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A History of Molecular Chaperone Structures in the Protein Data Bank. Int J Mol Sci 2019; 20:ijms20246195. [PMID: 31817979 PMCID: PMC6940948 DOI: 10.3390/ijms20246195] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2019] [Revised: 12/04/2019] [Accepted: 12/04/2019] [Indexed: 02/07/2023] Open
Abstract
Thirty years ago a class of proteins was found to prevent the aggregation of Rubisco. These proteins’ ability to prevent unwanted associations led to their being called chaperones. These chaperone proteins also increased in expression as a response to heat shock, hence their label as heat shock proteins (Hsps). However, neither label encompasses the breadth of these proteins’ functional capabilities. The term “unfoldases” has been proposed, as this basic function is shared by most members of this protein family. Onto this is added specializations that allow the different family members to perform various cellular functions. This current article focuses on the resolved structural bases for these functions. It reviews the currently available molecular structures in the Protein Data Bank for several classes of Hsps (Hsp60, Hsp70, Hsp90, and Hsp104). When possible, it discusses the complete structures for these proteins, and the types of molecular machines to which they have been assigned. The structures of domains and the associated functions are discussed in order to illustrate the rationale for the proposed unfoldase function.
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Richardson JS, Williams CJ, Videau LL, Chen VB, Richardson DC. Assessment of detailed conformations suggests strategies for improving cryoEM models: Helix at lower resolution, ensembles, pre-refinement fixups, and validation at multi-residue length scale. J Struct Biol 2018; 204:301-312. [PMID: 30107233 PMCID: PMC6163098 DOI: 10.1016/j.jsb.2018.08.007] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2018] [Revised: 08/01/2018] [Accepted: 08/08/2018] [Indexed: 11/17/2022]
Abstract
We find that the overall quite good methods used in the CryoEM Model Challenge could still benefit greatly from several strategies for improving local conformations. Our assessments primarily use validation criteria from the MolProbity web service. Those criteria include MolProbity's all-atom contact analysis, updated versions of standard conformational validations for protein and RNA, plus two recent additions: first, flags for cis-nonPro and twisted peptides, and second, the CaBLAM system for diagnosing secondary structure, validating Cα backbone, and validating adjacent peptide CO orientations in the context of the Cα trace. In general, automated ab initio building of starting models is quite good at backbone connectivity but often fails at local conformation or sequence register, especially at poorer than 3.5 Å resolution. However, we show that even if criteria (such as Ramachandran or rotamer) are explicitly restrained to improve refinement behavior and overall validation scores, automated optimization of a deposited structure seldom corrects specific misfittings that start in the wrong local minimum, but just hides them. Therefore, local problems should be identified, and as many as possible corrected, before starting refinement. Secondary structures are confusing at 3-4 Å but can be better recognized at 6-8 Å. In future model challenges, specific steps being tested (such as segmentation) and the required documentation (such as PDB code of starting model) should each be explicitly defined, so competing methods on a given task can be meaningfully compared. Individual local examples are presented here, to understand what local mistakes and corrections look like in 3D, how they probably arise, and what possible improvements to methodology might help avoid them. At these resolutions, both structural biologists and end-users need meaningful estimates of local uncertainty, perhaps through explicit ensembles. Fitting problems can best be diagnosed by validation that spans multiple residues; CaBLAM is such a multi-residue tool, and its effectiveness is demonstrated.
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Affiliation(s)
| | | | - Lizbeth L Videau
- Department of Biochemistry, Duke University, Durham, NC 27710, USA
| | - Vincent B Chen
- Department of Biochemistry, Duke University, Durham, NC 27710, USA
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3
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Grabowski M, Langner KM, Cymborowski M, Porebski PJ, Sroka P, Zheng H, Cooper DR, Zimmerman MD, Elsliger MA, Burley SK, Minor W. A public database of macromolecular diffraction experiments. Acta Crystallogr D Struct Biol 2016; 72:1181-1193. [PMID: 27841751 PMCID: PMC5108346 DOI: 10.1107/s2059798316014716] [Citation(s) in RCA: 91] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2016] [Accepted: 09/17/2016] [Indexed: 12/28/2022] Open
Abstract
The low reproducibility of published experimental results in many scientific disciplines has recently garnered negative attention in scientific journals and the general media. Public transparency, including the availability of `raw' experimental data, will help to address growing concerns regarding scientific integrity. Macromolecular X-ray crystallography has led the way in requiring the public dissemination of atomic coordinates and a wealth of experimental data, making the field one of the most reproducible in the biological sciences. However, there remains no mandate for public disclosure of the original diffraction data. The Integrated Resource for Reproducibility in Macromolecular Crystallography (IRRMC) has been developed to archive raw data from diffraction experiments and, equally importantly, to provide related metadata. Currently, the database of our resource contains data from 2920 macromolecular diffraction experiments (5767 data sets), accounting for around 3% of all depositions in the Protein Data Bank (PDB), with their corresponding partially curated metadata. IRRMC utilizes distributed storage implemented using a federated architecture of many independent storage servers, which provides both scalability and sustainability. The resource, which is accessible via the web portal at http://www.proteindiffraction.org, can be searched using various criteria. All data are available for unrestricted access and download. The resource serves as a proof of concept and demonstrates the feasibility of archiving raw diffraction data and associated metadata from X-ray crystallographic studies of biological macromolecules. The goal is to expand this resource and include data sets that failed to yield X-ray structures in order to facilitate collaborative efforts that will improve protein structure-determination methods and to ensure the availability of `orphan' data left behind for various reasons by individual investigators and/or extinct structural genomics projects.
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Affiliation(s)
- Marek Grabowski
- Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, VA 22904, USA
| | - Karol M. Langner
- Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, VA 22904, USA
| | - Marcin Cymborowski
- Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, VA 22904, USA
| | - Przemyslaw J. Porebski
- Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, VA 22904, USA
- Jerzy Haber Institute of Catalysis and Surface Chemistry, Polish Academy of Sciences, Niezapominajek 8, 30-239 Cracow, Poland
| | - Piotr Sroka
- Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, VA 22904, USA
| | - Heping Zheng
- Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, VA 22904, USA
| | - David R. Cooper
- Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, VA 22904, USA
| | - Matthew D. Zimmerman
- Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, VA 22904, USA
| | - Marc-André Elsliger
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 90237, USA
| | - Stephen K. Burley
- RCSB Protein Data Bank; Center for Integrative Proteomics Research; Institute for Quantitative Biomedicine; Rutgers Cancer Institute of New Jersey; Department of Chemistry and Chemical Biology, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA
- San Diego Supercomputer Center and Skaggs School of Pharmacological Sciences, University of California, San Diego, La Jolla, CA 92093, USA
| | - Wladek Minor
- Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, VA 22904, USA
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4
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Owen RL, Juanhuix J, Fuchs M. Current advances in synchrotron radiation instrumentation for MX experiments. Arch Biochem Biophys 2016; 602:21-31. [PMID: 27046341 PMCID: PMC5505570 DOI: 10.1016/j.abb.2016.03.021] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2015] [Revised: 03/16/2016] [Accepted: 03/21/2016] [Indexed: 11/15/2022]
Abstract
Following pioneering work 40 years ago, synchrotron beamlines dedicated to macromolecular crystallography (MX) have improved in almost every aspect as instrumentation has evolved. Beam sizes and crystal dimensions are now on the single micron scale while data can be collected from proteins with molecular weights over 10 MDa and from crystals with unit cell dimensions over 1000 Å. Furthermore it is possible to collect a complete data set in seconds, and obtain the resulting structure in minutes. The impact of MX synchrotron beamlines and their evolution is reflected in their scientific output, and MX is now the method of choice for a variety of aims from ligand binding to structure determination of membrane proteins, viruses and ribosomes, resulting in a much deeper understanding of the machinery of life. A main driving force of beamline evolution have been advances in almost every aspect of the instrumentation comprising a synchrotron beamline. In this review we aim to provide an overview of the current status of instrumentation at modern MX experiments. The most critical optical components are discussed, as are aspects of endstation design, sample delivery, visualisation and positioning, the sample environment, beam shaping, detectors and data acquisition and processing.
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Affiliation(s)
- Robin L Owen
- Diamond Light Source, Harwell Science and Innovation Campus, Didcot, OX11 0DE, UK.
| | - Jordi Juanhuix
- Alba Synchrotron, Carrer de la llum 2-26, Cerdanyola, 08192, Spain.
| | - Martin Fuchs
- National Synchrotron Light Source II, Brookhaven National Lab, Upton, NY, 11973, USA.
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5
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Abstract
Experimental phasing by single- or multi-wavelength anomalous dispersion (SAD or MAD) has become the most popular method of de novo macromolecular structure determination. Continuous advances at third-generation synchrotron sources have enabled the deployment of rapid data collection protocols that are capable of recording SAD or MAD data sets. However, procedural simplifications driven by the pursuit of high throughput have led to a loss of sophistication in data collection strategies, adversely affecting measurement accuracy from the viewpoint of anomalous phasing. In this chapter, we detail optimized strategies for collecting high-quality data for experimental phasing, with particular emphasis on minimizing errors from radiation damage as well as from the instrument. This chapter also emphasizes data processing for "on-the-fly" decision-making during data collection, a critical process when data quality depends directly on information gathered while at the synchrotron.
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Reardon-Robinson ME, Osipiuk J, Jooya N, Chang C, Joachimiak A, Das A, Ton-That H. A thiol-disulfide oxidoreductase of the Gram-positive pathogen Corynebacterium diphtheriae is essential for viability, pilus assembly, toxin production and virulence. Mol Microbiol 2015; 98:1037-50. [PMID: 26294390 PMCID: PMC4981772 DOI: 10.1111/mmi.13172] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/19/2015] [Indexed: 12/19/2022]
Abstract
The Gram-positive pathogen Corynebacterium diphtheriae exports through the Sec apparatus many extracellular proteins that include the key virulence factors diphtheria toxin and the adhesive pili. How these proteins attain their native conformations after translocation as unfolded precursors remains elusive. The fact that the majority of these exported proteins contain multiple cysteine residues and that several membrane-bound oxidoreductases are encoded in the corynebacterial genome suggests the existence of an oxidative protein-folding pathway in this organism. Here we show that the shaft pilin SpaA harbors a disulfide bond in vivo and alanine substitution of these cysteines abrogates SpaA polymerization and leads to the secretion of degraded SpaA peptides. We then identified a thiol-disulfide oxidoreductase (MdbA), whose structure exhibits a conserved thioredoxin-like domain with a CPHC active site. Remarkably, deletion of mdbA results in a severe temperature-sensitive cell division phenotype. This mutant also fails to assemble pilus structures and is greatly defective in toxin production. Consistent with these defects, the ΔmdbA mutant is attenuated in a guinea pig model of diphtheritic toxemia. Given its diverse cellular functions in cell division, pilus assembly and toxin production, we propose that MdbA is a component of the general oxidative folding machine in C. diphtheriae.
