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Jeffery CJ. Current successes and remaining challenges in protein function prediction. FRONTIERS IN BIOINFORMATICS 2023; 3:1222182. [PMID: 37576715 PMCID: PMC10415035 DOI: 10.3389/fbinf.2023.1222182] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2023] [Accepted: 07/03/2023] [Indexed: 08/15/2023] Open
Abstract
In recent years, improvements in protein function prediction methods have led to increased success in annotating protein sequences. However, the functions of over 30% of protein-coding genes remain unknown for many sequenced genomes. Protein functions vary widely, from catalyzing chemical reactions to binding DNA or RNA or forming structures in the cell, and some types of functions are challenging to predict due to the physical features associated with those functions. Other complications in understanding protein functions arise due to the fact that many proteins have more than one function or very small differences in sequence or structure that correspond to different functions. We will discuss some of the recent developments in predicting protein functions and some of the remaining challenges.
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Affiliation(s)
- Constance J. Jeffery
- Department of Biological Sciences, University of Illinois at Chicago, Chicago, IL, United States
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2
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Allen KN, Whitman CP. The Birth of Genomic Enzymology: Discovery of the Mechanistically Diverse Enolase Superfamily. Biochemistry 2021; 60:3515-3528. [PMID: 34664940 DOI: 10.1021/acs.biochem.1c00494] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
Enzymes are categorized into superfamilies by sequence, structural, and mechanistic similarities. The evolutionary implications can be profound. Until the mid-1990s, the approach was fragmented largely due to limited sequence and structural data. However, in 1996, Babbitt et al. published a paper in Biochemistry that demonstrated the potential power of mechanistically diverse superfamilies to identify common ancestry, predict function, and, in some cases, predict specificity. This Perspective describes the findings of the original work and reviews the current understanding of structure and mechanism in the founding family members. The outcomes of the genomic enzymology approach have reached far beyond the functional assignment of members of the enolase superfamily, inspiring the study of superfamilies and the adoption of sequence similarity networks and genome context and yielding fundamental insights into enzyme evolution.
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Affiliation(s)
- Karen N Allen
- Department of Chemistry, Boston University, Boston, Massachusetts 02215, United States
| | - Christian P Whitman
- Division of Chemical Biology and Medicinal Chemistry, College of Pharmacy, The University of Texas at Austin, Austin, Texas 78712, United States
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3
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Jeffery CJ, Dorgan KM, Pysh L. Promoting a more integrated approach to structure and function. Integr Comp Biol 2021; 61:2020-2030. [PMID: 34180524 DOI: 10.1093/icb/icab144] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
The connection between structure and function is one of the fundamental tenets of biology: a biological unit's structure determines its function, and, conversely, its function depends upon its structure. Historically, important advances have been made either when understanding of structure leads to questions about function or when understanding of function raises questions about the structures involved. Consequently, considering the connections between structure and function from a broader perspective might lead to the development of novel hypotheses that move our understanding of the fundamental connections between structure and function forward. Better integration of structure and function is a key component in the broader goal of reintegrating biology within and across scales. Here, we provide examples of how integrating studies of structure and function as well as comparing structure-function relationships across biological scales can lead to scientific advances. We also emphasize the potential of integrating studies of structure and function across scales for bio-inspired design and for improving biology education.
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Affiliation(s)
- Constance J Jeffery
- Department of Biological Sciences, University of Illinois at Chicago, Chicago, IL 60607, USA
| | | | - Leonard Pysh
- Biology Department, Roanoke College, Salem, VA, 24153, USA
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4
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Jeffery CJ. Enzymes, pseudoenzymes, and moonlighting proteins: diversity of function in protein superfamilies. FEBS J 2020; 287:4141-4149. [PMID: 32534477 DOI: 10.1111/febs.15446] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2019] [Revised: 03/20/2020] [Accepted: 06/08/2020] [Indexed: 12/31/2022]
Abstract
As more genome sequences are elucidated, there is an increasing need for information about the functions of the millions of proteins they encode. The function of a newly sequenced protein is often estimated by sequence alignment with the sequences of proteins with known functions. However, protein superfamilies can contain members that share significant amino acid sequence and structural homology yet catalyze different reactions or act on different substrates. Some homologous proteins differ by having a second or even third function, called moonlighting proteins. More recently, it was found that most protein superfamilies also include pseudoenzymes, a protein, or a domain within a protein, that has a three-dimensional fold that resembles a conventional catalytically active enzyme, but has no catalytic activity. In this review, we discuss several examples of protein families that contain enzymes, pseudoenzymes, and moonlighting proteins. It is becoming clear that pseudoenzymes and moonlighting proteins are widespread in the evolutionary tree, and in many protein families, and they are often very similar in sequence and structure to their monofunctional and catalytically active counterparts. A greater understanding is needed to clarify when similarities and differences in amino acid sequences and structures correspond to similarities and differences in biochemical functions and cellular roles. This information can help improve programs that identify protein functions from sequence or structure and assist in more accurate annotation of sequence and structural databases, as well as in our understanding of the broad diversity of protein functions.
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Affiliation(s)
- Constance J Jeffery
- Department of Biological Sciences, University of Illinois at Chicago, IL, USA
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Harty ML, Sharma AN, Bearne SL. Catalytic properties of the metal ion variants of mandelate racemase reveal alterations in the apparent electrophilicity of the metal cofactor. Metallomics 2020; 11:707-723. [PMID: 30843025 DOI: 10.1039/c8mt00330k] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
Mandalate racemase (MR) from Pseudomonas putida requires a divalent metal cation, usually Mg2+, to catalyse the interconversion of the enantiomers of mandelate. Although the active site Mg2+ may be replaced by Mn2+, Co2+, or Ni2+, substitution by these metal ions does not markedly (<10-fold) alter the kinetic parameters Kappm, kappcat, and (kcat/Km)app for the substrates (R)- and (S)-mandelate, and the alternative substrate (S)-trifluorolactate. Viscosity variation experiments with Mn2+-MR showed that the metal ion plays a role in the uniform binding of the transition states for enzyme-substrate association, the chemical step, and enzyme-product dissociation. Surprisingly, the competitive inhibition constants (Ki) for inhibition of each metalloenzyme variant by benzohydroxamate did not vary significantly with the identity of the metal ion unlike the marked variation of the stability constants (K1) observed for M2+·BzH complex formation in solution. A similar trend was observed for the inhibition of the metalloenzyme variants by F-, except for Mg2+-MR, which bound F- tighter than would be predicted based on the stability constants for formation of M2+·F- complexes in solution. Thus, the enzyme modifies the enatic state of the bound metal ion cofactor so that the apparent electrophilicity of Mg2+ is enhanced, while that of Ni2+ is attenuated, resulting in a levelling effect relative to the trends observed for the free metals in solution.
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Affiliation(s)
- Matthew L Harty
- Department of Biochemistry and Molecular Biology, Dalhousie University, Halifax, NS B3H 4R2, Canada.
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6
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Stampfli AR, Goncharenko KV, Meury M, Dubey BN, Schirmer T, Seebeck FP. An Alternative Active Site Architecture for O 2 Activation in the Ergothioneine Biosynthetic EgtB from Chloracidobacterium thermophilum. J Am Chem Soc 2019; 141:5275-5285. [PMID: 30883103 DOI: 10.1021/jacs.8b13023] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Sulfoxide synthases are nonheme iron enzymes that catalyze oxidative carbon-sulfur bond formation between cysteine derivatives and N-α-trimethylhistidine as a key step in the biosynthesis of thiohistidines. The complex catalytic mechanism of this enzyme reaction has emerged as the controversial subject of several biochemical and computational studies. These studies all used the structure of the γ-glutamyl cysteine utilizing sulfoxide synthase, MthEgtB from Mycobacterium thermophilum (EC 1.14.99.50), as a structural basis. To provide an alternative model system, we have solved the crystal structure of CthEgtB from Chloracidobacterium thermophilum (EC 1.14.99.51) that utilizes cysteine as a sulfur donor. This structure reveals a completely different configuration of active site residues that are involved in oxygen binding and activation. Furthermore, comparison of the two EgtB structures enables a classification of all ergothioneine biosynthetic EgtBs into five subtypes, each characterized by unique active-site features. This active site diversity provides an excellent platform to examine the catalytic mechanism of sulfoxide synthases by comparative enzymology, but also raises the question as to why so many different solutions to the same biosynthetic problem have emerged.
