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Lipowska J, Miks CD, Kwon K, Shuvalova L, Zheng H, Lewiński K, Cooper DR, Shabalin IG, Minor W. Pyrimidine biosynthesis in pathogens - Structures and analysis of dihydroorotases from Yersinia pestis and Vibrio cholerae. Int J Biol Macromol 2019; 136:1176-1187. [PMID: 31207330 PMCID: PMC6686667 DOI: 10.1016/j.ijbiomac.2019.05.149] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2019] [Revised: 05/01/2019] [Accepted: 05/14/2019] [Indexed: 02/06/2023]
Abstract
The de novo pyrimidine biosynthesis pathway is essential for the proliferation of many pathogens. One of the pathway enzymes, dihydroorotase (DHO), catalyzes the reversible interconversion of N-carbamoyl-l-aspartate to 4,5-dihydroorotate. The substantial difference between bacterial and mammalian DHOs makes it a promising drug target for disrupting bacterial growth and thus an important candidate to evaluate as a response to antimicrobial resistance on a molecular level. Here, we present two novel three-dimensional structures of DHOs from Yersinia pestis (YpDHO), the plague-causing pathogen, and Vibrio cholerae (VcDHO), the causative agent of cholera. The evaluations of these two structures led to an analysis of all available DHO structures and their classification into known DHO types. Comparison of all the DHO active sites containing ligands that are listed in DrugBank was facilitated by a new interactive, structure-comparison and presentation platform. In addition, we examined the genetic context of characterized DHOs, which revealed characteristic patterns for different types of DHOs. We also generated a homology model for DHO from Plasmodium falciparum.
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Affiliation(s)
- Joanna Lipowska
- Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, VA 22908, USA; Center for Structural Genomics of Infectious Diseases (CSGID), Charlottesville, VA 22908, USA; Faculty of Chemistry, Jagiellonian University, 30-387 Kraków, Poland
| | - Charles Dylan Miks
- Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, VA 22908, USA
| | - Keehwan Kwon
- Infectious Diseases Group, J. Craig Venter Institute, Rockville, MD 20850, USA
| | - Ludmilla Shuvalova
- Center for Structural Genomics of Infectious Diseases (CSGID), Chicago, IL 60611, USA
| | - Heping Zheng
- Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, VA 22908, USA; Center for Structural Genomics of Infectious Diseases (CSGID), Charlottesville, VA 22908, USA
| | | | - David R Cooper
- Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, VA 22908, USA; Center for Structural Genomics of Infectious Diseases (CSGID), Charlottesville, VA 22908, USA
| | - Ivan G Shabalin
- Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, VA 22908, USA; Center for Structural Genomics of Infectious Diseases (CSGID), Charlottesville, VA 22908, USA.
| | - Wladek Minor
- Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, VA 22908, USA; Center for Structural Genomics of Infectious Diseases (CSGID), Charlottesville, VA 22908, USA.
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Gerlt JA. Genomic Enzymology: Web Tools for Leveraging Protein Family Sequence-Function Space and Genome Context to Discover Novel Functions. Biochemistry 2017; 56:4293-4308. [PMID: 28826221 PMCID: PMC5569362 DOI: 10.1021/acs.biochem.7b00614] [Citation(s) in RCA: 136] [Impact Index Per Article: 19.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
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The exponentially increasing number
of protein and nucleic acid
sequences provides opportunities to discover novel enzymes, metabolic
pathways, and metabolites/natural products, thereby adding to our
knowledge of biochemistry and biology. The challenge has evolved from
generating sequence information to mining the databases to integrating
and leveraging the available information, i.e., the availability of
“genomic enzymology” web tools. Web tools that allow
identification of biosynthetic gene clusters are widely used by the
natural products/synthetic biology community, thereby facilitating
the discovery of novel natural products and the enzymes responsible
for their biosynthesis. However, many novel enzymes with interesting
mechanisms participate in uncharacterized small-molecule metabolic
pathways; their discovery and functional characterization also can
be accomplished by leveraging information in protein and nucleic acid
databases. This Perspective focuses on two genomic enzymology web
tools that assist the discovery novel metabolic pathways: (1) Enzyme
Function Initiative-Enzyme Similarity Tool (EFI-EST) for generating
sequence similarity networks to visualize and analyze sequence–function
space in protein families and (2) Enzyme Function Initiative-Genome
Neighborhood Tool (EFI-GNT) for generating genome neighborhood networks
to visualize and analyze the genome context in microbial and fungal
genomes. Both tools have been adapted to other applications to facilitate
target selection for enzyme discovery and functional characterization.