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Affiliation(s)
- Melissa E. Reardon-Robinson
- Department of Microbiology & Molecular Genetics, University of Texas Health Science Center, Houston, TX, USA
| | - Jerzy Osipiuk
- Midwest Center for Structural Genomics, Department of Biosciences, Argonne National Laboratory, Argonne, IL, USA
- Structural Biology Center, Department of Biosciences, Argonne National Laboratory, Argonne, IL, USA
| | - Neda Jooya
- Department of Microbiology & Molecular Genetics, University of Texas Health Science Center, Houston, TX, USA
| | - Chungyu Chang
- Department of Microbiology & Molecular Genetics, University of Texas Health Science Center, Houston, TX, USA
| | - Andrzej Joachimiak
- Midwest Center for Structural Genomics, Department of Biosciences, Argonne National Laboratory, Argonne, IL, USA
- Structural Biology Center, Department of Biosciences, Argonne National Laboratory, Argonne, IL, USA
| | - Asis Das
- Department of Molecular Biology and Biophysics, University of Connecticut Health Center, Farmington, CT, USA
| | - Hung Ton-That
- Department of Microbiology & Molecular Genetics, University of Texas Health Science Center, Houston, TX, USA
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Reardon-Robinson ME, Osipiuk J, Chang C, Wu C, Jooya N, Joachimiak A, Das A, Ton-That H. A Disulfide Bond-forming Machine Is Linked to the Sortase-mediated Pilus Assembly Pathway in the Gram-positive Bacterium Actinomyces oris. J Biol Chem 2015; 290:21393-405. [PMID: 26170452 PMCID: PMC4571867 DOI: 10.1074/jbc.m115.672253] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2015] [Indexed: 12/30/2022] Open
Abstract
Export of cell surface pilins in Gram-positive bacteria likely occurs by the translocation of unfolded precursor polypeptides; however, how the unfolded pilins gain their native conformation is presently unknown. Here, we present physiological studies to demonstrate that the FimA pilin of Actinomyces oris contains two disulfide bonds. Alanine substitution of cysteine residues forming the C-terminal disulfide bridge abrogates pilus assembly, in turn eliminating biofilm formation and polymicrobial interaction. Transposon mutagenesis of A. oris yielded a mutant defective in adherence to Streptococcus oralis, and revealed the essential role of a vitamin K epoxide reductase (VKOR) gene in pilus assembly. Targeted deletion of vkor results in the same defects, which are rescued by ectopic expression of VKOR, but not a mutant containing an alanine substitution in its conserved CXXC motif. Depletion of mdbA, which encodes a membrane-bound thiol-disulfide oxidoreductase, abrogates pilus assembly and alters cell morphology. Remarkably, overexpression of MdbA or a counterpart from Corynebacterium diphtheriae, rescues the Δvkor mutant. By alkylation assays, we demonstrate that VKOR is required for MdbA reoxidation. Furthermore, crystallographic studies reveal that A. oris MdbA harbors a thioredoxin-like fold with the conserved CXXC active site. Consistently, each MdbA enzyme catalyzes proper disulfide bond formation within FimA in vitro that requires the catalytic CXXC motif. Because the majority of signal peptide-containing proteins encoded by A. oris possess multiple Cys residues, we propose that MdbA and VKOR constitute a major folding machine for the secretome of this organism. This oxidative protein folding pathway may be a common feature in Actinobacteria.
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Affiliation(s)
- Melissa E. Reardon-Robinson
- From the Department of Microbiology and Molecular Genetics, University of Texas Health Science Center, Houston, Texas 77030
| | - Jerzy Osipiuk
- the Department of Biosciences, Midwest Center for Structural Genomics, and ,the Department of Biosciences, Structural Biology Center, Argonne National Laboratory, Argonne, Illinois 60439, and
| | - Chungyu Chang
- From the Department of Microbiology and Molecular Genetics, University of Texas Health Science Center, Houston, Texas 77030
| | - Chenggang Wu
- From the Department of Microbiology and Molecular Genetics, University of Texas Health Science Center, Houston, Texas 77030
| | - Neda Jooya
- From the Department of Microbiology and Molecular Genetics, University of Texas Health Science Center, Houston, Texas 77030
| | - Andrzej Joachimiak
- the Department of Biosciences, Midwest Center for Structural Genomics, and ,the Department of Biosciences, Structural Biology Center, Argonne National Laboratory, Argonne, Illinois 60439, and
| | - Asis Das
- the Department of Molecular Biology and Biophysics, University of Connecticut Health Center, Farmington, Connecticut 06030
| | - Hung Ton-That
- From the Department of Microbiology and Molecular Genetics, University of Texas Health Science Center, Houston, Texas 77030,
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Ramakrishnan V. The Diamond Light Source and the challenges ahead for structural biology: some informal remarks. PHILOSOPHICAL TRANSACTIONS. SERIES A, MATHEMATICAL, PHYSICAL, AND ENGINEERING SCIENCES 2015; 373:rsta.2013.0156. [PMID: 25624524 PMCID: PMC4308983 DOI: 10.1098/rsta.2013.0156] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
The remarkable advances in structural biology in the past three decades have led to the determination of increasingly complex structures that lie at the heart of many important biological processes. Many of these advances have been made possible by the use of X-ray crystallography using synchrotron radiation. In this short article, some of the challenges and prospects that lie ahead will be summarized.
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Affiliation(s)
- V Ramakrishnan
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, UK
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9
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Hammerstrom TG, Horton LB, Swick MC, Joachimiak A, Osipiuk J, Koehler TM. Crystal structure of Bacillus anthracis virulence regulator AtxA and effects of phosphorylated histidines on multimerization and activity. Mol Microbiol 2014; 95:426-41. [PMID: 25402841 DOI: 10.1111/mmi.12867] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/12/2014] [Indexed: 12/22/2022]
Abstract
The Bacillus anthracis virulence regulator AtxA controls transcription of the anthrax toxin genes and capsule biosynthetic operon. AtxA activity is elevated during growth in media containing glucose and CO(2)/bicarbonate, and there is a positive correlation between the CO(2)/bicarbonate signal, AtxA activity and homomultimerization. AtxA activity is also affected by phosphorylation at specific histidines. We show that AtxA crystallizes as a dimer. Distinct folds associated with predicted DNA-binding domains (HTH1 and HTH2) and phosphoenolpyruvate: carbohydrate phosphotransferase system-regulated domains (PRD1 and PRD2) are apparent. We tested AtxA variants containing single and double phosphomimetic (His→Asp) and phosphoablative (His→Ala) amino acid changes for activity in B. anthracis cultures and for protein-protein interactions in cell lysates. Reduced activity of AtxA H199A, lack of multimerization and activity of AtxAH379D variants, and predicted structural changes associated with phosphorylation support a model for control of AtxA function. We propose that (i) in the AtxA dimer, phosphorylation of H199 in PRD1 affects HTH2 positioning, influencing DNA-binding; and (ii) phosphorylation of H379 in PRD2 disrupts dimer formation. The AtxA structure is the first reported high-resolution full-length structure of a PRD-containing regulator, and can serve as a model for proteins of this family, especially those that link virulence to bacterial metabolism.
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Affiliation(s)
- Troy G Hammerstrom
- Department of Microbiology and Molecular Genetics, The University of Texas Health Science Center at Houston, Houston, TX, USA
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Bellini D, Caly DL, McCarthy Y, Bumann M, An SQ, Dow JM, Ryan RP, Walsh MA. Crystal structure of an HD-GYP domain cyclic-di-GMP phosphodiesterase reveals an enzyme with a novel trinuclear catalytic iron centre. Mol Microbiol 2013; 91:26-38. [PMID: 24176013 PMCID: PMC4159591 DOI: 10.1111/mmi.12447] [Citation(s) in RCA: 75] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/29/2013] [Indexed: 12/17/2022]
Abstract
Bis‐(3′,5′) cyclic di‐guanylate (c‐di‐GMP) is a key bacterial second messenger that is implicated in the regulation of many crucial processes that include biofilm formation, motility and virulence. Cellular levels of c‐di‐GMP are controlled through synthesis by GGDEF domain diguanylate cyclases and degradation by two classes of phosphodiesterase with EAL or HD‐GYP domains. Here, we have determined the structure of an enzymatically active HD‐GYP domain protein from Persephonella marina (PmGH) alone, in complex with substrate (c‐di‐GMP) and final reaction product (GMP). The structures reveal a novel trinuclear iron binding site, which is implicated in catalysis and identify residues involved in recognition of c‐di‐GMP. This structure completes the picture of all domains involved in c‐di‐GMP metabolism and reveals that the HD‐GYP family splits into two distinct subgroups containing bi‐ and trinuclear metal centres.
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Affiliation(s)
- Dom Bellini
- Diamond Light Source, Harwell Science and Innovation Campus, Didcot, Oxfordshire, OX11 0DE, UK; Research Complex at Harwell, Harwell Science and Innovation Campus, Didcot, Oxfordshire, OX11 0FA, UK
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11
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Tan K, Chang C, Cuff M, Osipiuk J, Landorf E, Mack JC, Zerbs S, Joachimiak A, Collart FR. Structural and functional characterization of solute binding proteins for aromatic compounds derived from lignin: p-coumaric acid and related aromatic acids. Proteins 2013; 81:1709-26. [PMID: 23606130 DOI: 10.1002/prot.24305] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2012] [Revised: 03/12/2013] [Accepted: 03/28/2013] [Indexed: 11/10/2022]
Abstract
Lignin comprises 15-25% of plant biomass and represents a major environmental carbon source for utilization by soil microorganisms. Access to this energy resource requires the action of fungal and bacterial enzymes to break down the lignin polymer into a complex assortment of aromatic compounds that can be transported into the cells. To improve our understanding of the utilization of lignin by microorganisms, we characterized the molecular properties of solute binding proteins of ATP-binding cassette transporter proteins that interact with these compounds. A combination of functional screens and structural studies characterized the binding specificity of the solute binding proteins for aromatic compounds derived from lignin such as p-coumarate, 3-phenylpropionic acid and compounds with more complex ring substitutions. A ligand screen based on thermal stabilization identified several binding protein clusters that exhibit preferences based on the size or number of aromatic ring substituents. Multiple X-ray crystal structures of protein-ligand complexes for these clusters identified the molecular basis of the binding specificity for the lignin-derived aromatic compounds. The screens and structural data provide new functional assignments for these solute-binding proteins which can be used to infer their transport specificity. This knowledge of the functional roles and molecular binding specificity of these proteins will support the identification of the specific enzymes and regulatory proteins of peripheral pathways that funnel these compounds to central metabolic pathways and will improve the predictive power of sequence-based functional annotation methods for this family of proteins.