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Affiliation(s)
- Anja R Stampfli
- Department of Chemistry , University of Basel , Mattenstrasse 24a , Basel 4002 , Switzerland.,Focal Area Structural Biology and Biophysics, Biozentrum , University of Basel , Basel 4056 , Switzerland
| | - Kristina V Goncharenko
- Department of Chemistry , University of Basel , Mattenstrasse 24a , Basel 4002 , Switzerland
| | - Marcel Meury
- Department of Chemistry , University of Basel , Mattenstrasse 24a , Basel 4002 , Switzerland
| | - Badri N Dubey
- Focal Area Structural Biology and Biophysics, Biozentrum , University of Basel , Basel 4056 , Switzerland
| | - Tilman Schirmer
- Focal Area Structural Biology and Biophysics, Biozentrum , University of Basel , Basel 4056 , Switzerland
| | - Florian P Seebeck
- Department of Chemistry , University of Basel , Mattenstrasse 24a , Basel 4002 , Switzerland
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Bearne SL, St Maurice M. A Paradigm for CH Bond Cleavage: Structural and Functional Aspects of Transition State Stabilization by Mandelate Racemase. ADVANCES IN PROTEIN CHEMISTRY AND STRUCTURAL BIOLOGY 2017; 109:113-160. [PMID: 28683916 DOI: 10.1016/bs.apcsb.2017.04.007] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
Mandelate racemase (MR) from Pseudomonas putida catalyzes the Mg2+-dependent, 1,1-proton transfer reaction that racemizes (R)- and (S)-mandelate. MR shares a partial reaction (i.e., the metal ion-assisted, Brønsted base-catalyzed proton abstraction of the α-proton of carboxylic acid substrates) and structural features ((β/α)7β-barrel and N-terminal α + β capping domains) with a vast group of homologous, yet functionally diverse, enzymes in the enolase superfamily. Mechanistic and structural studies have developed this enzyme into a paradigm for understanding how enzymes such as those of the enolase superfamily overcome kinetic and thermodynamic barriers to catalyze the abstraction of an α-proton from a carbon acid substrate with a relatively high pKa value. Structural studies on MR bound to intermediate/transition state analogues have delineated those structural features that MR uses to stabilize transition states and enhance reaction rates of proton abstraction. Kinetic, site-directed mutagenesis, and structural studies have also revealed that the phenyl ring of the substrate migrates through the hydrophobic cavity within the active site during catalysis and that the Brønsted acid-base catalysts (Lys 166 and His 297) may be utilized as binding determinants for inhibitor recognition. In addition, structural studies on the adduct formed from the irreversible inhibition of MR by 3-hydroxypyruvate revealed that MR can form and deprotonate a Schiff-base with 3-hydroxypyruvate to yield an enol(ate)-aldehyde adduct, suggesting a possible evolutionary link between MR and the Schiff-base forming aldolases. As the archetype of the enolase superfamily, mechanistic and structural studies on MR will continue to enhance our understanding of enzyme catalysis and furnish insights into the evolution of enzyme function.
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Maimanakos J, Chow J, Gaßmeyer SK, Güllert S, Busch F, Kourist R, Streit WR. Sequence-Based Screening for Rare Enzymes: New Insights into the World of AMDases Reveal a Conserved Motif and 58 Novel Enzymes Clustering in Eight Distinct Families. Front Microbiol 2016; 7:1332. [PMID: 27610105 PMCID: PMC4996985 DOI: 10.3389/fmicb.2016.01332] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2016] [Accepted: 08/11/2016] [Indexed: 12/11/2022] Open
Abstract
Arylmalonate Decarboxylases (AMDases, EC 4.1.1.76) are very rare and mostly underexplored enzymes. Currently only four known and biochemically characterized representatives exist. However, their ability to decarboxylate α-disubstituted malonic acid derivatives to optically pure products without cofactors makes them attractive and promising candidates for the use as biocatalysts in industrial processes. Until now, AMDases could not be separated from other members of the aspartate/glutamate racemase superfamily based on their gene sequences. Within this work, a search algorithm was developed that enables a reliable prediction of AMDase activity for potential candidates. Based on specific sequence patterns and screening methods 58 novel AMDase candidate genes could be identified in this work. Thereby, AMDases with the conserved sequence pattern of Bordetella bronchiseptica’s prototype appeared to be limited to the classes of Alpha-, Beta-, and Gamma-proteobacteria. Amino acid homologies and comparison of gene surrounding sequences enabled the classification of eight enzyme clusters. Particularly striking is the accumulation of genes coding for different transporters of the tripartite tricarboxylate transporters family, TRAP transporters and ABC transporters as well as genes coding for mandelate racemases/muconate lactonizing enzymes that might be involved in substrate uptake or degradation of AMDase products. Further, three novel AMDases were characterized which showed a high enantiomeric excess (>99%) of the (R)-enantiomer of flurbiprofen. These are the recombinant AmdA and AmdV from Variovorax sp. strains HH01 and HH02, originated from soil, and AmdP from Polymorphum gilvum found by a data base search. Altogether our findings give new insights into the class of AMDases and reveal many previously unknown enzyme candidates with high potential for bioindustrial processes.
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Affiliation(s)
- Janine Maimanakos
- Department of Microbiology and Biotechnology, Biocenter Klein Flottbek, University of Hamburg Hamburg, Germany
| | - Jennifer Chow
- Department of Microbiology and Biotechnology, Biocenter Klein Flottbek, University of Hamburg Hamburg, Germany
| | - Sarah K Gaßmeyer
- Junior Research Group for Microbial Biotechnology, Ruhr-University Bochum Bochum, Germany
| | - Simon Güllert
- Department of Microbiology and Biotechnology, Biocenter Klein Flottbek, University of Hamburg Hamburg, Germany
| | - Florian Busch
- Junior Research Group for Microbial Biotechnology, Ruhr-University Bochum Bochum, Germany
| | - Robert Kourist
- Junior Research Group for Microbial Biotechnology, Ruhr-University Bochum Bochum, Germany
| | - Wolfgang R Streit
- Department of Microbiology and Biotechnology, Biocenter Klein Flottbek, University of Hamburg Hamburg, Germany
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9
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Yun EJ, Lee S, Kim HT, Pelton JG, Kim S, Ko HJ, Choi IG, Kim KH. The novel catabolic pathway of 3,6-anhydro-L-galactose, the main component of red macroalgae, in a marine bacterium. Environ Microbiol 2014; 17:1677-88. [DOI: 10.1111/1462-2920.12607] [Citation(s) in RCA: 75] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2014] [Revised: 08/18/2014] [Accepted: 08/19/2014] [Indexed: 11/27/2022]
Affiliation(s)
- Eun Ju Yun
- Department of Biotechnology; Korea University Graduate School; Seoul 136-713 Korea
| | - Saeyoung Lee
- Department of Biotechnology; Korea University Graduate School; Seoul 136-713 Korea
| | - Hee Taek Kim
- Department of Biotechnology; Korea University Graduate School; Seoul 136-713 Korea
| | - Jeffrey G. Pelton
- Physical Biosciences Division; Lawrence Berkeley National Laboratory; Berkeley CA 94720 USA
| | - Sooah Kim
- Department of Biotechnology; Korea University Graduate School; Seoul 136-713 Korea
| | - Hyeok-Jin Ko
- Department of Biotechnology; Korea University Graduate School; Seoul 136-713 Korea
| | - In-Geol Choi
- Department of Biotechnology; Korea University Graduate School; Seoul 136-713 Korea
| | - Kyoung Heon Kim
- Department of Biotechnology; Korea University Graduate School; Seoul 136-713 Korea
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10
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Kolomytseva M, Ferraroni M, Chernykh A, Golovleva L, Scozzafava A. Structural basis for the substrate specificity and the absence of dehalogenation activity in 2-chloromuconate cycloisomerase from Rhodococcus opacus 1CP. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2014; 1844:1541-9. [DOI: 10.1016/j.bbapap.2014.04.008] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/07/2014] [Revised: 04/09/2014] [Accepted: 04/13/2014] [Indexed: 11/26/2022]
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11
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Catazaro J, Caprez A, Guru A, Swanson D, Powers R. Functional evolution of PLP-dependent enzymes based on active-site structural similarities. Proteins 2014; 82:2597-608. [PMID: 24920327 DOI: 10.1002/prot.24624] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2014] [Revised: 05/30/2014] [Accepted: 06/05/2014] [Indexed: 12/29/2022]
Abstract
Families of distantly related proteins typically have very low sequence identity, which hinders evolutionary analysis and functional annotation. Slowly evolving features of proteins, such as an active site, are therefore valuable for annotating putative and distantly related proteins. To date, a complete evolutionary analysis of the functional relationship of an entire enzyme family based on active-site structural similarities has not yet been undertaken. Pyridoxal-5'-phosphate (PLP) dependent enzymes are primordial enzymes that diversified in the last universal ancestor. Using the comparison of protein active site structures (CPASS) software and database, we show that the active site structures of PLP-dependent enzymes can be used to infer evolutionary relationships based on functional similarity. The enzymes successfully clustered together based on substrate specificity, function, and three-dimensional-fold. This study demonstrates the value of using active site structures for functional evolutionary analysis and the effectiveness of CPASS.
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Affiliation(s)
- Jonathan Catazaro
- Department of Chemistry, University of Nebraska-Lincoln, Lincoln, Nebraska, 68588-0304
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12
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Nosrati GR, Houk KN. Using catalytic atom maps to predict the catalytic functions present in enzyme active sites. Biochemistry 2012; 51:7321-9. [PMID: 22909276 DOI: 10.1021/bi3008438] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Catalytic atom maps (CAMs) are minimal models of enzyme active sites. The structures in the Protein Data Bank (PDB) were examined to determine if proteins with CAM-like geometries in their active sites all share the same catalytic function. We combined the CAM-based search protocol with a filter based on the weighted contact number (WCN) of the catalytic residues, a measure of the "crowdedness" of the microenvironment around a protein residue. Using this technique, a CAM based on the Ser-His-Asp catalytic triad of trypsin was able to correctly identify catalytic triads in other enzymes within 0.5 Å rmsd of the CAM with 96% accuracy. A CAM based on the Cys-Arg-(Asp/Glu) active site residues from the tyrosine phosphatase active site achieved 89% accuracy in identifying this type of catalytic functionality. Both of these CAMs were able to identify active sites across different fold types. Finally, the PDB was searched to locate proteins with catalytic functionality similar to that present in the active site of orotidine 5'-monophosphate decarboxylase (ODCase), whose mechanism is not known with certainty. A CAM, based on the conserved Lys-Asp-Lys-Asp tetrad in the ODCase active site, was used to search the PDB for enzymes with similar active sites. The ODCase active site has a geometry similar to that of Schiff base-forming Class I aldolases, with lowest aldolase rmsd to the ODCase CAM at 0.48 Å. The similarity between this CAM and the aldolase active site suggests that ODCase has the correct catalytic functionality present in its active site for the generation of a nucleophilic lysine.
