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Viola RE. The ammonia-lyases: enzymes that use a wide range of approaches to catalyze the same type of reaction. Crit Rev Biochem Mol Biol 2020; 54:467-483. [PMID: 31906712 DOI: 10.1080/10409238.2019.1708261] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Abstract
The paradigm that protein structure determines protein function has been clearly established. What is less clear is whether a specific protein structure is always required to carry out a specific function. Numerous cases are now known where there is no apparent connection between the biological function of a protein and the other members of its structural class, and where functionally related proteins can have quite diverse structures. A set of enzymes with these diverse properties, the ammonia-lyases, will be examined in this review. These are a class of enzymes that catalyze a relatively straightforward deamination reaction. However, the individual enzymes of this class possess a wide variety of different structures, utilize a diverse set of cofactors, and appear to catalyze this related reaction through a range of different mechanisms. This review aims to address a basic question: if there is not a specific protein structure and active site architecture that is both required and sufficient to define a catalyst for a given chemical reaction, then what factor(s) determine the structure and the mechanism that is selected to catalyze a particular reaction?
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Affiliation(s)
- Ronald E Viola
- Department of Chemistry and Biochemistry, University of Toledo, Toledo, OH, USA
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2
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Exploring the sequence, function, and evolutionary space of protein superfamilies using sequence similarity networks and phylogenetic reconstructions. Methods Enzymol 2019; 620:315-347. [PMID: 31072492 DOI: 10.1016/bs.mie.2019.03.015] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Integrative computational methods can facilitate the discovery of new protein functions and enzymatic reactions by enabling the observation and investigation of complex sequence-structure-function and evolutionary relationships within protein superfamilies. Here, we highlight the use of sequence similarity networks (SSNs) and phylogenetic reconstructions to map the functional divergence and evolutionary history of protein superfamilies. We exemplify this approach using the nitroreductase (NTR) flavoenzyme superfamily, demonstrating that SSN investigations can provide a rapid and effective means to classify groups of proteins, expose sequence similarity relationships across the global scale of a protein superfamily, and efficiently support detailed phylogenetic analyses. Integration of such approaches with systematic experimental characterization will expand our understanding of the functional diversity of enzymes, their evolution, and their associated physiological roles.
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3
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Copp JN, Akiva E, Babbitt PC, Tokuriki N. Revealing Unexplored Sequence-Function Space Using Sequence Similarity Networks. Biochemistry 2018; 57:4651-4662. [PMID: 30052428 DOI: 10.1021/acs.biochem.8b00473] [Citation(s) in RCA: 40] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The rapidly expanding number of protein sequences found in public databases can improve our understanding of how protein functions evolve. However, our current knowledge of protein function likely represents a small fraction of the diverse repertoire that exists in nature. Integrative computational methods can facilitate the discovery of new protein functions and enzymatic reactions through the observation and investigation of the complex sequence-structure-function relationships within protein superfamilies. Here, we highlight the use of sequence similarity networks (SSNs) to identify previously unexplored sequence and function space. We exemplify this approach using the nitroreductase (NTR) superfamily. We demonstrate that SSN investigations can provide a rapid and effective means to classify groups of proteins, therefore exposing experimentally unexplored sequences that may exhibit novel functionality. Integration of such approaches with systematic experimental characterization will expand our understanding of the functional diversity of enzymes and their associated physiological roles.
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Affiliation(s)
- Janine N Copp
- Michael Smith Laboratories , University of British Columbia , 2185 East Mall , Vancouver , British Columbia V6T 1Z4 , Canada
| | - Eyal Akiva
- Department of Bioengineering and Therapeutic Sciences , University of California , San Francisco , California 94158 , United States.,Quantitative Biosciences Institute , University of California , San Francisco , California 94143 , United States
| | - Patricia C Babbitt
- Department of Bioengineering and Therapeutic Sciences , University of California , San Francisco , California 94158 , United States.,Quantitative Biosciences Institute , University of California , San Francisco , California 94143 , United States
| | - Nobuhiko Tokuriki
- Michael Smith Laboratories , University of British Columbia , 2185 East Mall , Vancouver , British Columbia V6T 1Z4 , Canada
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4
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Abstract
Traditionally, only the 3',5'-cyclic monophosphates of adenosine and guanosine (produced by adenylyl cyclase and guanylyl cyclase, respectively) are regarded as true "second messengers" in the vascular wall, despite the presence of other cyclic nucleotides in different tissues. Among these noncanonical cyclic nucleotides, inosine 3',5'-cyclic monophosphate (cIMP) is synthesized by soluble guanylyl cyclase in porcine coronary arteries in response to hypoxia, when the enzyme is activated by endothelium-derived nitric oxide. Its production is associated with augmentation of vascular contraction mediated by stimulation of Rho kinase. Based on these findings, cIMP appears to meet most, if not all, of the criteria required for it to be accepted as a "second messenger," at least in the vascular wall.