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Affiliation(s)
- Kemin Tan
- Biosciences Division, Argonne National Laboratory, Lemont, Illinois, 60439; The Midwest Center for Structural Genomics, Argonne National Laboratory, Lemont, Illinois, 60439; Structural Biology Center, Argonne National Laboratory, Lemont, Illinois, 60439
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12
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Wu R, Gu M, Wilton R, Babnigg G, Kim Y, Pokkuluri PR, Szurmant H, Joachimiak A, Schiffer M. Insight into the sporulation phosphorelay: crystal structure of the sensor domain of Bacillus subtilis histidine kinase, KinD. Protein Sci 2013; 22:564-76. [PMID: 23436677 DOI: 10.1002/pro.2237] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2012] [Revised: 01/14/2013] [Accepted: 01/15/2013] [Indexed: 11/11/2022]
Abstract
The Bacillus subtilis KinD signal-transducing histidine kinase is a part of the sporulation phosphorelay known to regulate important developmental decisions such as sporulation and biofilm formation. We have determined crystal structures of the extracytoplasmic sensing domain of KinD, which was copurified and crystallized with a pyruvate ligand. The structure of a ligand-binding site mutant was also determined; it was copurified and crystallized with an acetate ligand. The structure of the KinD extracytoplasmic segment is similar to that of several other sensing domains of signal transduction proteins and is composed of tandem Per-Arnt-Sim (PAS)-like domains. The KinD ligand-binding site is located on the membrane distal PAS-like domain and appears to be highly selective; a single mutation, R131A, abolishes pyruvate binding and the mutant binds acetate instead. Differential scanning fluorimetry, using a variety of monocarboxylic and dicarboxylic acids, identified pyruvate, propionate, and butyrate but not lactate, acetate, or malate as KinD ligands. A recent report found that malate induces biofilm formation in a KinD-dependent manner. It was suggested that malate might induce a metabolic shift and increased secretion of the KinD ligand of unknown identity. The structure and binding assays now suggests that this ligand is pyruvate and/or other small monocarboxylic acids. In summary, this study gives a first insight into the identity of a molecular ligand for one of the five phosphorelay kinases of B. subtilis.
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Affiliation(s)
- R Wu
- The Midwest Center for Structural Genomics, Biosciences, Argonne National Laboratory, Argonne, Illinois 60439, USA
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Michalska K, Tan K, Li H, Hatzos-Skintges C, Bearden J, Babnigg G, Joachimiak A. GH1-family 6-P-β-glucosidases from human microbiome lactic acid bacteria. ACTA CRYSTALLOGRAPHICA. SECTION D, BIOLOGICAL CRYSTALLOGRAPHY 2013; 69:451-63. [PMID: 23519420 PMCID: PMC3605045 DOI: 10.1107/s0907444912049608] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/12/2012] [Accepted: 12/03/2012] [Indexed: 11/11/2022]
Abstract
In lactic acid bacteria and other bacteria, carbohydrate uptake is mostly governed by phosphoenolpyruvate-dependent phosphotransferase systems (PTSs). PTS-dependent translocation through the cell membrane is coupled with phosphorylation of the incoming sugar. After translocation through the bacterial membrane, the β-glycosidic bond in 6'-P-β-glucoside is cleaved, releasing 6-P-β-glucose and the respective aglycon. This reaction is catalyzed by 6-P-β-glucosidases, which belong to two glycoside hydrolase (GH) families: GH1 and GH4. Here, the high-resolution crystal structures of GH1 6-P-β-glucosidases from Lactobacillus plantarum (LpPbg1) and Streptococcus mutans (SmBgl) and their complexes with ligands are reported. Both enzymes show hydrolytic activity towards 6'-P-β-glucosides. The LpPbg1 structure has been determined in an apo form as well as in a complex with phosphate and a glucose molecule corresponding to the aglycon molecule. The S. mutans homolog contains a sulfate ion in the phosphate-dedicated subcavity. SmBgl was also crystallized in the presence of the reaction product 6-P-β-glucose. For a mutated variant of the S. mutans enzyme (E375Q), the structure of a 6'-P-salicin complex has also been determined. The presence of natural ligands enabled the definition of the structural elements that are responsible for substrate recognition during catalysis.
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Affiliation(s)
- Karolina Michalska
- Midwest Center for Structural Genomics, Biosciences Division, Argonne National Laboratory, Argonne, Illinois, USA
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14
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Yuan Y, Zhao W, Wang X, Gao Y, Niu L, Teng M. Dimeric Sfh3 has structural changes in its binding pocket that are associated with a dimer–monomer state transformation induced by substrate binding. ACTA CRYSTALLOGRAPHICA SECTION D: BIOLOGICAL CRYSTALLOGRAPHY 2013; 69:313-23. [DOI: 10.1107/s0907444912046161] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/18/2012] [Accepted: 11/08/2012] [Indexed: 12/31/2022]
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15
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Kim Y, Cunningham MA, Mire J, Tesar C, Sacchettini J, Joachimiak A. NDM-1, the ultimate promiscuous enzyme: substrate recognition and catalytic mechanism. FASEB J 2013; 27:1917-27. [PMID: 23363572 DOI: 10.1096/fj.12-224014] [Citation(s) in RCA: 96] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
The specter of a return to an era in which infectious disease looms as a significant threat to human health is not just hyperbole; there are serious concerns about the widespread overuse and misuse of antibiotics contributing to increased antibiotic resistance in pathogens. The recent discovery of a new enzyme, first identified in Klebsiella pneumoniae from a patient from New Delhi and denoted as NDM-1, represents an example of extreme promiscuity: It hydrolyzes and inactivates nearly all known β-lactam-based antibiotics with startling efficiency. NDM-1 can utilize different metal cofactors and seems to exploit an alternative mechanism based on the reaction conditions. Here we report the results of a combined experimental and theoretical study that examines the substrate, metal binding, and catalytic mechanism of the enzyme. We utilize structures obtained through X-ray crystallography, biochemical assays, and numerical simulation to construct a model of the enzyme catalytic pathway. The NDM-1 enzyme interacts with the substrate solely through zinc, or other metals, bound in the active site, explaining the observed lack of specificity against a broad range of β-lactam antibiotic agents. The zinc ions also serve to activate a water molecule that hydrolyzes the β-lactam ring through a proton shuttle.
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Affiliation(s)
- Youngchang Kim
- Midwest Center for Structural Genomics and Structural Biology Center, Biosciences, Argonne National Laboratory, Argonne, IL 60439, USA
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16
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Structural studies of SSB interaction with RecO. METHODS IN MOLECULAR BIOLOGY (CLIFTON, N.J.) 2013; 922:123-31. [PMID: 22976180 DOI: 10.1007/978-1-62703-032-8_7] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/20/2023]
Abstract
Interaction of recombination protein RecO with single-stranded (ss) DNA-binding protein (SSB) is essential for DNA damage repair and restart of stalled replication (Cox, Crit Rev Biochem Mol Biol 42(1):41-63, 2007). To understand mechanism of this interaction and its role in DNA repair, we deciphered a high-resolution structure of RecO complex with C-terminal tail of SSB (SSB-Ct). The structure revealed a key role of hydrophobic interactions between two proteins and suggests the mechanism of RecO recruitment to DNA during homologous recombination and strand annealing.
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17
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Michalska K, Chang C, Mack JC, Zerbs S, Joachimiak A, Collart FR. Characterization of transport proteins for aromatic compounds derived from lignin: benzoate derivative binding proteins. J Mol Biol 2012; 423:555-75. [PMID: 22925578 PMCID: PMC3836681 DOI: 10.1016/j.jmb.2012.08.017] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2012] [Revised: 07/27/2012] [Accepted: 08/20/2012] [Indexed: 10/28/2022]
Abstract
In vitro growth experiments have demonstrated that aromatic compounds derived from lignin can be metabolized and represent a major carbon resource for many soil bacteria. However, the proteins that mediate the movement of these metabolites across the cell membrane have not been thoroughly characterized. To address this deficiency, we used a library representative of lignin degradation products and a thermal stability screen to determine ligand specificity for a set of solute-binding proteins (SBPs) from ATP-binding cassette (ABC) transporters. The ligand mapping process identified a set of proteins from Alphaproteobacteria that recognize various benzoate derivatives. Seven high-resolution crystal structures of these proteins in complex with four different aromatic compounds were obtained. The protein-ligand complexes provide details of molecular recognition that can be used to infer binding specificity. This structure-function characterization provides new insight for the biological roles of these ABC transporters and their SBPs, which had been previously annotated as branched-chain amino-acid-binding proteins. The knowledge derived from the crystal structures provides a foundation for development of sequence-based methods to predict the ligand specificity of other uncharacterized transporters. These results also demonstrate that Alphaproteobacteria possess a diverse set of transport capabilities for lignin-derived compounds. Characterization of this new class of transporters improves genomic annotation projects and provides insight into the metabolic potential of soil bacteria.