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Affiliation(s)
- Geoffrey R Nosrati
- Department of Chemistry and Biochemistry, University of California, Los Angeles, California 90095-1569, United States
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Chen BY, Bandyopadhyay S. Modeling regionalized volumetric differences in protein-ligand binding cavities. Proteome Sci 2012; 10 Suppl 1:S6. [PMID: 22759583 PMCID: PMC3390949 DOI: 10.1186/1477-5956-10-s1-s6] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023] Open
Abstract
Identifying elements of protein structures that create differences in protein-ligand
binding specificity is an essential method for explaining the molecular mechanisms
underlying preferential binding. In some cases, influential mechanisms can be
visually identified by experts in structural biology, but subtler mechanisms, whose
significance may only be apparent from the analysis of many structures, are harder to
find. To assist this process, we present a geometric algorithm and two statistical
models for identifying significant structural differences in protein-ligand binding
cavities. We demonstrate these methods in an analysis of sequentially nonredundant
structural representatives of the canonical serine proteases and the enolase
superfamily. Here, we observed that statistically significant structural variations
identified experimentally established determinants of specificity. We also observed
that an analysis of individual regions inside cavities can reveal areas where small
differences in shape can correspond to differences in specificity.
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Affiliation(s)
- Brian Y Chen
- Department of Computer Science and Engineering, Lehigh University, Bethlehem, PA, USA.
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Andberg M, Maaheimo H, Boer H, Penttilä M, Koivula A, Richard P. Characterization of a novel Agrobacterium tumefaciens galactarolactone cycloisomerase enzyme for direct conversion of D-galactarolactone to 3-deoxy-2-keto-L-threo-hexarate. J Biol Chem 2012; 287:17662-17671. [PMID: 22493433 DOI: 10.1074/jbc.m111.335240] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Microorganisms use different pathways for D-galacturonate catabolism. In the known microbial oxidative pathway, D-galacturonate is oxidized to D-galactarolactone, the lactone hydrolyzed to galactarate, which is further converted to 3-deoxy-2-keto-hexarate and α-ketoglutarate. We have shown recently that Agrobacterium tumefaciens strain C58 contains an uronate dehydrogenase (At Udh) that oxidizes D-galacturonic acid to D-galactarolactone. Here we report identification of a novel enzyme from the same A. tumefaciens strain, which we named Galactarolactone cycloisomerase (At Gci) (E.C. 5.5.1.-), for the direct conversion of the D-galactarolactone to 3-deoxy-2-keto-hexarate. The At Gci enzyme is 378 amino acids long and belongs to the mandelate racemase subgroup in the enolase superfamily. At Gci was heterologously expressed in Escherichia coli, and the purified enzyme was found to exist as an octameric form. It is active both on D-galactarolactone and D-glucarolactone, but does not work on the corresponding linear hexaric acid forms. The details of the reaction mechanism were further studied by NMR and optical rotation demonstrating that the reaction product of At Gci from D-galactaro-1,4-lactone and D-glucaro-1,4-lactone conversion is in both cases the L-threo form of 3-deoxy-2-keto-hexarate.
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Affiliation(s)
- Martina Andberg
- VTT Technical Research Centre of Finland, P.O. Box 1000, FIN-02044 VTT, Finland.
| | - Hannu Maaheimo
- VTT Technical Research Centre of Finland, P.O. Box 1000, FIN-02044 VTT, Finland
| | - Harry Boer
- VTT Technical Research Centre of Finland, P.O. Box 1000, FIN-02044 VTT, Finland
| | - Merja Penttilä
- VTT Technical Research Centre of Finland, P.O. Box 1000, FIN-02044 VTT, Finland
| | - Anu Koivula
- VTT Technical Research Centre of Finland, P.O. Box 1000, FIN-02044 VTT, Finland
| | - Peter Richard
- VTT Technical Research Centre of Finland, P.O. Box 1000, FIN-02044 VTT, Finland
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15
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Skolnick J, Brylinski M. FINDSITE: a combined evolution/structure-based approach to protein function prediction. Brief Bioinform 2009; 10:378-91. [PMID: 19324930 DOI: 10.1093/bib/bbp017] [Citation(s) in RCA: 72] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
A key challenge of the post-genomic era is the identification of the function(s) of all the molecules in a given organism. Here, we review the status of sequence and structure-based approaches to protein function inference and ligand screening that can provide functional insights for a significant fraction of the approximately 50% of ORFs of unassigned function in an average proteome. We then describe FINDSITE, a recently developed algorithm for ligand binding site prediction, ligand screening and molecular function prediction, which is based on binding site conservation across evolutionary distant proteins identified by threading. Importantly, FINDSITE gives comparable results when high-resolution experimental structures as well as predicted protein models are used.
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Affiliation(s)
- Jeffrey Skolnick
- Center for the Study of Systems Biology, School of Biology, Georgia Institute of Technology 250 14th St NW, Atlanta, GA 30318, USA.
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16
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Sakai A, Fedorov AA, Fedorov EV, Schnoes AM, Glasner ME, Brown S, Rutter ME, Bain K, Chang S, Gheyi T, Sauder JM, Burley SK, Babbitt PC, Almo SC, Gerlt JA. Evolution of enzymatic activities in the enolase superfamily: stereochemically distinct mechanisms in two families of cis,cis-muconate lactonizing enzymes. Biochemistry 2009; 48:1445-53. [PMID: 19220063 PMCID: PMC2746992 DOI: 10.1021/bi802277h] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
The mechanistically diverse enolase superfamily is a paradigm for elucidating Nature's strategies for divergent evolution of enzyme function. Each of the different reactions catalyzed by members of the superfamily is initiated by abstraction of the alpha-proton of a carboxylate substrate that is coordinated to an essential Mg(2+). The muconate lactonizing enzyme (MLE) from Pseudomonas putida, a member of a family that catalyzes the syn-cycloisomerization of cis,cis-muconate to (4S)-muconolactone in the beta-ketoadipate pathway, has provided critical insights into the structural bases for evolution of function within the superfamily. A second, divergent family of homologous MLEs that catalyzes anti-cycloisomerization has been identified. Structures of members of both families liganded with the common (4S)-muconolactone product (syn, Pseudomonas fluorescens, gi 70731221 ; anti, Mycobacterium smegmatis, gi 118470554 ) document that the conserved Lys at the end of the second beta-strand in the (beta/alpha)(7)beta-barrel domain serves as the acid catalyst in both reactions. The different stereochemical courses (syn and anti) result from different structural strategies for determining substrate specificity: although the distal carboxylate group of the cis,cis-muconate substrate attacks the same face of the proximal double bond, opposite faces of the resulting enolate anion intermediate are presented to the conserved Lys acid catalyst. The discovery of two families of homologous, but stereochemically distinct, MLEs likely provides an example of "pseudoconvergent" evolution of the same function from different homologous progenitors within the enolase superfamily, in which different spatial arrangements of active site functional groups and substrate specificity determinants support catalysis of the same reaction.