As the natural products community has demonstrated, the enzymology
community needs to embrace the essential role of web tools that allow
the protein and genome sequence databases to be leveraged for novel
insights into enzymological problems.
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Affiliation(s)
- John A Gerlt
- Departments of Biochemistry and Chemistry, Institute for Genomic Biology, University of Illinois , Urbana-Champaign Urbana, Illinois 61801, United States
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Cirbes C, Tanski JM. Crystallographic and spectroscopic characterization of (R)-O-acetyl-mandelic acid. Acta Crystallogr E Crystallogr Commun 2016; 72:901-3. [PMID: 27555927 PMCID: PMC4992902 DOI: 10.1107/s2056989016008653] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2016] [Accepted: 05/29/2016] [Indexed: 11/11/2022]
Abstract
The title compound [systematic name: (R)-(-)-2-acet-oxy-2-phenyl-acetic acid], C10H10O4, is a resolved chiral ester derivative of mandelic acid. The compound contains an acetate group and a carb-oxy-lic acid group, which engage in inter-molecular hydrogen bonding, forming chains extending parallel to [001] with a short donor-acceptor hydrogen-bonding distance of 2.676 (2) Å.
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Affiliation(s)
- Cady Cirbes
- Department of Chemistry, Vassar College, Poughkeepsie, NY 12604, USA
| | - Joseph M. Tanski
- Department of Chemistry, Vassar College, Poughkeepsie, NY 12604, USA
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Holm L, Laakso LM. Dali server update. Nucleic Acids Res 2016; 44:W351-5. [PMID: 27131377 PMCID: PMC4987910 DOI: 10.1093/nar/gkw357] [Citation(s) in RCA: 708] [Impact Index Per Article: 88.5] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2016] [Accepted: 04/21/2016] [Indexed: 12/18/2022] Open
Abstract
The Dali server (http://ekhidna2.biocenter.helsinki.fi/dali) is a network service for comparing protein structures in 3D. In favourable cases, comparing 3D structures may reveal biologically interesting similarities that are not detectable by comparing sequences. The Dali server has been running in various places for over 20 years and is used routinely by crystallographers on newly solved structures. The latest update of the server provides enhanced analytics for the study of sequence and structure conservation. The server performs three types of structure comparisons: (i) Protein Data Bank (PDB) search compares one query structure against those in the PDB and returns a list of similar structures; (ii) pairwise comparison compares one query structure against a list of structures specified by the user; and (iii) all against all structure comparison returns a structural similarity matrix, a dendrogram and a multidimensional scaling projection of a set of structures specified by the user. Structural superimpositions are visualized using the Java-free WebGL viewer PV. The structural alignment view is enhanced by sequence similarity searches against Uniprot. The combined structure-sequence alignment information is compressed to a stack of aligned sequence logos. In the stack, each structure is structurally aligned to the query protein and represented by a sequence logo.