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Affiliation(s)
- Karolina Michalska
- Biosciences Division, Argonne National Laboratory, 9700 South Cass Avenue, Lemont, IL 60439, USA
- The Midwest Center for Structural Genomics, Argonne National Laboratory, Lemont, IL 60439, USA
| | - Changsoo Chang
- Biosciences Division, Argonne National Laboratory, 9700 South Cass Avenue, Lemont, IL 60439, USA
- The Midwest Center for Structural Genomics, Argonne National Laboratory, Lemont, IL 60439, USA
- Structural Biology Center, Argonne National Laboratory, Lemont, IL 60439, USA
| | - Jamey C. Mack
- Biosciences Division, Argonne National Laboratory, 9700 South Cass Avenue, Lemont, IL 60439, USA
- The Midwest Center for Structural Genomics, Argonne National Laboratory, Lemont, IL 60439, USA
| | - Sarah Zerbs
- Biosciences Division, Argonne National Laboratory, 9700 South Cass Avenue, Lemont, IL 60439, USA
| | - Andrzej Joachimiak
- Biosciences Division, Argonne National Laboratory, 9700 South Cass Avenue, Lemont, IL 60439, USA
- The Midwest Center for Structural Genomics, Argonne National Laboratory, Lemont, IL 60439, USA
- Structural Biology Center, Argonne National Laboratory, Lemont, IL 60439, USA
| | - Frank R. Collart
- Biosciences Division, Argonne National Laboratory, 9700 South Cass Avenue, Lemont, IL 60439, USA
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18
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Makowska-Grzyska M, Kim Y, Wu R, Wilton R, Gollapalli DR, Wang XK, Zhang R, Jedrzejczak R, Mack JC, Maltseva N, Mulligan R, Binkowski TA, Gornicki P, Kuhn ML, Anderson WF, Hedstrom L, Joachimiak A. Bacillus anthracis inosine 5'-monophosphate dehydrogenase in action: the first bacterial series of structures of phosphate ion-, substrate-, and product-bound complexes. Biochemistry 2012; 51:6148-63. [PMID: 22788966 DOI: 10.1021/bi300511w] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Abstract
Inosine 5'-monophosphate dehydrogenase (IMPDH) catalyzes the first unique step of the GMP branch of the purine nucleotide biosynthetic pathway. This enzyme is found in organisms of all three kingdoms. IMPDH inhibitors have broad clinical applications in cancer treatment, as antiviral drugs and as immunosuppressants, and have also displayed antibiotic activity. We have determined three crystal structures of Bacillus anthracis IMPDH, in a phosphate ion-bound (termed "apo") form and in complex with its substrate, inosine 5'-monophosphate (IMP), and product, xanthosine 5'-monophosphate (XMP). This is the first example of a bacterial IMPDH in more than one state from the same organism. Furthermore, for the first time for a prokaryotic enzyme, the entire active site flap, containing the conserved Arg-Tyr dyad, is clearly visible in the structure of the apoenzyme. Kinetic parameters for the enzymatic reaction were also determined, and the inhibitory effect of XMP and mycophenolic acid (MPA) has been studied. In addition, the inhibitory potential of two known Cryptosporidium parvum IMPDH inhibitors was examined for the B. anthracis enzyme and compared with those of three bacterial IMPDHs from Campylobacter jejuni, Clostridium perfringens, and Vibrio cholerae. The structures contribute to the characterization of the active site and design of inhibitors that specifically target B. anthracis and other microbial IMPDH enzymes.
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Affiliation(s)
- Magdalena Makowska-Grzyska
- Center for Structural Genomics of Infectious Diseases, University of Chicago, 5735 South Ellis Avenue, Chicago, IL 60637, USA
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19
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Osipiuk J, Mulligan R, Bargassa M, Hamilton JE, Cunningham MA, Joachimiak A. Characterization of member of DUF1888 protein family, self-cleaving and self-assembling endopeptidase. J Biol Chem 2012; 287:19452-61. [PMID: 22493430 DOI: 10.1074/jbc.m112.358069] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The crystal structure of SO1698 protein from Shewanella oneidensis was determined by a SAD method and refined to 1.57 Å. The structure is a β sandwich that unexpectedly consists of two polypeptides; the N-terminal fragment includes residues 1-116, and the C-terminal one includes residues 117-125. Electron density also displayed the Lys-98 side chain covalently linked to Asp-116. The putative active site residues involved in self-cleavage were identified; point mutants were produced and characterized structurally and in a biochemical assay. Numerical simulations utilizing molecular dynamics and hybrid quantum/classical calculations suggest a mechanism involving activation of a water molecule coordinated by a catalytic aspartic acid.
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Affiliation(s)
- Jerzy Osipiuk
- Midwest Center for Structural Genomics and Structural Biology Center, Biosciences, Argonne National Laboratory, Argonne, Illinois 60439, USA
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20
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Michalska K, Cuff ME, Tesar C, Feldmann B, Joachimiak A. Structure of 2-oxo-3-deoxygalactonate kinase from Klebsiella pneumoniae. ACTA CRYSTALLOGRAPHICA. SECTION D, BIOLOGICAL CRYSTALLOGRAPHY 2011; 67:678-89. [PMID: 21795809 PMCID: PMC3144851 DOI: 10.1107/s0907444911021834] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/08/2011] [Accepted: 06/06/2011] [Indexed: 11/10/2022]
Abstract
In most organisms, efficient D-galactose utilization requires the highly conserved Leloir pathway that converts D-galactose to D-glucose 1-phosphate. However, in some bacterial and fungal species alternative routes of D-galactose assimilation have been identified. In the so-called De Ley-Doudoroff pathway, D-galactose is metabolized into pyruvate and D-glyceraldehyde 3-phosphate in five consecutive reactions carried out by specific enzymes. The penultimate step in this pathway involves the phosphorylation of 2-oxo-3-deoxygalactonate to 2-oxo-3-deoxygalactonate 6-phosphate catalyzed by 2-oxo-3-deoxygalactonate kinase, with ATP serving as a phosphoryl-group donor. Here, a crystal structure of 2-oxo-3-deoxygalactonate kinase from Klebsiella pneumoniae determined at 2.1 Å resolution is reported, the first structure of an enzyme from the De Ley-Doudoroff pathway. Structural comparison indicates that the enzyme belongs to the ASKHA (acetate and sugar kinases/hsc70/actin) family of phosphotransferases. The protein is composed of two α/β domains, each of which contains a core common to all family members. Additional elements introduced between conserved structural motifs define the unique features of 2-oxo-3-deoxygalactonate kinase and possibly determine the biological function of the protein.
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Affiliation(s)
- Karolina Michalska
- Midwest Center for Structural Genomics, Biosciences Division, Argonne National Laboratory, USA
| | - Marianne E. Cuff
- Midwest Center for Structural Genomics, Biosciences Division, Argonne National Laboratory, USA
- Structural Biology Center, Biosciences Division, Argonne National Laboratory, USA
| | - Christine Tesar
- Midwest Center for Structural Genomics, Biosciences Division, Argonne National Laboratory, USA
| | - Brian Feldmann
- Midwest Center for Structural Genomics, Biosciences Division, Argonne National Laboratory, USA
| | - Andrzej Joachimiak
- Midwest Center for Structural Genomics, Biosciences Division, Argonne National Laboratory, USA
- Structural Biology Center, Biosciences Division, Argonne National Laboratory, USA
- Department of Biochemistry and Molecular Biology, University of Chicago, USA
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21
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Wang L, Wu M, Zang J. Crystal structure of Sa240: a ribose pyranase homolog with partial active site from Staphylococcus aureus. J Struct Biol 2011; 174:413-9. [PMID: 21276853 DOI: 10.1016/j.jsb.2011.01.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2010] [Revised: 12/16/2010] [Accepted: 01/20/2011] [Indexed: 11/17/2022]
Abstract
Ribose is transported into cells in its pyranose form and must be rearranged to its furanose form for further utilization. Ribose pyranase RbsD catalyzes the conversion of ribose from the pyranose to furanose form. This is the key step for substrate supply to ribokinase RbsK, which converts ribose to ribose-5-phosphate for further metabolism. Sequence analysis indicated Sa240 from Staphylococcus aureus was a ribose pyranase homolog. Here we showed that Sa240 formed dimeric structure both in solution and in crystal. S240-ribose complex structure showed a ribose binding site formed by an incomplete active site compared with RbsD. Because the catalytic activity of ribose pyranase depends on its oligomeric state, we propose Sa240 is catalytically inactive in its dimeric structure.
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Affiliation(s)
- Ling Wang
- School of Life Sciences, University of Science and Technology of China, 96 Jinzhai Road, Hefei, Anhui 230026, People's Republic of China
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22
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Nocek B, Stein AJ, Jedrzejczak R, Cuff ME, Li H, Volkart L, Joachimiak A. Structural studies of ROK fructokinase YdhR from Bacillus subtilis: insights into substrate binding and fructose specificity. J Mol Biol 2010; 406:325-42. [PMID: 21185308 DOI: 10.1016/j.jmb.2010.12.021] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2010] [Revised: 11/29/2010] [Accepted: 12/14/2010] [Indexed: 11/30/2022]
Abstract
The main pathway of bacterial sugar phosphorylation utilizes specific phosphoenolpyruvate phosphotransferase system (PTS) enzymes. In addition to the classic PTS system, a PTS-independent secondary system has been described in which nucleotide-dependent sugar kinases are used for monosaccharide phosphorylation. Fructokinase (FK), which phosphorylates d-fructose with ATP as a cofactor, has been shown to be a member of this secondary system. Bioinformatic analysis has shown that FK is a member of the "ROK" (bacterial Repressors, uncharacterized Open reading frames, and sugar Kinases) sequence family. In this study, we report the crystal structures of ROK FK from Bacillus subtilis (YdhR) (a) apo and in the presence of (b) ADP and (c) ADP/d-fructose. All structures show that YdhR is a homodimer with a monomer composed of two similar α/β domains forming a large cleft between domains that bind ADP and D-fructose. Enzymatic activity assays support YdhR function as an ATP-dependent fructose kinase.
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Affiliation(s)
- B Nocek
- Midwest Center for Structural Genomics and Structural Biology Center, Biosciences, Argonne National Laboratory, 9700 South Cass Avenue, Building 202, Argonne, IL 60439, USA
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23
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Duke EMH, Johnson LN. Macromolecular crystallography at synchrotron radiation sources: current status and future developments. Proc Math Phys Eng Sci 2010. [DOI: 10.1098/rspa.2010.0448] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
X-ray diffraction with synchrotron radiation (SR) has revealed the atomic structures of numerous biological macromolecules including proteins and protein complexes, nucleic acids and their protein complexes, viruses, membrane proteins and drug targets. The bright SR X-ray beam with its small divergence has made the study of weakly diffracting crystals of large biological molecules possible. The ability to tune the wavelength of the SR beam to the absorption edge of certain elements has allowed anomalous scattering to be exploited for phase determination. We review the developments at synchrotron sources and beamlines from the early days to the present time, and discuss the significance of the results in providing a deeper understanding of the biological function, the design of new therapeutic molecules and time-resolved studies of dynamic events using pump–probe techniques. Radiation damage, a problem with bright X-ray sources, has been partially alleviated by collecting data at low temperature (100 K) but work is ongoing. In the most recent development, free electron laser sources can offer a peak brightness of hard X-rays approximately 10
8
times brighter than that achieved at SR sources. We describe briefly how early experiments at FLASH and Linear Coherent Light Source have shown exciting possibilities for the future.