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Affiliation(s)
- Ayano Sakai
- Center for Biophysics and Computational Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801
| | - Alexander A. Fedorov
- Department of Biochemistry, Albert Einstein College of Medicine, Bronx, New York 10461,New York SGX Research Center for Structural Genomics (NYSGXRC), Albert Einstein College of Medicine, Bronx, New York 10461
| | - Elena V. Fedorov
- Department of Biochemistry, Albert Einstein College of Medicine, Bronx, New York 10461
| | - Alexandra M. Schnoes
- Department of Biopharmaceutical Sciences, School of Pharmacy and California Institute for Quantitative Biomedical Research, University of California, 1700 4th Street, San Francisco, California 94158
| | - Margaret E. Glasner
- Department of Biopharmaceutical Sciences, School of Pharmacy and California Institute for Quantitative Biomedical Research, University of California, 1700 4th Street, San Francisco, California 94158
| | - Shoshana Brown
- Department of Biopharmaceutical Sciences, School of Pharmacy and California Institute for Quantitative Biomedical Research, University of California, 1700 4th Street, San Francisco, California 94158
| | - Marc E. Rutter
- New York SGX Research Center for Structural Genomics (NYSGXRC), SGX Pharmaceuticals, Inc. 10505 Roselle St, San Diego, CA92121
| | - Kevin Bain
- New York SGX Research Center for Structural Genomics (NYSGXRC), SGX Pharmaceuticals, Inc. 10505 Roselle St, San Diego, CA92121
| | - Shawn Chang
- New York SGX Research Center for Structural Genomics (NYSGXRC), SGX Pharmaceuticals, Inc. 10505 Roselle St, San Diego, CA92121
| | - Tarun Gheyi
- New York SGX Research Center for Structural Genomics (NYSGXRC), SGX Pharmaceuticals, Inc. 10505 Roselle St, San Diego, CA92121
| | - J. Michael Sauder
- New York SGX Research Center for Structural Genomics (NYSGXRC), SGX Pharmaceuticals, Inc. 10505 Roselle St, San Diego, CA92121
| | - Stephen K. Burley
- New York SGX Research Center for Structural Genomics (NYSGXRC), SGX Pharmaceuticals, Inc. 10505 Roselle St, San Diego, CA92121
| | - Patricia C. Babbitt
- Department of Biopharmaceutical Sciences, School of Pharmacy and California Institute for Quantitative Biomedical Research, University of California, 1700 4th Street, San Francisco, California 94158,To whom correspondence should be addressed: J.A.G.: Department of Biochemistry, University of Illinois, 600 S. Mathews Avenue, Urbana, IL 61801. Phone: (217) 244-7414. Fax: (217) 244-6538. E-mail: S.C.A.: Department of Biochemistry, Albert Einstein College of Medicine, 1300 Morris Park Avenue, Bronx, NY 10461. Phone: (718) 430-2746. Fax: (718) 430-8565. E-mail: P.C.B., Department of Biopharmaceutical Sciences, University of California, San Francisco, 1700 South 4th Street, San Francisco, CA 94158. Phone: (415) 476-3784. Fax: (415) 514-4797. E-mail:
| | - Steven C. Almo
- Department of Biochemistry, Albert Einstein College of Medicine, Bronx, New York 10461,New York SGX Research Center for Structural Genomics (NYSGXRC), Albert Einstein College of Medicine, Bronx, New York 10461,To whom correspondence should be addressed: J.A.G.: Department of Biochemistry, University of Illinois, 600 S. Mathews Avenue, Urbana, IL 61801. Phone: (217) 244-7414. Fax: (217) 244-6538. E-mail: S.C.A.: Department of Biochemistry, Albert Einstein College of Medicine, 1300 Morris Park Avenue, Bronx, NY 10461. Phone: (718) 430-2746. Fax: (718) 430-8565. E-mail: P.C.B., Department of Biopharmaceutical Sciences, University of California, San Francisco, 1700 South 4th Street, San Francisco, CA 94158. Phone: (415) 476-3784. Fax: (415) 514-4797. E-mail:
| | - John A. Gerlt
- Departments of Biochemistry and Chemistry, University of Illinois at Urbana-Champaign, Urbana, IL 61801,To whom correspondence should be addressed: J.A.G.: Department of Biochemistry, University of Illinois, 600 S. Mathews Avenue, Urbana, IL 61801. Phone: (217) 244-7414. Fax: (217) 244-6538. E-mail: S.C.A.: Department of Biochemistry, Albert Einstein College of Medicine, 1300 Morris Park Avenue, Bronx, NY 10461. Phone: (718) 430-2746. Fax: (718) 430-8565. E-mail: P.C.B., Department of Biopharmaceutical Sciences, University of California, San Francisco, 1700 South 4th Street, San Francisco, CA 94158. Phone: (415) 476-3784. Fax: (415) 514-4797. E-mail:
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17
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Song L, Kalyanaraman C, Fedorov AA, Fedorov EV, Glasner ME, Brown S, Imker HJ, Babbitt PC, Almo SC, Jacobson MP, Gerlt JA. Prediction and assignment of function for a divergent N-succinyl amino acid racemase. Nat Chem Biol 2007; 3:486-91. [PMID: 17603539 DOI: 10.1038/nchembio.2007.11] [Citation(s) in RCA: 86] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2007] [Accepted: 06/10/2007] [Indexed: 11/08/2022]
Abstract
The protein databases contain many proteins with unknown function. A computational approach for predicting ligand specificity that requires only the sequence of the unknown protein would be valuable for directing experiment-based assignment of function. We focused on a family of unknown proteins in the mechanistically diverse enolase superfamily and used two approaches to assign function: (i) enzymatic assays using libraries of potential substrates, and (ii) in silico docking of the same libraries using a homology model based on the most similar (35% sequence identity) characterized protein. The results matched closely; an experimentally determined structure confirmed the predicted structure of the substrate-liganded complex. We assigned the N-succinyl arginine/lysine racemase function to the family, correcting the annotation (L-Ala-D/L-Glu epimerase) based on the function of the most similar characterized homolog. These studies establish that ligand docking to a homology model can facilitate functional assignment of unknown proteins by restricting the identities of the possible substrates that must be experimentally tested.
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Affiliation(s)
- Ling Song
- Department of Biochemistry, University of Illinois at Urbana-Champaign, 600 South Mathews Avenue, Urbana, Illinois 61801, USA
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18
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Woycechowsky KJ, Vamvaca K, Hilvert D. Novel enzymes through design and evolution. ADVANCES IN ENZYMOLOGY AND RELATED AREAS OF MOLECULAR BIOLOGY 2007; 75:241-94, xiii. [PMID: 17124869 DOI: 10.1002/9780471224464.ch4] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
The generation of enzymes with new catalytic activities remains a major challenge. So far, several different strategies have been developed to tackle this problem, including site-directed mutagenesis, random mutagenesis (directed evolution), antibody catalysis, computational redesign, and de novo methods. Using these techniques, a broad array of novel enzymes has been created (aldolases, decarboxylases, dehydratases, isomerases, oxidases, reductases, and others), although their low efficiencies (10 to 100 M(-1) s(-l)) compared to those of the best natural enzymes (10(6) to 10(8) M(-1) s(-1)) remains a significant concern. Whereas rational design might be the most promising and versatile approach to generating new activities, directed evolution seems to be the best way to optimize the catalytic properties of novel enzymes. Indeed, impressive successes in enzyme engineering have resulted from a combination of rational and random design.
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19
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Hemp J, Robinson DE, Martinez TJ, Kelleher NL, Gennis RB. Evolutionary migration of a post-translationally modified active-site residue in the proton-pumping heme-copper oxygen reductases. Biochemistry 2006; 45:15405-10. [PMID: 17176062 PMCID: PMC2535580 DOI: 10.1021/bi062026u] [Citation(s) in RCA: 59] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
In the respiratory chains of aerobic organisms, oxygen reductase members of the heme-copper superfamily couple the reduction of O2 to proton pumping, generating an electrochemical gradient. There are three distinct families of heme-copper oxygen reductases: A, B, and C types. The A- and B-type oxygen reductases have an active-site tyrosine that forms a unique cross-linked histidine-tyrosine cofactor. In the C-type oxygen reductases (also called cbb3 oxidases), an analogous active-site tyrosine has recently been predicted by molecular modeling to be located within a different transmembrane helix in comparison to the A- and B-type oxygen reductases. In this work, Fourier-transform mass spectrometry is used to show that the predicted tyrosine forms a histidine-tyrosine cross-linked cofactor in the active site of the C-type oxygen reductases. This is the first known example of the evolutionary migration of a post-translationally modified active-site residue. It also verifies the presence of a unique cofactor in all three families of proton-pumping respiratory oxidases, demonstrating that these enzymes likely share a common reaction mechanism and that the histidine-tyrosine cofactor may be a required component for proton pumping.
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Affiliation(s)
- James Hemp
- Department of Chemistry, University of Illinois, Urbana, IL 61801
- Center for Biophysics and Computational Biology, University of Illinois, Urbana, IL 61801
| | - Dana E. Robinson
- Department of Chemistry, University of Illinois, Urbana, IL 61801
| | - Todd J. Martinez
- Department of Chemistry, University of Illinois, Urbana, IL 61801
| | - Neil L. Kelleher
- Department of Chemistry, University of Illinois, Urbana, IL 61801
| | - Robert B. Gennis
- Department of Biochemistry, University of Illinois, 600 S. Mathews Street, Urbana, IL 61801
- Corresponding author: Department of Biochemistry, University of Illinois, 600 S. Mathews Street, Urbana, IL 61801 , FAX: 217-244-3186, TEL: 217-333-9075
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20
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Mercier KA, Baran M, Ramanathan V, Revesz P, Xiao R, Montelione GT, Powers R. FAST-NMR: functional annotation screening technology using NMR spectroscopy. J Am Chem Soc 2006; 128:15292-9. [PMID: 17117882 PMCID: PMC2529462 DOI: 10.1021/ja0651759] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
An abundance of protein structures emerging from structural genomics and the Protein Structure Initiative (PSI) are not amenable to ready functional assignment because of a lack of sequence and structural homology to proteins of known function. We describe a high-throughput NMR methodology (FAST-NMR) to annotate the biological function of novel proteins through the structural and sequence analysis of protein-ligand interactions. This is based on basic tenets of biochemistry where proteins with similar functions will have similar active sites and exhibit similar ligand binding interactions, despite global differences in sequence and structure. Protein-ligand interactions are determined through a tiered NMR screen using a library composed of compounds with known biological activity. A rapid co-structure is determined by combining the experimental identification of the ligand binding site from NMR chemical shift perturbations with the protein-ligand docking program AutoDock. Our CPASS (Comparison of Protein Active Site Structures) software and database are then used to compare this active site with proteins of known function. The methodology is demonstrated using unannotated protein SAV1430 from Staphylococcus aureus.
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Affiliation(s)
| | - Michael Baran
- Center for Advanced Biotechnology and Medicine, Department of Molecular Biology and Biochemistry, Rutgers University, Piscataway, NJ 08854, USA
| | - Viswanathan Ramanathan
- Department of Computer Science and Engineering, University of Nebraska-Lincoln, Lincoln, NE 68588, USA
| | - Peter Revesz
- Department of Computer Science and Engineering, University of Nebraska-Lincoln, Lincoln, NE 68588, USA
| | - Rong Xiao
- Center for Advanced Biotechnology and Medicine, Department of Molecular Biology and Biochemistry, Rutgers University, Piscataway, NJ 08854, USA
| | - Gaetano T. Montelione
- Center for Advanced Biotechnology and Medicine, Department of Molecular Biology and Biochemistry, Rutgers University, Piscataway, NJ 08854, USA
| | - Robert Powers
- To whom correspondence should be addressed: Department of Chemistry, 722 Hamilton Hall, University of Nebraska, Lincoln, NE 68588, Tel: (402) 472-3073; Fax (402) 472-9402,
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21
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Savolainen K, Bhaumik P, Schmitz W, Kotti TJ, Conzelmann E, Wierenga RK, Hiltunen JK. α-Methylacyl-CoA Racemase from Mycobacterium tuberculosis. J Biol Chem 2005; 280:12611-20. [PMID: 15632186 DOI: 10.1074/jbc.m409704200] [Citation(s) in RCA: 37] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Alpha-methylacyl-CoA racemase (Amacr) catalyzes the racemization of alpha-methyl-branched CoA esters. Sequence comparisons have shown that this enzyme is a member of the family III CoA transferases. The mammalian Amacr is involved in bile acid synthesis and branched-chain fatty acid degradation. In human, mutated variants of Amacr have been shown to be associated with disease states. Amino acid sequence alignment of Amacrs and its homologues from various species revealed 26 conserved protic residues, assumed to be potential candidates as catalytic residues. Amacr from Mycobacterium tuberculosis (MCR) was taken as a representative of the racemases. To determine their importance for efficient catalysis, each of these 26 protic residues of MCR was mutated into an alanine, respectively, and the mutated variants were overexpressed in Escherichia coli. It was found that four variants (R91A, H126A, D156A, and E241A) were properly folded but had much decreased catalytic efficiency. Apparently, Arg91, His126, Asp156, and Glu241 are important catalytic residues of MCR. The importance of these residues for catalysis can be rationalized by the 1.8 A resolution crystal structure of MCR, which shows that the catalytic site is at the interface between the large and small domain of two different subunits of the dimeric enzyme. This crystal structure is the first structure of a complete enzyme of the bile acid synthesis pathway. It shows that MCR has unique structural features, not seen in the structures of the sequence related formyl-CoA transferases, suggesting that the family III CoA transferases can be subdivided in at least two classes, being racemases and CoA transferases.
