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Kim GE, Lee SY, Park HH. A high-resolution (1.2 Å) crystal structure of the anti-CRISPR protein AcrIF9. FEBS Open Bio 2020; 10:2532-2540. [PMID: 32990416 PMCID: PMC7714069 DOI: 10.1002/2211-5463.12986] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2020] [Revised: 09/15/2020] [Accepted: 09/22/2020] [Indexed: 12/11/2022] Open
Abstract
Prokaryotic adaptive immunity by CRISPR‐Cas systems, which confer resistance to foreign genetic elements, has been used by bacteria to combat viruses. To cope, viruses evolved multiple anti‐CRISPR proteins, which can inhibit system function through various mechanisms. Although the structures and mechanisms of several anti‐CRISPR proteins have been elucidated, those of the AcrIF9 family have not yet been identified. To understand the molecular basis underlying AcrIF9 anti‐CRISPR function, we determined the 1.2 Å crystal structure of AcrIF9. Structural and biochemical studies showed that AcrIF9 exists in monomeric form in solution and can directly interact with DNA using a positively charged cleft. Based on analysis of the structure, we suggest part of the anti‐CRISPR molecular mechanism by AcrIF9.
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Affiliation(s)
- Gi Eob Kim
- Department of Global Innovative Drugs, Graduate School of Chung-Ang University, Seoul, Korea.,College of Pharmacy, Chung-Ang University, Seoul, Korea
| | - So Yeon Lee
- Department of Global Innovative Drugs, Graduate School of Chung-Ang University, Seoul, Korea.,College of Pharmacy, Chung-Ang University, Seoul, Korea
| | - Hyun Ho Park
- Department of Global Innovative Drugs, Graduate School of Chung-Ang University, Seoul, Korea.,College of Pharmacy, Chung-Ang University, Seoul, Korea
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Watanabe Y, Yanai H, Kanagawa M, Suzuki S, Tamura S, Okada K, Baba S, Kumasaka T, Agari Y, Chen L, Fu ZQ, Chrzas J, Wang BC, Nakagawa N, Ebihara A, Masui R, Kuramitsu S, Yokoyama S, Sampei GI, Kawai G. Crystal structures of a subunit of the formylglycinamide ribonucleotide amidotransferase, PurS, from Thermus thermophilus, Sulfolobus tokodaii and Methanocaldococcus jannaschii. Acta Crystallogr F Struct Biol Commun 2016; 72:627-35. [PMID: 27487927 PMCID: PMC4973304 DOI: 10.1107/s2053230x1600978x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2016] [Accepted: 06/16/2016] [Indexed: 11/10/2022] Open
Abstract
The crystal structures of a subunit of the formylglycinamide ribonucleotide amidotransferase, PurS, from Thermus thermophilus, Sulfolobus tokodaii and Methanocaldococcus jannaschii were determined and their structural characteristics were analyzed. For PurS from T. thermophilus, two structures were determined using two crystals that were grown in different conditions. The four structures in the dimeric form were almost identical to one another despite their relatively low sequence identities. This is also true for all PurS structures determined to date. A few residues were conserved among PurSs and these are located at the interaction site with PurL and PurQ, the other subunits of the formylglycinamide ribonucleotide amidotransferase. Molecular-dynamics simulations of the PurS dimer as well as a model of the complex of the PurS dimer, PurL and PurQ suggest that PurS plays some role in the catalysis of the enzyme by its bending motion.