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Affiliation(s)
- E. M. H. Duke
- Diamond Light Source, Harwell Science and Innovation Campus, Didcot OX11 0DE, UK
| | - L. N. Johnson
- Diamond Light Source, Harwell Science and Innovation Campus, Didcot OX11 0DE, UK
- Laboratory of Molecular Biophysics, Department of Biochemistry, University of Oxford, Oxford OX1 3QU, UK
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24
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Kim Y, Zhou M, Moy S, Morales J, Cunningham MA, Joachimiak A. High-resolution structure of the nitrile reductase QueF combined with molecular simulations provide insight into enzyme mechanism. J Mol Biol 2010; 404:127-37. [PMID: 20875425 DOI: 10.1016/j.jmb.2010.09.042] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2010] [Revised: 09/09/2010] [Accepted: 09/17/2010] [Indexed: 10/19/2022]
Abstract
Here, we report the 1.53-Å crystal structure of the enzyme 7-cyano-7-deazaguanine reductase (QueF) from Vibrio cholerae, which is responsible for the complete reduction of a nitrile (CN) bond to a primary amine (H(2)C-NH(2)). At present, this is the only example of a biological pathway that includes reduction of a nitrile bond, establishing QueF as particularly noteworthy. The structure of the QueF monomer resembles two connected ferrodoxin-like domains that assemble into dimers. Ligands identified in the crystal structure suggest the likely binding conformation of the native substrates NADPH and 7-cyano-7-deazaguanine. We also report on a series of numerical simulations that have shed light on the mechanism by which this enzyme affects the transfer of four protons (and electrons) to the 7-cyano-7-deazaguanine substrate. In particular, the simulations suggest that the initial step of the catalytic process is the formation of a covalent adduct with the residue Cys194, in agreement with previous studies. The crystal structure also suggests that two conserved residues (His233 and Asp102) play an important role in the delivery of a fourth proton to the substrate.
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Affiliation(s)
- Youngchang Kim
- The Midwest Center for Structural Genomics and Structural Biology Center, Biosciences, Argonne National Laboratory, 9700 South Cass Avenue, Argonne, IL 60439, USA
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25
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Abstract
An expert system for macromolecular crystallography data reduction is presented, which builds on existing software to automate the complete data reduction process from images to merged structure factor amplitudes. This can automatically identify multi-wedge, multi-pass and multiwavelength data sets and includes explicit procedures to test for crystallographic special cases. With the push towards high-thoughput crystallography at synchrotron beamlines and automation of structure solution, the ability to reduce data with no user input fills an important gap in the pipeline.
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26
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Joachimiak A. High-throughput crystallography for structural genomics. Curr Opin Struct Biol 2009; 19:573-84. [PMID: 19765976 DOI: 10.1016/j.sbi.2009.08.002] [Citation(s) in RCA: 96] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2009] [Revised: 08/14/2009] [Accepted: 08/20/2009] [Indexed: 11/20/2022]
Abstract
Protein X-ray crystallography recently celebrated its 50th anniversary. The structures of myoglobin and hemoglobin determined by Kendrew and Perutz provided the first glimpses into the complex protein architecture and chemistry. Since then, the field of structural molecular biology has experienced extraordinary progress and now more than 55000 protein structures have been deposited into the Protein Data Bank. In the past decade many advances in macromolecular crystallography have been driven by world-wide structural genomics efforts. This was made possible because of third-generation synchrotron sources, structure phasing approaches using anomalous signal, and cryo-crystallography. Complementary progress in molecular biology, proteomics, hardware and software for crystallographic data collection, structure determination and refinement, computer science, databases, robotics and automation improved and accelerated many processes. These advancements provide the robust foundation for structural molecular biology and assure strong contribution to science in the future. In this report we focus mainly on reviewing structural genomics high-throughput X-ray crystallography technologies and their impact.
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Affiliation(s)
- Andrzej Joachimiak
- Midwest Center for Structural Genomics, Structural Biology Center, Biosciences Division, Argonne National Laboratory, 9700 S Class Ave., Argonne, IL 60439, USA.
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27
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Radiation stability of proteinase K crystals grown by LB nanotemplate method. J Struct Biol 2009; 168:409-18. [PMID: 19686853 DOI: 10.1016/j.jsb.2009.08.005] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2009] [Revised: 07/29/2009] [Accepted: 08/12/2009] [Indexed: 11/23/2022]
Abstract
A detailed analysis of structural and intensity changes induced by X-ray radiation is presented for two types of proteinase K crystals: crystal grown by classical hanging drop method and those grown by Langmuir-Blodgett (LB) nanotemplate. The comparison of various parameters (e.g. intensity per sigma ratio, unit-cell volume, number of unique reflections, B-factors) and electron density maps as a function of radiation dose, demonstrates that crystals, grown by the LB nanotemplate method, appear to be more resistant against radiation damage than crystals grown by the classical hanging drop method.
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28
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Cuff M, Li H, Moy S, Watson J, Cipriani A, Joachimiak A. Crystal structure of an acetyltransferase protein from Vibrio cholerae strain N16961. Proteins 2009; 69:422-7. [PMID: 17623843 PMCID: PMC2885949 DOI: 10.1002/prot.21417] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- M.E. Cuff
- Midwest Center for Structural Genomics, Biosciences Division, Argonne National Laboratory, Argonne, Illinois 60439
- Structural Biology Center, Biosciences Division, Argonne National Laboratory, Argonne, Illinois 60439
| | - H. Li
- Midwest Center for Structural Genomics, Biosciences Division, Argonne National Laboratory, Argonne, Illinois 60439
| | - S. Moy
- Midwest Center for Structural Genomics, Biosciences Division, Argonne National Laboratory, Argonne, Illinois 60439
| | - J. Watson
- Midwest Center for Structural Genomics, Biomolecular Structure and Modeling Group, European Bioinformatics Institute, Birkbeck College, Cambridge, CB10 1SD, United Kingdom
| | - A. Cipriani
- Midwest Center for Structural Genomics, Biosciences Division, Argonne National Laboratory, Argonne, Illinois 60439
| | - A. Joachimiak
- Midwest Center for Structural Genomics, Biosciences Division, Argonne National Laboratory, Argonne, Illinois 60439
- Structural Biology Center, Biosciences Division, Argonne National Laboratory, Argonne, Illinois 60439
- Correspondence to: Dr. Andrzej Joachimiak, Biosciences Division, Midwest Center for Structural Genomics and Structural Biology Center, Argonne National Laboratory, 9700 S. Cass Ave. Argonne, IL 60439.
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29
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Wu R, Richter S, Zhang RG, Anderson VJ, Missiakas D, Joachimiak A. Crystal structure of Bacillus anthracis transpeptidase enzyme CapD. J Biol Chem 2009; 284:24406-14. [PMID: 19535342 DOI: 10.1074/jbc.m109.019034] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Bacillus anthracis elaborates a poly-gamma-d-glutamic acid capsule that protects bacilli from phagocytic killing during infection. The enzyme CapD generates amide bonds with peptidoglycan cross-bridges to anchor capsular material within the cell wall envelope of B. anthracis. The capsular biosynthetic pathway is essential for virulence during anthrax infections and can be targeted for anti-infective inhibition with small molecules. Here, we present the crystal structures of the gamma-glutamyltranspeptidase CapD with and without alpha-l-Glu-l-Glu dipeptide, a non-hydrolyzable analog of poly-gamma-d-glutamic acid, in the active site. Purified CapD displays transpeptidation activity in vitro, and its structure reveals an active site broadly accessible for poly-gamma-glutamate binding and processing. Using structural and biochemical information, we derive a mechanistic model for CapD catalysis whereby Pro(427), Gly(428), and Gly(429) activate the catalytic residue of the enzyme, Thr(352), and stabilize an oxyanion hole via main chain amide hydrogen bonds.
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Affiliation(s)
- Ruiying Wu
- Biosciences Division, Midwest Center for Structural Genomics and Structural Biology Center, Argonne National Laboratory, Argonne, Illinois 60439, USA
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30
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Kim Y, Quartey P, Ng R, Zarembinski TI, Joachimiak A. Crystal structure of YfeU protein from Haemophilus influenzae: a predicted etherase involved in peptidoglycan recycling. ACTA ACUST UNITED AC 2009; 10:151-6. [PMID: 19234762 DOI: 10.1007/s10969-009-9063-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2008] [Accepted: 02/05/2009] [Indexed: 11/30/2022]
Abstract
The crystal structure of the H. influenzae YfeU protein, was determined at 1.90 A resolution using multi-wavelength anomalous diffraction. YfeU belongs to a very large conserved family of proteins found mainly in bacteria but also in archaea and eukaryota. The protein is a homolog of eukaryotic glucokinase regulator and is predicted to be a sugar phosphate isomerase or aminotransferase. Here we describe the structure of YfeU and discuss the possible function as an etherase possibly involved in peptidoglycan recycling.
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Affiliation(s)
- Y Kim
- Midwest Center for Structural Genomics and Structural Biology Center, Biosciences, Argonne National Laboratory, Argonne, IL 60439, USA
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31
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Osipiuk J, Zhou M, Moy S, Collart F, Joachimiak A. X-ray crystal structure of GarR-tartronate semialdehyde reductase from Salmonella typhimurium. ACTA ACUST UNITED AC 2009; 10:249-53. [PMID: 19184529 DOI: 10.1007/s10969-009-9059-x] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2008] [Accepted: 01/02/2009] [Indexed: 10/21/2022]
Abstract
Tartronate semialdehyde reductases (TSRs), also known as 2-hydroxy-3-oxopropionate reductases, catalyze the reduction of tartronate semialdehyde using NAD as cofactor in the final stage of D-glycerate biosynthesis. These enzymes belong to family of structurally and mechanically related beta-hydroxyacid dehydrogenases which differ in substrate specificity and catalyze reactions in specific metabolic pathways. Here, we present the crystal structure of GarR a TSR from Salmonella typhimurium determined by the single-wavelength anomalous diffraction method and refined to 1.65 A resolution. The active site of the enzyme contains L-tartrate which most likely mimics a position of a glycerate which is a product of the enzyme reaction. The analysis of the TSR structure shows also a putative NADPH binding site in the enzyme.