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Affiliation(s)
- Kalle Savolainen
- Biocenter Oulu and Department of Biochemistry, University of Oulu, Linnanmaa, P. O. Box 3000, FIN-90014 University of Oulu, Finland
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22
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Gerlt JA, Babbitt PC, Rayment I. Divergent evolution in the enolase superfamily: the interplay of mechanism and specificity. Arch Biochem Biophys 2005; 433:59-70. [PMID: 15581566 DOI: 10.1016/j.abb.2004.07.034] [Citation(s) in RCA: 180] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2004] [Revised: 07/15/2004] [Indexed: 11/17/2022]
Abstract
The members of the mechanistically diverse enolase superfamily catalyze different overall reactions. Each shares a partial reaction in which an active site base abstracts the alpha-proton of the carboxylate substrate to generate an enolate anion intermediate that is stabilized by coordination to the essential Mg(2+) ion; the intermediates are then directed to different products in the different active sites. In this minireview, our current understanding of structure/function relationships in the divergent members of the superfamily is reviewed, and the use of this knowledge for our future studies is proposed.
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Affiliation(s)
- John A Gerlt
- Departments of Biochemistry and Chemistry, University of Illinois, Urbana, IL 61801, USA.
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23
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Partanen ST, Novikov DK, Popov AN, Mursula AM, Hiltunen JK, Wierenga RK. The 1.3 A crystal structure of human mitochondrial Delta3-Delta2-enoyl-CoA isomerase shows a novel mode of binding for the fatty acyl group. J Mol Biol 2004; 342:1197-208. [PMID: 15351645 DOI: 10.1016/j.jmb.2004.07.039] [Citation(s) in RCA: 35] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2004] [Revised: 07/02/2004] [Accepted: 07/06/2004] [Indexed: 11/18/2022]
Abstract
The crystal structure of Delta3-Delta2-enoyl-CoA isomerase from human mitochondria (hmEci), complexed with the substrate analogue octanoyl-CoA, has been refined at 1.3 A resolution. This enzyme takes part in the beta-oxidation of unsaturated fatty acids by converting both cis-3 and trans-3-enoyl-CoA esters (with variable length of the acyl group) to trans-2-enoyl-CoA. hmEci belongs to the hydratase/isomerase (crotonase) superfamily. Most of the enzymes belonging to this superfamily are hexamers, but hmEci is shown to be a trimer. The mode of binding of the ligand, octanoyl-CoA, shows that the omega-end of the acyl group binds in a hydrophobic tunnel formed by residues of the loop preceding helix H4 as well as by side-chains of the kinked helix H9. From the structure of the complex it can be seen that Glu136 is the only catalytic residue. The importance of Glu136 for catalysis is confirmed by mutagenesis studies. A cavity analysis shows the presence of two large, adjacent empty hydrophobic cavities near the active site, which are shaped by side-chains of helices H1, H2, H3 and H4. The structure comparison of hmEci with structures of other superfamily members, in particular of rat mitochondrial hydratase (crotonase) and yeast peroxisomal enoyl-CoA isomerase, highlights the variable mode of binding of the fatty acid moiety in this superfamily.
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Affiliation(s)
- Sanna T Partanen
- Biocenter Oulu and Department of Biochemistry, University of Oulu, PO Box 3000, FIN-90014 University of Oulu, Finland
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24
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Kalinina OV, Mironov AA, Gelfand MS, Rakhmaninova AB. Automated selection of positions determining functional specificity of proteins by comparative analysis of orthologous groups in protein families. Protein Sci 2004; 13:443-56. [PMID: 14739328 PMCID: PMC2286703 DOI: 10.1110/ps.03191704] [Citation(s) in RCA: 92] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
The increasing volume of genomic data opens new possibilities for analysis of protein function. We introduce a method for automated selection of residues that determine the functional specificity of proteins with a common general function (the specificity-determining positions [SDP] prediction method). Such residues are assumed to be conserved within groups of orthologs (that may be assumed to have the same specificity) and to vary between paralogs. Thus, considering a multiple sequence alignment of a protein family divided into orthologous groups, one can select positions where the distribution of amino acids correlates with this division. Unlike previously published techniques, the introduced method directly takes into account nonuniformity of amino acid substitution frequencies. In addition, it does not require setting arbitrary thresholds. Instead, a formal procedure for threshold selection using the Bernoulli estimator is implemented. We tested the SDP prediction method on the LacI family of bacterial transcription factors and a sample of bacterial water and glycerol transporters belonging to the major intrinsic protein (MIP) family. In both cases, the comparison with available experimental and structural data strongly supported our predictions.
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Affiliation(s)
- Olga V Kalinina
- State Scientific Center GosNIIGenetika, 1st Dorozhny pr., 1, Moscow 113545, Russia
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25
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Wang WC, Chiu WC, Hsu SK, Wu CL, Chen CY, Liu JS, Hsu WH. Structural Basis for Catalytic Racemization and Substrate Specificity of an N-Acylamino Acid Racemase Homologue from Deinococcus radiodurans. J Mol Biol 2004; 342:155-69. [PMID: 15313614 DOI: 10.1016/j.jmb.2004.07.023] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2004] [Revised: 07/01/2004] [Accepted: 07/06/2004] [Indexed: 10/26/2022]
Abstract
N-acylamino acid racemase (NAAAR) catalyzes the racemization of N-acylamino acids and can be used in concert with an aminoacylase to produce enantiopure alpha-amino acids, a process that has potential industrial applications. Here we have cloned and characterized an NAAAR homologue from a radiation-resistant ancient bacterium, Deinococcus radiodurans. The expressed NAAAR racemized various substrates at an optimal temperature of 60 degrees C and had Km values of 24.8 mM and 12.3 mM for N-acetyl-D-methionine and N-acetyl-L-methionine, respectively. The crystal structure of NAAAR was solved to 1.3 A resolution using multiwavelength anomalous dispersion (MAD) methods. The structure consists of a homooctamer in which each subunit has an architecture characteristic of enolases with a capping domain and a (beta/alpha)7 beta barrel domain. The NAAAR.Mg2+ and NAAAR.N-acetyl-L-glutamine.Mg2+ structures were also determined, allowing us to define the Lys170-Asp195-Glu220-Asp245-Lys269 framework for catalyzing 1,1-proton exchange of N-acylamino acids. Four subsites enclosing the substrate are identified: catalytic site, metal-binding site, side-chain-binding region, and a flexible lid region. The high conservation of catalytic and metal-binding sites in different enolases reflects the essentiality of a common catalytic platform, allowing these enzymes to robustly abstract alpha-protons of various carboxylate substrates efficiently. The other subsites involved in substrate recognition are less conserved, suggesting that divergent evolution has led to functionally distinct enzymes.
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Affiliation(s)
- Wen-Ching Wang
- Institute of Molecular and Cellular Biology, National Tsing Hua University, Hsinchu 300, Taiwan, ROC.
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26
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Matsuda K, Nishioka T, Kinoshita K, Kawabata T, Go N. Finding evolutionary relations beyond superfamilies: fold-based superfamilies. Protein Sci 2004; 12:2239-51. [PMID: 14500881 PMCID: PMC2366925 DOI: 10.1110/ps.0383603] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
Superfamily classifications are based variably on similarity of sequences, global folds, local structures, or functions. We have examined the possibility of defining superfamilies purely from the viewpoint of the global fold/function relationship. For this purpose, we first classified protein domains according to the beta-sheet topology. We then introduced the concept of kinship relations among the classified beta-sheet topology by assuming that the major elementary event leading to creation of a new beta-sheet topology is either an addition or deletion of one beta-strand at the edge of an existing beta-sheet during the molecular evolution. Based on this kinship relation, a network of protein domains was constructed so that the distance between a pair of domains represents the number of evolutionary events that lead one from the other domain. We then mapped on it all known domains with a specific core chemical function (here taken, as an example, that involving ATP or its analogs). Careful analyses revealed that the domains are found distributed on the network as >20 mutually disjointed clusters. The proteins in each cluster are defined to form a fold-based superfamily. The results indicate that >20 ATP-binding protein superfamilies have been invented independently in the process of molecular evolution, and the conservative evolutionary diffusion of global folds and functions is the origin of the relationship between them.