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Affiliation(s)
- Liisa Holm
- Institute of Biotechnology, University of Helsinki, PO Box 56, Finland Department of Biosciences, University of Helsinki, PO Box 56, Finland
| | - Laura M Laakso
- Institute of Biotechnology, University of Helsinki, PO Box 56, Finland
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Miller DV, Brown AM, Xu H, Bevan DR, White RH. Purine salvage inMethanocaldococcus jannaschii: Elucidating the role of a conserved cysteine in adenine deaminase. Proteins 2016; 84:828-40. [DOI: 10.1002/prot.25033] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2015] [Revised: 01/22/2016] [Accepted: 03/06/2016] [Indexed: 12/16/2022]
Affiliation(s)
- Danielle V. Miller
- Department of Biochemistry; Virginia Polytechnic Institute and State University; Blacksburg Virginia 24061
| | - Anne M. Brown
- Department of Biochemistry; Virginia Polytechnic Institute and State University; Blacksburg Virginia 24061
| | - Huimin Xu
- Department of Biochemistry; Virginia Polytechnic Institute and State University; Blacksburg Virginia 24061
| | - David R. Bevan
- Department of Biochemistry; Virginia Polytechnic Institute and State University; Blacksburg Virginia 24061
| | - Robert H. White
- Department of Biochemistry; Virginia Polytechnic Institute and State University; Blacksburg Virginia 24061
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Xiang DF, Patskovsky Y, Nemmara VV, Toro R, Almo SC, Raushel FM. Function discovery and structural characterization of a methylphosphonate esterase. Biochemistry 2015; 54:2919-30. [PMID: 25873441 PMCID: PMC4477287 DOI: 10.1021/acs.biochem.5b00199] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
Pmi1525, an enzyme of unknown function from Proteus mirabilis HI4320 and the amidohydrolase superfamily, was cloned, purified to homogeneity, and functionally characterized. The three-dimensional structure of Pmi1525 was determined with zinc and cacodylate bound in the active site (PDB id: 3RHG ). The structure was also determined with manganese and butyrate in the active site (PDB id: 4QSF ). Pmi1525 folds as a distorted (β/α)8-barrel that is typical for members of the amidohydrolase superfamily and cog1735. The substrate profile for Pmi1525 was determined via a strategy that marshaled the utilization of bioinformatics, structural characterization, and focused library screening. The protein was found to efficiently catalyze the hydrolysis of organophosphonate and carboxylate esters. The best substrates identified for Pmi1525 are ethyl 4-nitrophenylmethyl phosphonate (kcat and kcat/Km values of 580 s(-1) and 1.2 × 10(5) M(-1) s(-1), respectively) and 4-nitrophenyl butyrate (kcat and kcat/Km values of 140 s(-1) and 1.4 × 10(5) M(-1) s(-1), respectively). Pmi1525 is stereoselective for the hydrolysis of chiral methylphosphonate esters. The enzyme hydrolyzes the (SP)-enantiomer of isobutyl 4-nitrophenyl methylphosphonate 14 times faster than the corresponding (RP)-enantiomer. The catalytic properties of this enzyme make it an attractive template for the evolution of novel enzymes for the detection, destruction, and detoxification of organophosphonate nerve agents.
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Affiliation(s)
- Dao Feng Xiang
- Department of Chemistry, P.O. Box 30012, Texas A&M University, College Station, Texas 77842-3012
| | - Yury Patskovsky
- Department of Biochemistry, Einstein College of Medicine, 1300 Morris Park Avenue, Bronx, New York, 10461
| | - Venkatesh V. Nemmara
- Department of Chemistry, P.O. Box 30012, Texas A&M University, College Station, Texas 77842-3012
| | - Rafael Toro
- Department of Biochemistry, Einstein College of Medicine, 1300 Morris Park Avenue, Bronx, New York, 10461
| | - Steven C. Almo
- Department of Biochemistry, Einstein College of Medicine, 1300 Morris Park Avenue, Bronx, New York, 10461,To whom correspondence may be sent: (FMR) Telephone: 979-845-3373; , (SCA) Telephone: 718-430-2746;
| | - Frank M. Raushel
- Department of Chemistry, P.O. Box 30012, Texas A&M University, College Station, Texas 77842-3012,To whom correspondence may be sent: (FMR) Telephone: 979-845-3373; , (SCA) Telephone: 718-430-2746;
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Korczynska M, Xiang DF, Zhang Z, Xu C, Narindoshvili T, Kamat SS, Williams HJ, Chang SS, Kolb P, Hillerich B, Sauder JM, Burley SK, Almo SC, Swaminathan S, Shoichet BK, Raushel FM. Functional annotation and structural characterization of a novel lactonase hydrolyzing D-xylono-1,4-lactone-5-phosphate and L-arabino-1,4-lactone-5-phosphate. Biochemistry 2014; 53:4727-38. [PMID: 24955762 PMCID: PMC4108184 DOI: 10.1021/bi500595c] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Abstract
A novel lactonase from Mycoplasma synoviae 53 (MS53_0025) and Mycoplasma agalactiae PG2 (MAG_6390) was characterized by protein structure determination, molecular docking, gene context analysis, and library screening. The crystal structure of MS53_0025 was determined to a resolution of 2.06 Å. This protein adopts a typical amidohydrolase (β/α)8-fold and contains a binuclear zinc center located at the C-terminal end of the β-barrel. A phosphate molecule was bound in the active site and hydrogen bonds to Lys217, Lys244, Tyr245, Arg275, and Tyr278. Both docking and gene context analysis were used to narrow the theoretical substrate profile of the enzyme, thus directing empirical screening to identify that MS53_0025 and MAG_6390 catalyze the hydrolysis of d-xylono-1,4-lactone-5-phosphate (2) with kcat/Km values of 4.7 × 10(4) and 5.7 × 10(4) M(-1) s(-1) and l-arabino-1,4-lactone-5-phosphate (7) with kcat/Km values of 1.3 × 10(4) and 2.2 × 10(4) M(-1) s(-1), respectively. The identification of the substrate profile of these two phospho-furanose lactonases emerged only when all methods were integrated and therefore provides a blueprint for future substrate identification of highly related amidohydrolase superfamily members.