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Affiliation(s)
- J Osipiuk
- Biosciences Division, Midwest Center for Structural Genomics, Argonne National Laboratory, Bldg 202, Argonne, IL 60439, USA
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32
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Crystal structure of fatty acid/phospholipid synthesis protein PlsX from Enterococcus faecalis. ACTA ACUST UNITED AC 2008; 10:157-63. [PMID: 19058030 DOI: 10.1007/s10969-008-9052-9] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2008] [Accepted: 11/12/2008] [Indexed: 10/21/2022]
Abstract
PlsX is a key enzyme that coordinates the production of fatty acids and membrane phospholipids. The plsX gene is co-localized with a bacterial fab gene cluster which encodes several key fatty acid biosynthetic enzymes. The protein is a member of a large, conserved protein family (Pfam02504) found exclusively in bacteria. The PlsX sequence homologues include both phosphate acetyltransferases and phosphate butaryltransferases that catalyze the transfer of an acetyl or butaryl group to orthophosphate. We have determined the crystal structure of PlsX from the human pathogen Enterococcus faecalis. PlsX is a alpha/beta/alpha sandwich that resembles a Rossmann fold and forms a dimer. A putative catalytic site has been identified within a deep groove on the interface between monomers. This site showed strong surface similarity to epimerases and reductases. It was recently proposed that PlsX is a phosphate acyltransferase that catalyzes the formation of acyl-phosphate from the acyl-acyl carrier protein; however the specific biochemical function of the PlsX protein awaits further experimental scrutiny.
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Nocek B, Bigelow L, Abdullah J, Joachimiak A. Structure of SO2946 orphan from Shewanella oneidensis shows "jelly-roll" fold with carbohydrate-binding module. JOURNAL OF STRUCTURAL AND FUNCTIONAL GENOMICS 2008; 9:1-6. [PMID: 18566914 PMCID: PMC2678837 DOI: 10.1007/s10969-008-9040-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/12/2008] [Accepted: 05/20/2008] [Indexed: 05/26/2023]
Abstract
The crystal structure of the uncharacterized protein SO2946 from Shewanella oneidensis MR-1 was determined with single-wavelength anomalous diffraction (SAD) and refined to 2.0 A resolution. The SO2946 protein consists of a short helical N-terminal domain and a large C-terminal domain with the "jelly-roll" topology. The protein assembles into a propeller consisting of three C-terminal blades arranged around a central core formed by the N-terminal domains. The function of SO2946 could not be inferred from the sequence since the protein represents an orphan with no sequence homologs, but the protein's structure bears a fold similar to that of proteins containing carbohydrate-binding modules. Features such as fold conservation, the presence of a conserved groove and a metal binding region are indicative that SO2946 may be an enzyme and could be involved in binding carbohydrate molecules.
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Affiliation(s)
- B. Nocek
- Midwest Center for Structural Genomics and Structural Biology Center, Biosciences Division, Argonne National Laboratory, 9700 South Cass Avenue, Building 202, Argonne, IL 60439, USA
| | - L. Bigelow
- Midwest Center for Structural Genomics and Structural Biology Center, Biosciences Division, Argonne National Laboratory, 9700 South Cass Avenue, Building 202, Argonne, IL 60439, USA
| | - J. Abdullah
- Midwest Center for Structural Genomics and Structural Biology Center, Biosciences Division, Argonne National Laboratory, 9700 South Cass Avenue, Building 202, Argonne, IL 60439, USA
| | - A. Joachimiak
- Midwest Center for Structural Genomics and Structural Biology Center, Biosciences Division, Argonne National Laboratory, 9700 South Cass Avenue, Building 202, Argonne, IL 60439, USA
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Structural and functional analysis of AsbF: origin of the stealth 3,4-dihydroxybenzoic acid subunit for petrobactin biosynthesis. Proc Natl Acad Sci U S A 2008; 105:17133-8. [PMID: 18955706 DOI: 10.1073/pnas.0808118105] [Citation(s) in RCA: 42] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
Petrobactin, a virulence-associated siderophore produced by Bacillus anthracis, chelates ferric iron through the rare 3,4-isomer of dihydroxybenzoic acid (3,4-DHBA). Most catechol siderophores, including bacillibactin and enterobactin, use 2,3-DHBA as a biosynthetic subunit. Significantly, siderocalin, a factor involved in human innate immunity, sequesters ferric siderophores bearing the more typical 2,3-DHBA moiety, thereby impeding uptake of iron by the pathogenic bacterial cell. In contrast, the unusual 3,4-DHBA component of petrobactin renders the siderocalin system incapable of obstructing bacterial iron uptake. Although recent genetic and biochemical studies have revealed selected early steps in petrobactin biosynthesis, the origin of 3,4-DHBA as well as the function of the protein encoded by the final gene in the B. anthracis siderophore biosynthetic (asb) operon, asbF (BA1986), has remained unclear. In this study we demonstrate that 3,4-DHBA is produced through conversion of the common bacterial metabolite 3-dehydroshikimate (3-DHS) by AsbF-a 3-DHS dehydratase. Elucidation of the cocrystal structure of AsbF with 3,4-DHBA, in conjunction with a series of biochemical studies, supports a mechanism in which an enolate intermediate is formed through the action of this 3-DHS dehydratase metalloenzyme. Structural and functional parallels are evident between AsbF and other enzymes within the xylose isomerase TIM-barrel family. Overall, these data indicate that microbial species shown to possess homologs of AsbF may, like B. anthracis, also rely on production of the unique 3,4-DHBA metabolite to achieve full viability in the environment or virulence within the host.
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Qiu Y, Zhang R, Binkowski TA, Tereshko V, Joachimiak A, Kossiakoff A. The 1.38 A crystal structure of DmsD protein from Salmonella typhimurium, a proofreading chaperone on the Tat pathway. Proteins 2008; 71:525-33. [PMID: 18175314 DOI: 10.1002/prot.21828] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
The DmsD protein is necessary for the biogenesis of dimethyl sulphoxide (DMSO) reductase in many prokaryotes. It performs a critical chaperone function initiated through its binding to the twin-arginine signal peptide of DmsA, the catalytic subunit of DMSO reductase. Upon binding to DmsD, DmsA is translocated to the periplasm via the so-called twin-arginine translocation (Tat) pathway. Here we report the 1.38 A crystal structure of the protein DmsD from Salmonella typhimurium and compare it with a close functional homolog, TorD. DmsD has an all-alpha fold structure with a notable helical extension located at its N-terminus with two solvent exposed hydrophobic residues. A major difference between DmsD and TorD is that TorD structure is a domain-swapped dimer, while DmsD exists as a monomer. Nevertheless, these two proteins have a number of common features suggesting they function by using similar mechanisms. A possible signal peptide-binding site is proposed based on structural similarities. Computational analysis was used to identify a potential GTP binding pocket on similar surfaces of DmsD and TorD structures.
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Affiliation(s)
- Yang Qiu
- Department of Biochemistry and Molecular Biology, The University of Chicago, Chicago, Illinois 60637, USA
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36
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Manjasetty BA, Turnbull AP, Panjikar S, Büssow K, Chance MR. Automated technologies and novel techniques to accelerate protein crystallography for structural genomics. Proteomics 2008; 8:612-25. [PMID: 18210369 DOI: 10.1002/pmic.200700687] [Citation(s) in RCA: 48] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
The sequence infrastructure that has arisen through large-scale genomic projects dedicated to protein analysis, has provided a wealth of information and brought together scientists and institutions from all over the world. As a consequence, the development of novel technologies and methodologies in proteomics research is helping to unravel the biochemical and physiological mechanisms of complex multivariate diseases at both a functional and molecular level. In the late sixties, when X-ray crystallography had just been established, the idea of determining protein structure on an almost universal basis was akin to an impossible dream or a miracle. Yet only forty years after, automated protein structure determination platforms have been established. The widespread use of robotics in protein crystallography has had a huge impact at every stage of the pipeline from protein cloning, over-expression, purification, crystallization, data collection, structure solution, refinement, validation and data management- all of which have become more or less automated with minimal human intervention necessary. Here, recent advances in protein crystal structure analysis in the context of structural genomics will be discussed. In addition, this review aims to give an overview of recent developments in high throughput instrumentation, and technologies and strategies to accelerate protein structure/function analysis.
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Affiliation(s)
- Babu A Manjasetty
- Case Center for Synchrotron Biosciences, National Synchrotron Light Source, Brookhaven National Laboratory, Upton, NY11973, USA.
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37
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Nocek B, Mulligan R, Bargassa M, Collart F, Joachimiak A. Crystal structure of aminopeptidase N from human pathogen Neisseria meningitidis. Proteins 2008; 70:273-9. [PMID: 17876832 PMCID: PMC2885950 DOI: 10.1002/prot.21276] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Affiliation(s)
- B. Nocek
- Midwest Center for Structural Genomics and Structural Biology Center, Biosciences Division, Argonne National Laboratory, Argonne, Illinois 60439
| | - R. Mulligan
- Midwest Center for Structural Genomics and Structural Biology Center, Biosciences Division, Argonne National Laboratory, Argonne, Illinois 60439
| | - M. Bargassa
- Midwest Center for Structural Genomics and Structural Biology Center, Biosciences Division, Argonne National Laboratory, Argonne, Illinois 60439
| | - F. Collart
- Midwest Center for Structural Genomics and Structural Biology Center, Biosciences Division, Argonne National Laboratory, Argonne, Illinois 60439
| | - A. Joachimiak
- Midwest Center for Structural Genomics and Structural Biology Center, Biosciences Division, Argonne National Laboratory, Argonne, Illinois 60439
- Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, Illinois 60637
- Correspondence to: Andrzej Joachimiak, Midwest Center for Structural Genomics and Structural Biology Center, Biosciences Division, Argonne National Laboratory, Argonne, Illinois 60439.
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38
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Maresso AW, Wu R, Kern JW, Zhang R, Janik D, Missiakas DM, Duban ME, Joachimiak A, Schneewind O. Activation of inhibitors by sortase triggers irreversible modification of the active site. J Biol Chem 2007; 282:23129-39. [PMID: 17545669 PMCID: PMC3366505 DOI: 10.1074/jbc.m701857200] [Citation(s) in RCA: 84] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023] Open
Abstract
Sortases anchor surface proteins to the cell wall of Gram-positive pathogens through recognition of specific motif sequences. Loss of sortase leads to large reductions in virulence, which identifies sortase as a target for the development of antibacterials. By screening 135,625 small molecules for inhibition, we report here that aryl (beta-amino)ethyl ketones inhibit sortase enzymes from staphylococci and bacilli. Inhibition of sortases occurs through an irreversible, covalent modification of their active site cysteine. Sortases specifically activate this class of molecules via beta-elimination, generating a reactive olefin intermediate that covalently modifies the cysteine thiol. Analysis of the three-dimensional structure of Bacillus anthracis sortase B with and without inhibitor provides insights into the mechanism of inhibition and reveals binding pockets that can be exploited for drug discovery.