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Affiliation(s)
- Keiko Matsuda
- Graduate School of Information Science, Nara Institute of Science and Technology, Ikoma, 630-0101, Japan
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27
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Beebe K, Merriman E, Ribas De Pouplana L, Schimmel P. A domain for editing by an archaebacterial tRNA synthetase. Proc Natl Acad Sci U S A 2004; 101:5958-63. [PMID: 15079065 PMCID: PMC395905 DOI: 10.1073/pnas.0401530101] [Citation(s) in RCA: 50] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The rules of the genetic code are established by aminoacylations of transfer RNAs by aminoacyl tRNA synthetases. New codon assignments, and the introduction of new kinds of amino acids, are blocked by vigorous tRNA-dependent editing reactions occurring at hydrolytic sites embedded within specialized domains in the synthetases. For some synthetases, these domains were present at the time of the last common ancestor and were fixed in evolution through all three of the kingdoms of life. Significantly, a well characterized domain for editing found in bacterial and eukaryotic threonyl- and all alanyl-tRNA synthetases is missing from archaebacterial threonine enzymes. Here we show that the archaebacterial Methanosarcina mazei ThrRS efficiently misactivates serine, but does not fuse serine to tRNA. Consistent with this observation, the enzyme cleared serine that was linked to threonine-specific tRNAs. M. mazei and most other archaebacterial ThrRSs have a domain, N2(A), fused to the N terminus and not found in bacterial or eukaryotic orthologs. Mutations at conserved residues in this domain led to an inability to clear threonine-specific tRNA mischarged with serine. Thus, these results demonstrate a domain for editing that is distinct from all others, is restricted to just one branch of the tree of life, and was most likely added to archaebacterial ThrRSs after the eukaryote/archaebacteria split.
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Affiliation(s)
- Kirk Beebe
- The Skaggs Institute for Chemical Biology, The Scripps Research Institute, Beckman Center, BCC379, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA
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28
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Abstract
We show that three-dimensional signatures consisting of only a few functionally important residues can be diagnostic of membership in superfamilies of enzymes. Using the enolase superfamily as a model system, we demonstrate that such a signature, or template, can identify superfamily members in structural databases with high sensitivity and specificity. This is remarkable because superfamilies can be highly diverse, with members catalyzing many different overall reactions; the unifying principle can be a conserved partial reaction or chemical capability. Our definition of a superfamily thus hinges on the disposition of residues involved in a conserved function, rather than on fold similarity alone. A clear advantage of basing structure searches on such active site templates rather than on fold similarity is the specificity with which superfamilies with distinct functional characteristics can be identified within a large set of proteins with the same fold, such as the (beta/alpha)8 barrels. Preliminary results are presented for an additional group of enzymes with a different fold, the haloacid dehalogenase superfamily, suggesting that this approach may be generally useful for assigning reading frames of unknown function to specific superfamilies and thereby allowing inference of some of their functional properties.
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Affiliation(s)
- Elaine C Meng
- Department of Pharmaceutical Chemistry, University of California, Genentech Hall, 600 Sixteenth Street, San Francisco, CA 94143-2240, USA
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29
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Young DM, D'Argenio DA, Jen M, Parke D, Nicholas Ornston L. Gunsalus and Stanier set the stage for selection of cold-sensitive mutants apparently impaired in movement of FAD within 4-hydroxybenzoate hydroxylase. Biochem Biophys Res Commun 2004; 312:153-60. [PMID: 14630034 DOI: 10.1016/j.bbrc.2003.09.240] [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: 10/26/2022]
Affiliation(s)
- David M Young
- Department of Microbiology and Molecular Genetics, Harvard Medical School, 200 Longwood Ave., D1-219, Boston, MA 02115, USA
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30
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31
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Wise EL, Graham DE, White RH, Rayment I. The structural determination of phosphosulfolactate synthase from Methanococcus jannaschii at 1.7-A resolution: an enolase that is not an enolase. J Biol Chem 2003; 278:45858-63. [PMID: 12952952 DOI: 10.1074/jbc.m307486200] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Members of the enolase mechanistically diverse superfamily catalyze a wide variety of chemical reactions that are related by a common mechanistic feature, the abstraction of a proton adjacent to a carboxylate group. Recent investigations into the function and mechanism of the phosphosulfolactate synthase encoded by the ComA gene in Methanococcus jannaschii have suggested that ComA, which catalyzes the stereospecific Michael addition of sulfite to phosphoenolpyruvate to form phosphosulfolactate, may be a member of the enolase superfamily. The ComA-catalyzed reaction, the first step in the coenzyme M biosynthetic pathway, likely proceeds via a Mg2+ ion-stabilized enolate intermediate in a manner similar to that observed for members of the enolase superfamily. ComA, however, has no significant sequence similarity to any known enolase. Here we report the x-ray crystal structure of ComA to 1.7-A resolution. The overall fold for ComA is an (alpha/beta)8 barrel that assembles with two other ComA molecules to form a trimer in which three active sites are created at the subunit interfaces. From the positions of two ordered sulfate ions in the active site, a model for the binding of phosphoenolpyruvate and sulfite is proposed. Despite its mechanistic similarity to the enolase superfamily, the overall structure and active site architecture of ComA are unlike any member of the enolase superfamily, which suggests that ComA is not a member of the enolase superfamily but instead acquired an enolase-type mechanism through convergent evolution.
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Affiliation(s)
- Eric L Wise
- Department of Biochemistry, University of Wisconsin, Madison, Wisconsin 53706, USA
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Kajander T, Lehtiö L, Schlömann M, Goldman A. The structure of Pseudomonas P51 Cl-muconate lactonizing enzyme: co-evolution of structure and dynamics with the dehalogenation function. Protein Sci 2003; 12:1855-64. [PMID: 12930985 PMCID: PMC2323983 DOI: 10.1110/ps.0388503] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
Bacterial muconate lactonizing enzymes (MLEs) catalyze the conversion of cis,cis-muconate as a part of the beta-ketoadipate pathway, and some MLEs are also able to dehalogenate chlorinated muconates (Cl-MLEs). The basis for the Cl-MLEs dehalogenating activity is still unclear. To further elucidate the differences between MLEs and Cl-MLEs, we have solved the structure of Pseudomonas P51 Cl-MLE at 1.95 A resolution. Comparison of Pseudomonas MLE and Cl-MLE structures reveals the presence of a large cavity in the Cl-MLEs. The cavity may be related to conformational changes on substrate binding in Cl-MLEs, at Gly52. Site-directed mutagenesis on Pseudomonas MLE core positions to the equivalent Cl-MLE residues showed that the variant Thr52Gly was rather inactive, whereas the Thr52Gly-Phe103Ser variant had regained part of the activity. These residues form a hydrogen bond in the Cl-MLEs. The Cl-MLE structure, as a result of the Thr-to-Gly change, is more flexible than MLE: As a mobile loop closes over the active site, a conformational change at Gly52 is observed in Cl-MLEs. The loose packing and structural motions in Cl-MLE may be required for the rotation of the lactone ring in the active site necessary for the dehalogenating activity of Cl-MLEs. Furthermore, we also suggest that differences in the active site mobile loop sequence between MLEs and Cl-MLEs result in lower active site polarity in Cl-MLEs, possibly affecting catalysis. These changes could result in slower product release from Cl-MLEs and make it a better enzyme for dehalogenation of substrate.
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Affiliation(s)
- Tommi Kajander
- Research Program in Structural Biology and Biophysics, Institute of Biotechnology, University of Helsinki, FIN-00014 Helsinki, Finland
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33
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Parschat K, Hauer B, Kappl R, Kraft R, Huttermann J, Fetzner S. Gene cluster of Arthrobacter ilicis Ru61a involved in the degradation of quinaldine to anthranilate: characterization and functional expression of the quinaldine 4-oxidase qoxLMS genes. J Biol Chem 2003; 278:27483-94. [PMID: 12730200 DOI: 10.1074/jbc.m301330200] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
A genetic analysis of the anthranilate pathway of quinaldine degradation was performed. A 23-kb region of DNA from Arthrobacter ilicis Rü61a was cloned into the cosmid pVK100. Although Escherichia coli clones containing the recombinant cosmid did not transform quinaldine, cosmids harboring the 23-kb region, or a 10.8-kb stretch of this region, conferred to Pseudomonas putida KT2440 the ability to cometabolically convert quinaldine to anthranilate. The 10.8-kb fragment thus contains the genes coding for quinaldine 4-oxidase (Qox), 1H-4-oxoquinaldine 3-monooxygenase, 1H-3-hydroxy-4-oxoquinaldine 2,4-dioxygenase, and N-acetylanthranilate amidase. The qoxLMS genes coding for the molybdopterin cytosine dinucleotide-(MCD-), FeSI-, FeSII-, and FAD-containing Qox were inserted into the expression vector pJB653, generating pKP1. Qox is the first MCD-containing enzyme to be synthesized in a catalytically fully competent form by a heterologous host, P. putida KT2440 pKP1; the catalytic properties and the UV-visible and EPR spectra of Qox purified from P. putida KT2440 pKP1 were essentially like those of wild-type Qox. This provides a starting point for the construction of protein variants of Qox by site-directed mutagenesis. Downstream of the qoxLMS genes, a putative gene whose deduced amino acid sequence showed 37% similarity to the cofactor-inserting chaperone XdhC was located. Additional open reading frames identified on the 23-kb segment may encode further enzymes (a glutamyl tRNA synthetase, an esterase, two short-chain dehydrogenases/reductases, an ATPase belonging to the AAA family, a 2-hydroxyhepta-2,4-diene-1,7-dioate isomerase/5-oxopent-3-ene-1,2,5-tricarboxylate decarboxylase-like protein, and an enzyme of the mandelate racemase group) and hypothetical proteins involved in transcriptional regulation, and metabolite transport.