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Affiliation(s)
- Yuzo Watanabe
- Department of Life and Environmental Sciences, Faculty of Engineering, Chiba Institute of Technology, 2-17-1 Tsudanuma, Narashino, Chiba 275-0016, Japan
| | - Hisaaki Yanai
- RIKEN SPring-8 Center, Harima Institute, 1-1-1 Kouto, Sayo, Hyogo 679-5148, Japan
| | - Mayumi Kanagawa
- RIKEN SPring-8 Center, Harima Institute, 1-1-1 Kouto, Sayo, Hyogo 679-5148, Japan
| | - Sakiko Suzuki
- Department of Life and Environmental Sciences, Faculty of Engineering, Chiba Institute of Technology, 2-17-1 Tsudanuma, Narashino, Chiba 275-0016, Japan
| | - Satoko Tamura
- Department of Life and Environmental Sciences, Faculty of Engineering, Chiba Institute of Technology, 2-17-1 Tsudanuma, Narashino, Chiba 275-0016, Japan
| | - Kiyoshi Okada
- Department of Engineering Science, Graduate School of Informatics and Engineering, The University of Electro-Communications, 1-5-1 Chofugaoka, Chofu, Tokyo 182-8585, Japan
| | - Seiki Baba
- Structural Biology Group, SPring-8/JASRI, 1-1-1 Kouto, Sayo, Hyogo 679-5198, Japan
| | - Takashi Kumasaka
- Structural Biology Group, SPring-8/JASRI, 1-1-1 Kouto, Sayo, Hyogo 679-5198, Japan
| | - Yoshihiro Agari
- RIKEN SPring-8 Center, Harima Institute, 1-1-1 Kouto, Sayo, Hyogo 679-5148, Japan
| | - Lirong Chen
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA 30602, USA
| | - Zheng-Qing Fu
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA 30602, USA
- SER-CAT, Advanced Photon Source, Argonne National Laboratory, 9700 South Cass Avenue, Argonne, IL 60439-4861, USA
| | - John Chrzas
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA 30602, USA
- SER-CAT, Advanced Photon Source, Argonne National Laboratory, 9700 South Cass Avenue, Argonne, IL 60439-4861, USA
| | - Bi-Cheng Wang
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA 30602, USA
| | - Noriko Nakagawa
- Department of Biological Sciences, Graduate School of Science, Osaka University, 1-1 Machikaneyama-cho, Toyonaka, Osaka 560-0043, Japan
| | - Akio Ebihara
- RIKEN SPring-8 Center, Harima Institute, 1-1-1 Kouto, Sayo, Hyogo 679-5148, Japan
| | - Ryoji Masui
- Department of Biological Sciences, Graduate School of Science, Osaka University, 1-1 Machikaneyama-cho, Toyonaka, Osaka 560-0043, Japan
| | - Seiki Kuramitsu
- Department of Biological Sciences, Graduate School of Science, Osaka University, 1-1 Machikaneyama-cho, Toyonaka, Osaka 560-0043, Japan
| | - Shigeyuki Yokoyama
- RIKEN SPring-8 Center, Harima Institute, 1-1-1 Kouto, Sayo, Hyogo 679-5148, Japan
| | - Gen-ichi Sampei
- RIKEN SPring-8 Center, Harima Institute, 1-1-1 Kouto, Sayo, Hyogo 679-5148, Japan
- Department of Engineering Science, Graduate School of Informatics and Engineering, The University of Electro-Communications, 1-5-1 Chofugaoka, Chofu, Tokyo 182-8585, Japan
| | - Gota Kawai
- Department of Life and Environmental Sciences, Faculty of Engineering, Chiba Institute of Technology, 2-17-1 Tsudanuma, Narashino, Chiba 275-0016, Japan
- RIKEN SPring-8 Center, Harima Institute, 1-1-1 Kouto, Sayo, Hyogo 679-5148, Japan
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Misra SK, Moussan Désirée Aké F, Wu Z, Milohanic E, Cao TN, Cossart P, Deutscher J, Monnet V, Archambaud C, Henry C. Quantitative proteome analyses identify PrfA-responsive proteins and phosphoproteins in Listeria monocytogenes. J Proteome Res 2014; 13:6046-57. [PMID: 25383790 DOI: 10.1021/pr500929u] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Protein phosphorylation is a major mechanism of signal transduction in bacteria. Here, we analyzed the proteome and phosphoproteome of a wild-type strain of the food-borne pathogen Listeria monocytogenes that was grown in either chemically defined medium or rich medium containing glucose. We then compared these results with those obtained from an isogenic prfA* mutant that produced a constitutively active form of PrfA, the main transcriptional activator of virulence genes. In the prfA* mutant grown in rich medium, we identified 256 peptides that were phosphorylated on serine (S), threonine (T), or tyrosine (Y) residues, with a S/T/Y ratio of 155:75:12. Strikingly, we detected five novel phosphosites on the virulence protein ActA. This protein was known to be phosphorylated by a cellular kinase in the infected host, but phosphorylation by a listerial kinase had not previously been reported. Unexpectedly, SILAC experiments with the prfA* mutant grown in chemically defined medium revealed that, in addition to previously described PrfA-regulated proteins, several other proteins were significantly overproduced, among them were several proteins involved in purine biosynthesis. This work provides new information for our understanding of the correlation among protein phosphorylation, virulence mechanisms, and carbon metabolism.