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Affiliation(s)
- Anthony W Maresso
- Department of Microbiology, University of Chicago, Chicago, Illinois 60637, USA
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40
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Carmieli R, Larsen TM, Reed GH, Zein S, Neese F, Goldfarb D. The catalytic Mn2+ sites in the enolase-inhibitor complex: crystallography, single-crystal EPR, and DFT calculations. J Am Chem Soc 2007; 129:4240-52. [PMID: 17367133 PMCID: PMC2538446 DOI: 10.1021/ja066124e] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Crystals of Zn2+/Mn2+ yeast enolase with the inhibitor PhAH (phosphonoacetohydroxamate) were grown under conditions with a slight preference for binding of Zn2+ at the higher affinity site, site I. The structure of the Zn2+/Mn2+-PhAH complex was solved at a resolution of 1.54 A, and the two catalytic metal binding sites, I and II, show only subtle displacement compared to that of the corresponding complex with the native Mg2+ ions. Low-temperature echo-detected high-field (W-band, 95 GHz) EPR (electron paramagnetic resonance) and 1H ENDOR (electron-nuclear double resonance) were carried out on a single crystal, and rotation patterns were acquired in two perpendicular planes. Analysis of the rotation patterns resolved a total of six Mn2+ sites, four symmetry-related sites of one type and two out of the four of the other type. The observation of two chemically inequivalent Mn2+ sites shows that Mn2+ ions populate both sites I and II and the zero-field splitting (ZFS) tensors of the Mn2+ in the two sites were determined. The Mn2+ site with the larger D value was assigned to site I based on the 1H ENDOR spectra, which identified the relevant water ligands. This assignment is consistent with the seemingly larger deviation of site I from octahedral symmetry, compared to that of site II. The ENDOR results gave the coordinates of the protons of two water ligands, and adding them to the crystal structure revealed their involvement in a network of H bonds stabilizing the binding of the metal ions and PhAH. Although specific hyperfine interactions with the inhibitor were not determined, the spectroscopic properties of the Mn2+ in the two sites were consistent with the crystal structure. Density functional theory (DFT) calculations carried out on a cluster representing the catalytic site, with Mn2+ in site I and Zn2+ in site II, and vice versa, gave overestimated D values on the order of the experimental ones, although the larger D value was found for Mn2+ in site II rather than in site I. This discrepancy was attributed to the high sensitivity of the ZFS parameters to the Mn-O bond lengths and orientations, such that small, but significant, differences between the optimized and crystal structures alter the ZFS considerably, well above the difference between the two sites.
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Affiliation(s)
- Raanan Carmieli
- Department of Chemical Physics, The Weizmann Institute of Science, Rehovot, Israel
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41
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Lesnyak DV, Osipiuk J, Skarina T, Sergiev PV, Bogdanov AA, Edwards A, Savchenko A, Joachimiak A, Dontsova OA. Methyltransferase that modifies guanine 966 of the 16 S rRNA: functional identification and tertiary structure. J Biol Chem 2007; 282:5880-7. [PMID: 17189261 PMCID: PMC2885967 DOI: 10.1074/jbc.m608214200] [Citation(s) in RCA: 72] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
N(2)-Methylguanine 966 is located in the loop of Escherichia coli 16 S rRNA helix 31, forming a part of the P-site tRNA-binding pocket. We found yhhF to be a gene encoding for m(2)G966 specific 16 S rRNA methyltransferase. Disruption of the yhhF gene by kanamycin resistance marker leads to a loss of modification at G966. The modification could be rescued by expression of recombinant protein from the plasmid carrying the yhhF gene. Moreover, purified m(2)G966 methyltransferase, in the presence of S-adenosylomethionine (AdoMet), is able to methylate 30 S ribosomal subunits that were purified from yhhF knock-out strain in vitro. The methylation is specific for G966 base of the 16 S rRNA. The m(2)G966 methyltransferase was crystallized, and its structure has been determined and refined to 2.05A(.) The structure closely resembles RsmC rRNA methyltransferase, specific for m(2)G1207 of the 16 S rRNA. Structural comparisons and analysis of the enzyme active site suggest modes for binding AdoMet and rRNA to m(2)G966 methyltransferase. Based on the experimental data and current nomenclature the protein expressed from the yhhF gene was renamed to RsmD. A model for interaction of RsmD with ribosome has been proposed.
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Affiliation(s)
- Dmitry V. Lesnyak
- Department of Bioinformatics and Bioengineering, Moscow State University, Moscow 119992, Russia
| | - Jerzy Osipiuk
- Midwest Center for Structural Genomics and Structural Biology Center, Biosciences Division, Argonne National Laboratory, Argonne, Illinois 60439
| | - Tatiana Skarina
- Banting and Best Department of Medical Research, University of Toronto, Toronto, Ontario M5G IL6, Canada
| | - Petr V. Sergiev
- Department of Chemistry and A.N. Belozersky Institute of Physico-Chemical Biology, Moscow State University, Moscow 119992, Russia
| | - Alexey A. Bogdanov
- Department of Chemistry and A.N. Belozersky Institute of Physico-Chemical Biology, Moscow State University, Moscow 119992, Russia
| | - Aled Edwards
- Banting and Best Department of Medical Research, University of Toronto, Toronto, Ontario M5G IL6, Canada
| | - Alexei Savchenko
- Banting and Best Department of Medical Research, University of Toronto, Toronto, Ontario M5G IL6, Canada
| | - Andrzej Joachimiak
- Midwest Center for Structural Genomics and Structural Biology Center, Biosciences Division, Argonne National Laboratory, Argonne, Illinois 60439
| | - Olga A. Dontsova
- Department of Chemistry and A.N. Belozersky Institute of Physico-Chemical Biology, Moscow State University, Moscow 119992, Russia
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42
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Koroleva O, Makharashvili N, Courcelle CT, Courcelle J, Korolev S. Structural conservation of RecF and Rad50: implications for DNA recognition and RecF function. EMBO J 2007; 26:867-77. [PMID: 17255941 PMCID: PMC1794394 DOI: 10.1038/sj.emboj.7601537] [Citation(s) in RCA: 45] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2006] [Accepted: 12/08/2006] [Indexed: 11/09/2022] Open
Abstract
RecF, together with RecO and RecR, belongs to a ubiquitous group of recombination mediators (RMs) that includes eukaryotic proteins such as Rad52 and BRCA2. RMs help maintain genome stability in the presence of DNA damage by loading RecA-like recombinases and displacing single-stranded DNA-binding proteins. Here, we present the crystal structure of RecF from Deinococcus radiodurans. RecF exhibits a high degree of structural similarity with the head domain of Rad50, but lacks its long coiled-coil region. The structural homology between RecF and Rad50 is extensive, encompassing the ATPase subdomain and the so-called 'Lobe II' subdomain of Rad50. The pronounced structural conservation between bacterial RecF and evolutionarily diverged eukaryotic Rad50 implies a conserved mechanism of DNA binding and recognition of the boundaries of double-stranded DNA regions. The RecF structure, mutagenesis of conserved motifs and ATP-dependent dimerization of RecF are discussed with respect to its role in promoting presynaptic complex formation at DNA damage sites.
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Affiliation(s)
- Olga Koroleva
- Edward A Doisy Department of Biochemistry and Molecular Biology, Saint Louis University School of Medicine, St Louis, MO, USA
| | - Nodar Makharashvili
- Edward A Doisy Department of Biochemistry and Molecular Biology, Saint Louis University School of Medicine, St Louis, MO, USA
| | | | - Justin Courcelle
- Department of Biology, Portland State University, Portland, OR, USA
| | - Sergey Korolev
- Edward A Doisy Department of Biochemistry and Molecular Biology, Saint Louis University School of Medicine, St Louis, MO, USA
- Department of Biochemistry and Molecular Biology, St Louis University School of Medicine, 1402 South Grand Blvd, St Louis, MO 63104, USA. Tel.: +1 314 977 9261; Fax: +1 314 977 9205; E-mail:
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43
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Osipiuk J, Maltseva N, Dementieva I, Clancy S, Collart F, Joachimiak A. Structure of YidB protein from Shigella flexneri shows a new fold with homeodomain motif. Proteins 2006; 65:509-13. [PMID: 16927377 PMCID: PMC2885951 DOI: 10.1002/prot.21054] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Affiliation(s)
| | | | | | | | | | - Andrzej Joachimiak
- Correspondence to: Dr. Andrzej Joachimiak, Biosciences Division, Midwest Center for Structural Genomics and Structural Biology Center, Argonne National Laboratory, 9700 S Cass Ave. Argonne, IL 60439.
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44
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Zhang R, Joachimiak G, Jiang S, Cipriani A, Collart F, Joachimiak A. Structure of phage protein BC1872 from Bacillus cereus, a singleton with new fold. Proteins 2006; 64:280-3. [PMID: 16596646 PMCID: PMC2792010 DOI: 10.1002/prot.20910] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Affiliation(s)
| | | | | | | | | | - A. Joachimiak
- Correspondence to: Andrzej Joachimiak, Structural Biology Center and Midwest Center for Structural Genomics, Biosciences, Argonne National Laboratory, 9700 South Cass Ave., Bldg. 202, Argonne, IL 60439.
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45
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Kim Y, Maltseva N, Dementieva I, Collart F, Holzle D, Joachimiak A. Crystal structure of hypothetical protein YfiH from Shigella flexneri at 2 A resolution. Proteins 2006; 63:1097-101. [PMID: 16498617 PMCID: PMC2792012 DOI: 10.1002/prot.20589] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
| | | | | | | | | | - Andrzej Joachimiak
- Correspondence to: Andrzej Joachimiak, Biosciences Division, Midwest Center for Structural Genomics and Structural Biology, Center, Argonne National Laboratory, 9700 South Cass Avenue, Argonne, IL 60439.