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Affiliation(s)
- Katja Parschat
- AG Mikrobiologie, Institut für Chemie und Biologie des Meeres, Carl von Ossietzky Universität Oldenburg, D-26111 Oldenburg, Germany
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Breinbauer R, Vetter IR, Waldmann H. From protein domains to drug candidates--natural products as guiding principles in compound library design and synthesis. ERNST SCHERING RESEARCH FOUNDATION WORKSHOP 2003:167-88. [PMID: 12664541 DOI: 10.1007/978-3-662-05314-0_11] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/01/2023]
Affiliation(s)
- R Breinbauer
- Max-Planck-Institut für Molekulare Physiologie, Department of Chemical Biology, Otto-Hahn-Str. 11, 44227 Dortmund, Germany.
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35
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Dokholyan NV, Shakhnovich B, Shakhnovich EI. Expanding protein universe and its origin from the biological Big Bang. Proc Natl Acad Sci U S A 2002; 99:14132-6. [PMID: 12384571 PMCID: PMC137849 DOI: 10.1073/pnas.202497999] [Citation(s) in RCA: 153] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The bottom-up approach to understanding the evolution of organisms is by studying molecular evolution. With the large number of protein structures identified in the past decades, we have discovered peculiar patterns that nature imprints on protein structural space in the course of evolution. In particular, we have discovered that the universe of protein structures is organized hierarchically into a scale-free network. By understanding the cause of these patterns, we attempt to glance at the very origin of life.
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Affiliation(s)
- Nikolay V Dokholyan
- Department of Chemistry and Chemical Biology, Harvard University, 12 Oxford Street, Cambridge, MA 02138, USA.
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36
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Mirny LA, Gelfand MS. Using orthologous and paralogous proteins to identify specificity-determining residues in bacterial transcription factors. J Mol Biol 2002; 321:7-20. [PMID: 12139929 DOI: 10.1016/s0022-2836(02)00587-9] [Citation(s) in RCA: 117] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
Concepts of orthology and paralogy are become increasingly important as whole-genome comparison allows their identification in complete genomes. Functional specificity of proteins is assumed to be conserved among orthologs and is different among paralogs. We used this assumption to identify residues which determine specificity of protein-DNA and protein-ligand recognition. Finding such residues is crucial for understanding mechanisms of molecular recognition and for rational protein and drug design. Assuming conservation of specificity among orthologs and different specificity of paralogs, we identify residues that correlate with this grouping by specificity. The method is taking advantage of complete genomes to find multiple orthologs and paralogs. The central part of this method is a procedure to compute statistical significance of the predictions. The procedure is based on a simple statistical model of protein evolution. When applied to a large family of bacterial transcription factors, our method identified 12 residues that are presumed to determine the protein-DNA and protein-ligand recognition specificity. Structural analysis of the proteins and available experimental results strongly support our predictions. Our results suggest new experiments aimed at rational re-design of specificity in bacterial transcription factors by a minimal number of mutations.
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Affiliation(s)
- Leonid A Mirny
- Harvard-MIT Division of Health Science and Technology, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge 02139, USA.
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37
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Abstract
The expectation is that any similarity in reaction chemistry shared by enzyme homologues is mediated by common functional groups conserved through evolution. However, detailed enzyme studies have revealed the flexibility of many active sites, in that different functional groups, unconserved with respect to position in the primary sequence, mediate the same mechanistic role. Nevertheless, the catalytic atoms might be spatially equivalent. More rarely, the active sites have completely different locations in the protein scaffold. This variability could result from: (1) the hopping of functional groups from one position to another to optimize catalysis; (2) the independent specialization of a low-activity primordial enzyme in different phylogenetic lineages; (3) functional convergence after evolutionary divergence; or (4) circular permutation events.
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Affiliation(s)
- Annabel E Todd
- Biochemistry and Molecular Biology Department, University College London, Gower Street, London, UK WC1E 6BT
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38
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Gerlt JA, Babbitt PC. Divergent evolution of enzymatic function: mechanistically diverse superfamilies and functionally distinct suprafamilies. Annu Rev Biochem 2002; 70:209-46. [PMID: 11395407 DOI: 10.1146/annurev.biochem.70.1.209] [Citation(s) in RCA: 439] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
The protein sequence and structure databases are now sufficiently representative that strategies nature uses to evolve new catalytic functions can be identified. Groups of divergently related enzymes whose members catalyze different reactions but share a common partial reaction, intermediate, or transition state (mechanistically diverse superfamilies) have been discovered, including the enolase, amidohydrolase, thiyl radical, crotonase, vicinal-oxygen-chelate, and Fe-dependent oxidase superfamilies. Other groups of divergently related enzymes whose members catalyze different overall reactions that do not share a common mechanistic strategy (functionally distinct suprafamilies) have also been identified: (a) functionally distinct suprafamilies whose members catalyze successive transformations in the tryptophan and histidine biosynthetic pathways and (b) functionally distinct suprafamilies whose members catalyze different reactions in different metabolic pathways. An understanding of the structural bases for the catalytic diversity observed in super- and suprafamilies may provide the basis for discovering the functions of proteins and enzymes in new genomes as well as provide guidance for in vitro evolution/engineering of new enzymes.
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Affiliation(s)
- J A Gerlt
- Departments of Biochemistry and Chemistry, University of Illinois, Urbana, Illinois 61801, USA.
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39
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Asuncion M, Blankenfeldt W, Barlow JN, Gani D, Naismith JH. The structure of 3-methylaspartase from Clostridium tetanomorphum functions via the common enolase chemical step. J Biol Chem 2002; 277:8306-11. [PMID: 11748244 DOI: 10.1074/jbc.m111180200] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Methylaspartate ammonia-lyase (3-methylaspartase, MAL; EC ) catalyzes the reversible anti elimination of ammonia from L-threo-(2S,3S)-3-methylaspartic acid to give mesaconic acid. This reaction lies on the main catabolic pathway for glutamate in Clostridium tetanomorphum. MAL requires monovalent and divalent cation cofactors for full catalytic activity. The enzyme has attracted interest because of its potential use as a biocatalyst. The structure of C. tetanomorphum MAL has been solved to 1.9-A resolution by the single-wavelength anomalous diffraction method. A divalent metal ion complex of the protein has also been determined. MAL is a homodimer with each monomer consisting of two domains. One is an alpha/beta-barrel, and the other smaller domain is mainly beta-strands. The smaller domain partially occludes the C terminus of the barrel and forms a large cleft. The structure identifies MAL as belonging to the enolase superfamily of enzymes. The metal ion site is located in a large cleft between the domains. Potential active site residues have been identified based on a combination of their proximity to a metal ion site, molecular modeling, and sequence homology. In common with all members of the enolase superfamily, the carboxylic acid of the substrate is co-ordinated by the metal ions, and a proton adjacent to a carboxylic acid group of the substrate is abstracted by a base. In MAL, it appears that Lys(331) removes the alpha-proton of methylaspartic acid. This motif is the defining mechanistic characteristic of the enolase superfamily of which all have a common fold. The degree of structural conservation is remarkable given only four residues are absolutely conserved.
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Affiliation(s)
- Miryam Asuncion
- The Centre for Biomolecular Sciences, The University, St. Andrews, Scotland, United Kingdom KY16 9ST
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40
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Abstract
The viability of living systems requires that C--H bonds of biological molecules be stable in water, but that there also be a mechanism for shortening the timescale for their heterolytic cleavage through enzymatic catalysis of a variety of catabolic and metabolic reactions. An understanding of the mechanism of enzymatic catalysis of proton transfer at carbon requires the integration of results of studies to determine the structure of the enzyme-substrate complex with model studies on the mechanism for the non-enzymatic reaction in water, and the effect of the local protein environment on the stability of the transition state for this reaction. A common theme is the importance of electrostatic interactions in providing stabilization of bound carbanion intermediates of enzyme-catalyzed proton-transfer reactions.
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Affiliation(s)
- J P Richard
- Department of Chemistry, University at Buffalo, SUNY, Buffalo, NY 14260-3000, USA.
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41
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Todd AE, Orengo CA, Thornton JM. Evolution of function in protein superfamilies, from a structural perspective. J Mol Biol 2001; 307:1113-43. [PMID: 11286560 DOI: 10.1006/jmbi.2001.4513] [Citation(s) in RCA: 459] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
The recent growth in protein databases has revealed the functional diversity of many protein superfamilies. We have assessed the functional variation of homologous enzyme superfamilies containing two or more enzymes, as defined by the CATH protein structure classification, by way of the Enzyme Commission (EC) scheme. Combining sequence and structure information to identify relatives, the majority of superfamilies display variation in enzyme function, with 25 % of superfamilies in the PDB having members of different enzyme types. We determined the extent of functional similarity at different levels of sequence identity for 486,000 homologous pairs (enzyme/enzyme and enzyme/non-enzyme), with structural and sequence relatives included. For single and multi-domain proteins, variation in EC number is rare above 40 % sequence identity, and above 30 %, the first three digits may be predicted with an accuracy of at least 90 %. For more distantly related proteins sharing less than 30 % sequence identity, functional variation is significant, and below this threshold, structural data are essential for understanding the molecular basis of observed functional differences. To explore the mechanisms for generating functional diversity during evolution, we have studied in detail 31 diverse structural enzyme superfamilies for which structural data are available. A large number of variations and peculiarities are observed, at the atomic level through to gross structural rearrangements. Almost all superfamilies exhibit functional diversity generated by local sequence variation and domain shuffling. Commonly, substrate specificity is diverse across a superfamily, whilst the reaction chemistry is maintained. In many superfamilies, the position of catalytic residues may vary despite playing equivalent functional roles in related proteins. The implications of functional diversity within supefamilies for the structural genomics projects are discussed. More detailed information on these superfamilies is available at http://www.biochem.ucl.ac.uk/bsm/FAM-EC/.