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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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7
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Gerlt JA, Bouvier JT, Davidson DB, Imker HJ, Sadkhin B, Slater DR, Whalen KL. Enzyme Function Initiative-Enzyme Similarity Tool (EFI-EST): A web tool for generating protein sequence similarity networks. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2015; 1854:1019-37. [PMID: 25900361 DOI: 10.1016/j.bbapap.2015.04.015] [Citation(s) in RCA: 578] [Impact Index Per Article: 64.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/15/2015] [Revised: 03/30/2015] [Accepted: 04/14/2015] [Indexed: 11/19/2022]
Abstract
The Enzyme Function Initiative, an NIH/NIGMS-supported Large-Scale Collaborative Project (EFI; U54GM093342; http://enzymefunction.org/), is focused on devising and disseminating bioinformatics and computational tools as well as experimental strategies for the prediction and assignment of functions (in vitro activities and in vivo physiological/metabolic roles) to uncharacterized enzymes discovered in genome projects. Protein sequence similarity networks (SSNs) are visually powerful tools for analyzing sequence relationships in protein families (H.J. Atkinson, J.H. Morris, T.E. Ferrin, and P.C. Babbitt, PLoS One 2009, 4, e4345). However, the members of the biological/biomedical community have not had access to the capability to generate SSNs for their "favorite" protein families. In this article we announce the EFI-EST (Enzyme Function Initiative-Enzyme Similarity Tool) web tool (http://efi.igb.illinois.edu/efi-est/) that is available without cost for the automated generation of SSNs by the community. The tool can create SSNs for the "closest neighbors" of a user-supplied protein sequence from the UniProt database (Option A) or of members of any user-supplied Pfam and/or InterPro family (Option B). We provide an introduction to SSNs, a description of EFI-EST, and a demonstration of the use of EFI-EST to explore sequence-function space in the OMP decarboxylase superfamily (PF00215). This article is designed as a tutorial that will allow members of the community to use the EFI-EST web tool for exploring sequence/function space in protein families.
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Affiliation(s)
- John A Gerlt
- Institute for Genomic Biology, University of Illinois, Urbana-Champaign, Urbana, IL 61801 USA; Department of Biochemistry, University of Illinois, Urbana-Champaign, Urbana, IL 61801 USA; Department of Chemistry, University of Illinois, Urbana-Champaign, Urbana, IL 61801 USA.