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46
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Nocek B, Cuff M, Evdokimova E, Edwards A, Joachimiak A, Savchenko A. 1.6 A crystal structure of a PA2721 protein from pseudomonas aeruginosa--a potential drug-resistance protein. Proteins 2006; 63:1102-5. [PMID: 16493657 PMCID: PMC2792011 DOI: 10.1002/prot.20659] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- B. Nocek
- Midwest Center for Structural Genomics and Structural Biology Center, Biosciences Division, Argonne National Laboratory, Argonne, Illinois
| | - M. Cuff
- Midwest Center for Structural Genomics and Structural Biology Center, Biosciences Division, Argonne National Laboratory, Argonne, Illinois
| | - E. Evdokimova
- Banting and Best Department of Medical Research, University of Toronto, Toronto, Ontario, Canada
| | - A. Edwards
- Banting and Best Department of Medical Research, University of Toronto, Toronto, Ontario, Canada
- Clinical Genomics Centre/Proteomics, University Health Network, Toronto, Ontario, Canada
- Correspondence to: Andrzej Joachimiak, Midwest Center for Structural Genomics and Structural Biology Center, Biosciences Division, Argonne National Laboratory, 9700 South Cass Avenue, Building 202, Argonne, IL 60439.
| | - A. Joachimiak
- Midwest Center for Structural Genomics and Structural Biology Center, Biosciences Division, Argonne National Laboratory, Argonne, Illinois
- The University of Chicago, Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, Illinois
- Correspondence to: Andrzej Joachimiak, Midwest Center for Structural Genomics and Structural Biology Center, Biosciences Division, Argonne National Laboratory, 9700 South Cass Avenue, Building 202, Argonne, IL 60439.
| | - A. Savchenko
- Banting and Best Department of Medical Research, University of Toronto, Toronto, Ontario, Canada
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47
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Zhang R, Minh T, Lezondra L, Korolev S, Moy S, Collart F, Joachimiak A. 1.6 A crystal structure of YteR protein from Bacillus subtilis, a predicted lyase. Proteins 2006; 60:561-5. [PMID: 15906318 PMCID: PMC2792013 DOI: 10.1002/prot.20410] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Affiliation(s)
- R. Zhang
- Structural Biology Center, Midwest Center for Structural Genomics, Biosciences, Argonne National Laboratory
| | - T. Minh
- Structural Biology Center, Midwest Center for Structural Genomics, Biosciences, Argonne National Laboratory
- College of Chemistry, University of California at Berkeley, Berkeley, CA
| | - L. Lezondra
- Structural Biology Center, Midwest Center for Structural Genomics, Biosciences, Argonne National Laboratory
| | - S. Korolev
- Structural Biology Center, Midwest Center for Structural Genomics, Biosciences, Argonne National Laboratory
| | - S.F. Moy
- Structural Biology Center, Midwest Center for Structural Genomics, Biosciences, Argonne National Laboratory
| | - F. Collart
- Structural Biology Center, Midwest Center for Structural Genomics, Biosciences, Argonne National Laboratory
| | - A. Joachimiak
- Structural Biology Center, Midwest Center for Structural Genomics, Biosciences, Argonne National Laboratory
- Correspondence to: Andrzej Joachimiak, Structural Biology Center, Midwest Center for Structural Genomics, Biosciences, Argonne National Laboratory, 9700 South Cass Ave., Bldg. 202, Argonne, IL 60439.
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48
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Qiu Y, Tereshko V, Kim Y, Zhang R, Collart F, Yousef M, Kossiakoff A, Joachimiak A. The crystal structure of Aq_328 from the hyperthermophilic bacteria Aquifex aeolicus shows an ancestral histone fold. Proteins 2006; 62:8-16. [PMID: 16287087 PMCID: PMC2792020 DOI: 10.1002/prot.20590] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
The structure of Aq_328, an uncharacterized protein from hyperthermophilic bacteria Aquifex aeolicus, has been determined to 1.9 A by using multi-wavelength anomalous diffraction (MAD) phasing. Although the amino acid sequence analysis shows that Aq_328 has no significant similarity to proteins with a known structure and function, the structure comparison by using the Dali server reveals that it: (1) assumes a histone-like fold, and (2) is similar to an ancestral nuclear histone protein (PDB code 1F1E) with z-score 8.1 and RMSD 3.6 A over 124 residues. A sedimentation equilibrium experiment indicates that Aq_328 is a monomer in solution, with an average sedimentation coefficient of 2.4 and an apparent molecular weight of about 20 kDa. The overall architecture of Aq_328 consists of two noncanonical histone domains in tandem repeat within a single chain, and is similar to eukaryotic heterodimer (H2A/H2B and H3/H4) and an archaeal histone heterodimer (HMfA/HMfB). The sequence comparisons between the two histone domains of Aq_328 and six eukaryotic/archaeal histones demonstrate that most of the conserved residues that underlie the Aq_328 architecture are used to build and stabilize the two cross-shaped antiparallel histone domains. The high percentage of salt bridges in the structure could be a factor in the protein's thermostability. The structural similarities to other histone-like proteins, molecular properties, and potential function of Aq_328 are discussed in this paper.
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Affiliation(s)
- Yang Qiu
- The University of Chicago, Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, Illinois
| | - Valentina Tereshko
- The University of Chicago, Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, Illinois
| | - Youngchang Kim
- Structural Biology Center and Midwest Center for Structural Genomics, Biosciences Division, Argonne National Laboratory, Argonne, Illinois
| | - Rongguang Zhang
- Structural Biology Center and Midwest Center for Structural Genomics, Biosciences Division, Argonne National Laboratory, Argonne, Illinois
| | - Frank Collart
- Structural Biology Center and Midwest Center for Structural Genomics, Biosciences Division, Argonne National Laboratory, Argonne, Illinois
| | - Mohammed Yousef
- The University of Chicago, Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, Illinois
| | - Anthony Kossiakoff
- The University of Chicago, Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, Illinois
| | - Andrzej Joachimiak
- The University of Chicago, Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, Illinois
- Structural Biology Center and Midwest Center for Structural Genomics, Biosciences Division, Argonne National Laboratory, Argonne, Illinois
- Correspondence to: Andrzej Joachimiak, Structural Biology Center and Midwest Center for Structural Genomics, Biosciences Division, Argonne National Laboratory, 9700 South Cass Avenue, Building 202, Argonne, Illinois 60439. and Anthony Kossia-koff, The University of Chicago, Department of Biochemistry and Molecular Biology, University of Chicago, 920 E. 58 St., Chicago, IL 60637.
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49
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Nocek B, Chang C, Li H, Lezondra L, Holzle D, Collart F, Joachimiak A. Crystal structures of delta1-pyrroline-5-carboxylate reductase from human pathogens Neisseria meningitides and Streptococcus pyogenes. J Mol Biol 2005; 354:91-106. [PMID: 16233902 PMCID: PMC2792033 DOI: 10.1016/j.jmb.2005.08.036] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2005] [Revised: 08/12/2005] [Accepted: 08/17/2005] [Indexed: 10/25/2022]
Abstract
L-proline is an amino acid that plays an important role in proteins uniquely contributing to protein folding, structure, and stability, and this amino acid serves as a sequence-recognition motif. Proline biosynthesis can occur via two pathways, one from glutamate and the other from arginine. In both pathways, the last step of biosynthesis, the conversion of delta1-pyrroline-5-carboxylate (P5C) to L-proline, is catalyzed by delta1-pyrroline-5-carboxylate reductase (P5CR) using NAD(P)H as a cofactor. We have determined the first crystal structure of P5CR from two human pathogens, Neisseria meningitides and Streptococcus pyogenes, at 2.0 angstroms and 2.15 angstroms resolution, respectively. The catalytic unit of P5CR is a dimer composed of two domains, but the biological unit seems to be species-specific. The N-terminal domain of P5CR is an alpha/beta/alpha sandwich, a Rossmann fold. The C-terminal dimerization domain is rich in alpha-helices and shows domain swapping. Comparison of the native structure of P5CR to structures complexed with L-proline and NADP+ in two quite different primary sequence backgrounds provides unique information about key functional features: the active site and the catalytic mechanism. The inhibitory L-proline has been observed in the crystal structure.
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Affiliation(s)
- B. Nocek
- Midwest Center for Structural Genomics and Structural Biology Center, Biosciences Division, Argonne National Laboratory, 9700 South Cass Avenue, Building 202, Argonne IL 60439, USA
| | - C. Chang
- Midwest Center for Structural Genomics and Structural Biology Center, Biosciences Division, Argonne National Laboratory, 9700 South Cass Avenue, Building 202, Argonne IL 60439, USA
| | - H. Li
- Midwest Center for Structural Genomics and Structural Biology Center, Biosciences Division, Argonne National Laboratory, 9700 South Cass Avenue, Building 202, Argonne IL 60439, USA
| | - L. Lezondra
- Midwest Center for Structural Genomics and Structural Biology Center, Biosciences Division, Argonne National Laboratory, 9700 South Cass Avenue, Building 202, Argonne IL 60439, USA
| | - D. Holzle
- Midwest Center for Structural Genomics and Structural Biology Center, Biosciences Division, Argonne National Laboratory, 9700 South Cass Avenue, Building 202, Argonne IL 60439, USA
| | - F. Collart
- Midwest Center for Structural Genomics and Structural Biology Center, Biosciences Division, Argonne National Laboratory, 9700 South Cass Avenue, Building 202, Argonne IL 60439, USA
| | - A. Joachimiak
- Midwest Center for Structural Genomics and Structural Biology Center, Biosciences Division, Argonne National Laboratory, 9700 South Cass Avenue, Building 202, Argonne IL 60439, USA
- The University of Chicago Department of Biochemistry and Molecular Biology, University of Chicago, 920 E. 58th St. Chicago, IL 60637, USA
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Carugo O, Djinović Carugo K. When X-rays modify the protein structure: radiation damage at work. Trends Biochem Sci 2005; 30:213-9. [PMID: 15817398 DOI: 10.1016/j.tibs.2005.02.009] [Citation(s) in RCA: 99] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The majority of 3D structures of macromolecules are currently determined by macromolecular crystallography, which employs the diffraction of X-rays on single crystals. However, during diffraction experiments, the X-rays can damage the protein crystals by ionization processes, especially when powerful X-ray sources at synchrotron facilities are used. This process of radiation damage generates photo-electrons that can get trapped in protein moieties. The 3D structure derived from such experiments can differ remarkably from the structure of the native molecule. Recently, the crystal structures of different oxidation states of horseradish peroxidase and nickel-containing superoxide dismutase were determined using crystallographic redox titration performed during the exposure of the crystals to the incident X-ray beam. Previous crystallographic analyses have not shown the distinct structures of the active sites associated with the redox state of the structural features of these enzymes. These new studies show that, for protein moieties that are susceptible to radiation damage and prone to reduction by photo-electrons, care is required in both the design of the diffraction experiment and the analysis and interpretation.
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Affiliation(s)
- Oliviero Carugo
- Department of General Chemistry, University of Pavia, Via Taramelli 12, 27100 Pavia, Italy.
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