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Affiliation(s)
- A E Todd
- Biochemistry and Molecular Biology Department, University College London, Gower Street, London, WC1E 6BT, UK
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42
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Abstract
Recent studies on triosephosphate isomerase (TIM)-barrel enzymes highlight the remarkable versatility of the TIM-barrel scaffold. At least 15 distinct enzyme families use this framework to generate the appropriate active site geometry, always at the C-terminal end of the eight parallel beta-strands of the barrel. Sequence and structure comparisons now suggest that many of the TIM-barrel enzymes are evolutionarily related. Common structural properties of TIM-barrel enzymes are discussed.
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Affiliation(s)
- R K Wierenga
- Biocenter Oulu and Department of Biochemistry, University of Oulu, Linnanmaa, Oulu, Finland.
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43
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Linial M, Yona G. Methodologies for target selection in structural genomics. PROGRESS IN BIOPHYSICS AND MOLECULAR BIOLOGY 2001; 73:297-320. [PMID: 11063777 DOI: 10.1016/s0079-6107(00)00011-0] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
As the number of complete genomes that have been sequenced keeps growing, unknown areas of the protein space are revealed and new horizons open up. Most of this information will be fully appreciated only when the structural information about the encoded proteins becomes available. The goal of structural genomics is to direct large-scale efforts of protein structure determination, so as to increase the impact of these efforts. This review focuses on current approaches in structural genomics aimed at selecting representative proteins as targets for structure determination. We will discuss the concept of representative structures/folds, the current methodologies for identifying those proteins, and computational techniques for identifying proteins which are expected to adopt new structural folds.
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Affiliation(s)
- M Linial
- Department of Biological Chemistry, Institute of Life Sciences, Hebrew University, 91904, Jerusalem, Israel.
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44
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Cosper NJ, Collier LS, Clark TJ, Scott RA, Neidle EL. Mutations in catB, the gene encoding muconate cycloisomerase, activate transcription of the distal ben genes and contribute to a complex regulatory circuit in Acinetobacter sp. strain ADP1. J Bacteriol 2000; 182:7044-52. [PMID: 11092867 PMCID: PMC94832 DOI: 10.1128/jb.182.24.7044-7052.2000] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Mutants of the bacterium Acinetobacter sp. strain ADP1 were selected to grow on benzoate without the BenM transcriptional activator. In the wild type, BenM responds to benzoate and cis,cis-muconate to activate expression of the benABCDE operon, which is involved in benzoate catabolism. This operon encodes enzymes that convert benzoate to catechol, a compound subsequently degraded by cat gene-encoded enzymes. In this report, four spontaneous mutants were found to carry catB mutations that enabled BenM-independent growth on benzoate. catB encodes muconate cycloisomerase, an enzyme required for benzoate catabolism. Its substrate, cis,cis-muconate, is enzymatically produced from catechol by the catA-encoded catechol 1,2-dioxygenase. Muconate cycloisomerase was purified to homogeneity from the wild type and the catB mutants. Each purified enzyme was active, although there were differences in the catalytic properties of the wild type and variant muconate cycloisomerases. Strains with a chromosomal benA::lacZ transcriptional fusion were constructed and used to investigate how catB mutations affect growth on benzoate. All of the catB mutations increased cis,cis-muconate-activated ben gene expression in strains lacking BenM. A model is presented in which the catB mutations reduce muconate cycloisomerase activity during growth on benzoate, thereby increasing intracellular cis, cis-muconate concentrations. This, in turn, may allow CatM, an activator similar to BenM in sequence and function, to activate ben gene transcription. CatM normally responds to cis,cis-muconate to activate cat gene expression. Consistent with this model, muconate cylcoisomerase specific activities in cell extracts of benzoate-grown catB mutants were low relative to that of the wild type. Moreover, the catechol 1,2-dioxygenase activities of the mutants were elevated, which may result from CatM responding to the altered intracellular levels of cis,cis-muconate and increasing catA expression. Collectively, these results support the important role of metabolite concentrations in controlling benzoate degradation via a complex transcriptional regulatory circuit.
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Affiliation(s)
- N J Cosper
- Center for Metalloenzyme Studies, University of Georgia, Athens, Georgia 30602, USA
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45
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Lang D, Thoma R, Henn-Sax M, Sterner R, Wilmanns M. Structural evidence for evolution of the beta/alpha barrel scaffold by gene duplication and fusion. Science 2000; 289:1546-50. [PMID: 10968789 DOI: 10.1126/science.289.5484.1546] [Citation(s) in RCA: 250] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
Abstract
The atomic structures of two proteins in the histidine biosynthesis pathway consist of beta/alpha barrels with a twofold repeat pattern. It is likely that these proteins evolved by twofold gene duplication and gene fusion from a common half-barrel ancestor. These ancestral domains are not visible as independent domains in the extant proteins but can be inferred from a combination of sequence and structural analysis. The detection of subdomain structures may be useful in efforts to search genome sequences for functionally and structurally related proteins.
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Affiliation(s)
- D Lang
- European Molecular Biology Laboratory (EMBL) Hamburg Outstation, EMBL c/o Deutsches Elektronen- Synchrotron (DESY), Notkestrasse 85, D-22603 Hamburg, Germany
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46
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Jürgens C, Strom A, Wegener D, Hettwer S, Wilmanns M, Sterner R. Directed evolution of a (beta alpha)8-barrel enzyme to catalyze related reactions in two different metabolic pathways. Proc Natl Acad Sci U S A 2000; 97:9925-30. [PMID: 10944186 PMCID: PMC27628 DOI: 10.1073/pnas.160255397] [Citation(s) in RCA: 146] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2000] [Accepted: 06/02/2000] [Indexed: 11/18/2022] Open
Abstract
Enzymes participating in different metabolic pathways often have similar catalytic mechanisms and structures, suggesting their evolution from a common ancestral precursor enzyme. We sought to create a precursor-like enzyme for N'-[(5'-phosphoribosyl)formimino]-5-aminoimidazole-4-carboxamide ribonucleotide (ProFAR) isomerase (HisA; EC ) and phosphoribosylanthranilate (PRA) isomerase (TrpF; EC ), which catalyze similar reactions in the biosynthesis of the amino acids histidine and tryptophan and have a similar (betaalpha)(8)-barrel structure. Using random mutagenesis and selection, we generated several HisA variants that catalyze the TrpF reaction both in vivo and in vitro, and one of these variants retained significant HisA activity. A more detailed analysis revealed that a single amino acid exchange could establish TrpF activity on the HisA scaffold. These findings suggest that HisA and TrpF may have evolved from an ancestral enzyme of broader substrate specificity and underscore that (betaalpha)(8)-barrel enzymes are very suitable for the design of new catalytic activities.
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Affiliation(s)
- C Jürgens
- Abteilung Molekulare Genetik und Präparative Molekularbiologie, Institut für Mikrobiologie und Genetik, Georg-August-Universität Göttingen, Grisebachstrasse 8, D-37077 Göttingen, Germany
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47
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Weiss KM, Fullerton SM. Phenogenetic drift and the evolution of genotype-phenotype relationships. Theor Popul Biol 2000; 57:187-95. [PMID: 10828213 DOI: 10.1006/tpbi.2000.1460] [Citation(s) in RCA: 134] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Affiliation(s)
- K M Weiss
- Departments of Anthropology and Biology, Penn State University, 409 Carpenter, University Park, Pennsylvania 16802, USA.
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48
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Altamirano MM, Blackburn JM, Aguayo C, Fersht AR. Directed evolution of new catalytic activity using the alpha/beta-barrel scaffold. Nature 2000; 403:617-22. [PMID: 10688189 DOI: 10.1038/35001001] [Citation(s) in RCA: 143] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
In biological systems, enzymes catalyse the efficient synthesis of complex molecules under benign conditions, but widespread industrial use of these biocatalysts depends crucially on the development of new enzymes with useful catalytic functions. The evolution of enzymes in biological systems often involves the acquisition of new catalytic or binding properties by an existing protein scaffold. Here we mimic this strategy using the most common fold in enzymes, the alpha/beta-barrel, as the scaffold. By combining an existing binding site for structural elements of phosphoribosylanthranilate with a catalytic template required for isomerase activity, we are able to evolve phosphoribosylanthranilate isomerase activity from the scaffold of indole-3-glycerol-phosphate synthase. We find that targeting the catalytic template for in vitro mutagenesis and recombination, followed by in vivo selection, results in a new phosphoribosylanthranilate isomerase that has catalytic properties similar to those of the natural enzyme, with an even higher specificity constant. Our demonstration of divergent evolution and the widespread occurrence of the alpha/beta-barrel suggest that this scaffold may be a fold of choice for the directed evolution of new biocatalysts.
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Affiliation(s)
- M M Altamirano
- Cambridge Centre for Protein Engineering, and Cambridge University Chemical Laboratory, MRC Centre, UK
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49
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Abstract
The recent growth in structural data, and ensuing analyses, have revealed the structural and functional versatility of protein families. With respect to enzymes, local active-site mutations, variations in surface loops and recruitment of additional domains accommodate the diverse substrate specificities and catalytic activities observed within several superfamilies. Conversely, some functions have more than one structural solution, having evolved independently several times during evolution. Combined with the existence of multi-functional genes, which have arisen by gene recruitment, these phenomena must be considered in the process of genome annotation.
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Affiliation(s)
- A E Todd
- Biomolecular Structure and Modelling Unit Department of Biochemistry and Molecular Biology, University College London, Gower Street, London,WC1E 6BT, UK
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50
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Schell U, Helin S, Kajander T, Schl�mann M, Goldman A. Structural basis for the activity of two muconate cycloisomerase variants toward substituted muconates. Proteins 1999. [DOI: 10.1002/(sici)1097-0134(19990101)34:1<125::aid-prot10>3.0.co;2-y] [Citation(s) in RCA: 21] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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