| | - Jason T Bouvier
- Institute for Genomic Biology, University of Illinois, Urbana-Champaign, Urbana, IL 61801 USA; Department of Biochemistry, University of Illinois, Urbana-Champaign, Urbana, IL 61801 USA
| | - Daniel B Davidson
- Institute for Genomic Biology, University of Illinois, Urbana-Champaign, Urbana, IL 61801 USA
| | - Heidi J Imker
- Institute for Genomic Biology, University of Illinois, Urbana-Champaign, Urbana, IL 61801 USA
| | - Boris Sadkhin
- Institute for Genomic Biology, University of Illinois, Urbana-Champaign, Urbana, IL 61801 USA
| | - David R Slater
- Institute for Genomic Biology, University of Illinois, Urbana-Champaign, Urbana, IL 61801 USA
| | - Katie L Whalen
- Institute for Genomic Biology, University of Illinois, Urbana-Champaign, Urbana, IL 61801 USA
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Zhang H, Luo Q, Gao H, Feng Y. A new regulatory mechanism for bacterial lipoic acid synthesis. Microbiologyopen 2015; 4:282-300. [PMID: 25611823 PMCID: PMC4398509 DOI: 10.1002/mbo3.237] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2014] [Revised: 12/01/2014] [Accepted: 12/09/2014] [Indexed: 01/15/2023] Open
Abstract
Lipoic acid, an essential enzyme cofactor, is required in three domains of life. In the past 60 years since its discovery, most of the pathway for lipoic acid synthesis and metabolism has been elucidated. However, genetic control of lipoic acid synthesis remains unclear. Here, we report integrative evidence that bacterial cAMP-dependent signaling is linked to lipoic acid synthesis in Shewanella species, the certain of unique marine-borne bacteria with special ability of metal reduction. Physiological requirement of protein lipoylation in γ-proteobacteria including Shewanella oneidensis was detected using Western blotting with rabbit anti-lipoyl protein primary antibody. The two genes (lipB and lipA) encoding lipoic acid synthesis pathway were proved to be organized into an operon lipBA in Shewanella, and the promoter was mapped. Electrophoretic mobility shift assays confirmed that the putative CRP-recognizable site (AAGTGTGATCTATCTTACATTT) binds to cAMP-CRP protein with origins of both Escherichia coli and Shewanella. The native lipBA promoter of Shewanella was fused to a LacZ reporter gene to create a chromosome lipBA-lacZ transcriptional fusion in E. coli and S. oneidensis, allowing us to directly assay its expression level by β-galactosidase activity. As anticipated, the removal of E. coli crp gene gave above fourfold increment of lipBA promoter-driven β-gal expression. The similar scenario was confirmed by both the real-time quantitative PCR and the LacZ transcriptional fusion in the crp mutant of Shewanella. Furthermore, the glucose effect on the lipBA expression of Shewanella was evaluated in the alternative microorganism E. coli. As anticipated, an addition of glucose into media effectively induces the transcriptional level of Shewanella lipBA in that the lowered cAMP level relieves the repression of lipBA by cAMP-CRP complex. Therefore, our finding might represent a first paradigm mechanism for genetic control of bacterial lipoic acid synthesis.
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Affiliation(s)
- Huimin Zhang
- Center for Infection and Immunity, Department of Medical Microbiology and Parasitology, School of Basic Medical Sciences, Zhejiang University, Hangzhou, Zhejiang, China
| | - Qixia Luo
- Institute of Microbiology, College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang, China
| | - Haichun Gao
- Institute of Microbiology, College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang, China
| | - Youjun Feng
- Center for Infection and Immunity, Department of Medical Microbiology and Parasitology, School of Basic Medical Sciences, Zhejiang University, Hangzhou, Zhejiang, China
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A facile and sensitive method for quantification of cyclic nucleotide monophosphates in mammalian organs: basal levels of eight cNMPs and identification of 2',3'-cIMP. Biomolecules 2014; 4:1070-92. [PMID: 25513747 PMCID: PMC4279170 DOI: 10.3390/biom4041070] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2014] [Revised: 11/27/2014] [Accepted: 12/01/2014] [Indexed: 12/25/2022] Open
Abstract
A sensitive, versatile and economical method to extract and quantify cyclic nucleotide monophosphates (cNMPs) using LC-MS/MS, including both 3',5'-cNMPs and 2',3'-cNMPs, in mammalian tissues and cellular systems has been developed. Problems, such as matrix effects from complex biological samples, are addressed and have been optimized. This protocol allows for comparison of multiple cNMPs in the same system and was used to examine the relationship between tissue levels of cNMPs in a panel of rat organs. In addition, the study reports the first identification and quantification of 2',3'-cIMP. The developed method will allow for quantification of cNMPs levels in cells and tissues with varying disease states, which will provide insight into the role(s) and interplay of cNMP signalling pathways.