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Affiliation(s)
- Magdalena Korczynska
- Department of Pharmaceutical Chemistry, University of California, San Francisco , 1700 Fourth Street, San Francisco, California 94158-2330, United States
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Barelier S, Cummings J, Rauwerdink AM, Hitchcock DS, Farelli JD, Almo SC, Raushel FM, Allen KN, Shoichet BK. Substrate deconstruction and the nonadditivity of enzyme recognition. J Am Chem Soc 2014; 136:7374-82. [PMID: 24791931 PMCID: PMC4046767 DOI: 10.1021/ja501354q] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2014] [Indexed: 12/15/2022]
Abstract
Predicting substrates for enzymes of unknown function is a major postgenomic challenge. Substrate discovery, like inhibitor discovery, is constrained by our ability to explore chemotypes; it would be expanded by orders of magnitude if reactive sites could be probed with fragments rather than fully elaborated substrates, as is done for inhibitor discovery. To explore the feasibility of this approach, substrates of six enzymes from three different superfamilies were deconstructed into 41 overlapping fragments that were tested for activity or binding. Surprisingly, even those fragments containing the key reactive group had little activity, and most fragments did not bind measurably, until they captured most of the substrate features. Removing a single atom from a recognized substrate could often reduce catalytic recognition by 6 log-orders. To explore recognition at atomic resolution, the structures of three fragment complexes of the β-lactamase substrate cephalothin were determined by X-ray crystallography. Substrate discovery may be difficult to reduce to the fragment level, with implications for function discovery and for the tolerance of enzymes to metabolite promiscuity. Pragmatically, this study supports the development of libraries of fully elaborated metabolites as probes for enzyme function, which currently do not exist.
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Affiliation(s)
- Sarah Barelier
- Department
of Pharmaceutical Chemistry, University
of California - San Francisco, 1700 Fourth Street, Byers Hall, San Francisco, California 94158, United States
| | - Jennifer
A. Cummings
- Department
of Chemistry, Texas A&M University, College Station, Texas 77843, United States
| | - Alissa M. Rauwerdink
- Department
of Chemistry, Texas A&M University, College Station, Texas 77843, United States
| | - Daniel S. Hitchcock
- Department
of Biochemistry and Biophysics, Texas A&M
University, College Station, Texas, United States
| | - Jeremiah D. Farelli
- Department
of Chemistry, Boston University, 590 Commonwealth Avenue, Boston, Massachusetts 02215-2521, United States
| | - Steven C. Almo
- Department
of Biochemistry, Albert Einstein College
of Medicine, New York, New York 10461, United
States
| | - Frank M. Raushel
- Department
of Chemistry, Texas A&M University, College Station, Texas 77843, United States
- Department
of Biochemistry and Biophysics, Texas A&M
University, College Station, Texas, United States
| | - Karen N. Allen
- Department
of Chemistry, Boston University, 590 Commonwealth Avenue, Boston, Massachusetts 02215-2521, United States
| | - Brian K. Shoichet
- Department
of Pharmaceutical Chemistry, University
of California - San Francisco, 1700 Fourth Street, Byers Hall, San Francisco, California 94158, United States
- Faculty of
Pharmacy, University of Toronto, Donnelly Centre Suite 604, 160 College
Street, Toronto, Ontario, Canada, M5S 3E1
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