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Feng Y, Cronan JE. PdhR, the pyruvate dehydrogenase repressor, does not regulate lipoic acid synthesis. Res Microbiol 2014; 165:429-38. [PMID: 24816490 PMCID: PMC4134263 DOI: 10.1016/j.resmic.2014.04.005] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2014] [Revised: 04/23/2014] [Accepted: 04/24/2014] [Indexed: 12/17/2022]
Abstract
Lipoic acid is a covalently-bound enzyme cofactor required for central metabolism all three domains of life. In the last 20 years the pathway of lipoic acid synthesis and metabolism has been established in Escherichia coli. Expression of the genes of the lipoic acid biosynthesis pathway was believed to be constitutive. However, in 2010 Kaleta and coworkers (BMC Syst. Biol. 4:116) predicted a binding site for the pyruvate dehydrogenase operon repressor, PdhR (referred to lipA site 1) upstream of lipA, the gene encoding lipoic acid synthase and concluded that PdhR regulates lipA transcription. We report in vivo and in vitro evidence that lipA is not controlled by PdhR and that the putative regulatory site deduced by the prior workers is nonfunctional and physiologically irrelevant. E. coli PdhR was purified to homogeneity and used for electrophoretic mobility shift assays. The lipA site 1 of Kaleta and coworkers failed to bind PdhR. The binding detected by these workers is due to another site (lipA site 3) located far upstream of the lipA promoter. Relative to the canonical PdhR binding site lipA site 3 is a half-palindrome and as expected had only weak PdhR binding ability. Manipulation of lipA site 3 to construct a palindrome gave significantly enhanced PdhR binding affinity. The native lipA promoter and the version carrying the artificial lipA3 palindrome were transcriptionally fused to a LacZ reporter gene to directly assay lipA expression. Deletion of pdhR gave no significant change in lipA promoter-driven β-galactosidase activity with either the native or constructed palindrome upstream sequences, indicating that PdhR plays no physiological role in regulation of lipA expression.
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Affiliation(s)
- Youjun Feng
- Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases & State Key Laboratory for Diagnosis and Treatment of Infectious Disease, First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310058, PR China; Department of Medical Microbiology and Parasitology, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310058, PR China; Department of Microbiology, University of Illinois at Urbana-Champaign, IL 61801, USA
| | - John E Cronan
- Department of Microbiology, University of Illinois at Urbana-Champaign, IL 61801, USA; Department of Biochemistry, University of Illinois at Urbana-Champaign, IL 61801, USA.
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Feng Y, Zhang H, Wu Z, Wang S, Cao M, Hu D, Wang C. Streptococcus suis infection: an emerging/reemerging challenge of bacterial infectious diseases? Virulence 2014; 5:477-97. [PMID: 24667807 PMCID: PMC4063810 DOI: 10.4161/viru.28595] [Citation(s) in RCA: 158] [Impact Index Per Article: 15.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Streptococcus suis (S. suis) is a family of pathogenic gram-positive bacterial strains that represents a primary health problem in the swine industry worldwide. S. suis is also an emerging zoonotic pathogen that causes severe human infections clinically featuring with varied diseases/syndromes (such as meningitis, septicemia, and arthritis). Over the past few decades, continued efforts have made significant progress toward better understanding this zoonotic infectious entity, contributing in part to the elucidation of the molecular mechanism underlying its high pathogenicity. This review is aimed at presenting an updated overview of this pathogen from the perspective of molecular epidemiology, clinical diagnosis and typing, virulence mechanism, and protective antigens contributing to its zoonosis.
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Affiliation(s)
- Youjun Feng
- Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases & State Key Laboratory for Diagnosis and Treatment of Infectious Disease; First Affiliated Hospital; Zhejiang University School of Medicine; Hangzhou, Zhejiang, PR China; Department of Medical Microbiology and Parasitology; Zhejiang University School of Medicine; Hangzhou, Zhejiang, PR China
| | - Huimin Zhang
- University of Illinois at Urbana-Champaign (UIUC); Urbana, IL USA
| | - Zuowei Wu
- Department of Veterinary Microbiology and Preventive Medicine; Iowa State University; Ames, IA USA
| | - Shihua Wang
- College of Life Sciences; Fujian Agriculture and Forestry University; Fuzhou, Fujian, PR China
| | - Min Cao
- Department of Epidemiology; Research Institute for Medicine of Nanjing Command; Nanjing, Jiangsu, PR China
| | - Dan Hu
- Department of Epidemiology; Research Institute for Medicine of Nanjing Command; Nanjing, Jiangsu, PR China
| | - Changjun Wang
- Department of Epidemiology; Research Institute for Medicine of Nanjing Command; Nanjing, Jiangsu, PR China
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