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Abstract
Purine biosynthesis requires ten enzymatic transformations to generate inosine monophosphate. PurF, PurD, PurL, PurM, PurC, and PurB are common to all pathways, while PurN or PurT, PurK/PurE-I or PurE-II, PurH or PurP, and PurJ or PurO catalyze the same steps in different organisms. X-ray crystal structures are available for all 15 purine biosynthetic enzymes, including 7 ATP-dependent enzymes, 2 amidotransferases and 2 tetrahydrofolate-dependent enzymes. Here we summarize the structures of the purine biosynthetic enzymes, discuss similarities and differences, and present arguments for pathway evolution. Four of the ATP-dependent enzymes belong to the ATP-grasp superfamily and 2 to the PurM superfamily. The amidotransferases are unrelated, with one utilizing an N-terminal nucleophileglutaminase and the other utilizing a triad glutaminase. Likewise the tetrahydrofolate-dependent enzymes are unrelated. Ancestral proteins may have included a broad specificity enzyme instead of PurD, PurT, PurK, PurC, and PurP, and a separate enzyme instead of PurM and PurL.
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Affiliation(s)
- Y. Zhang
- Department of Chemistry and Chemical Biology, Baker Laboratory, Cornell University, Ithaca, NY 14853 USA
| | - M. Morar
- Department of Chemistry and Chemical Biology, Baker Laboratory, Cornell University, Ithaca, NY 14853 USA
| | - S. E. Ealick
- Department of Chemistry and Chemical Biology, Baker Laboratory, Cornell University, Ithaca, NY 14853 USA
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Morar M, Hoskins AA, Stubbe J, Ealick SE. Formylglycinamide ribonucleotide amidotransferase from Thermotoga maritima: structural insights into complex formation. Biochemistry 2008; 47:7816-30. [PMID: 18597481 PMCID: PMC2646663 DOI: 10.1021/bi800329p] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
In the fourth step of the purine biosynthetic pathway, formyl glycinamide ribonucleotide (FGAR) amidotransferase, also known as PurL, catalyzes the conversion of FGAR, ATP, and glutamine to formyl glycinamidine ribonucleotide (FGAM), ADP, P i, and glutamate. Two forms of PurL have been characterized, large and small. Large PurL, present in most Gram-negative bacteria and eukaryotes, consists of a single polypeptide chain and contains three major domains: the N-terminal domain, the FGAM synthetase domain, and the glutaminase domain, with a putative ammonia channel located between the active sites of the latter two. Small PurL, present in Gram-positive bacteria and archaea, is structurally homologous to the FGAM synthetase domain of large PurL, and forms a complex with two additional gene products, PurQ and PurS. The structure of the PurS dimer is homologous with the N-terminal domain of large PurL, while PurQ, whose structure has not been reported, contains the glutaminase activity. In Bacillus subtilis, the formation of the PurLQS complex is dependent on glutamine and ADP and has been demonstrated by size-exclusion chromatography. In this work, a structure of the PurLQS complex from Thermotoga maritima is described revealing a 2:1:1 stoichiometry of PurS:Q:L, respectively. The conformational changes observed in TmPurL upon complex formation elucidate the mechanism of metabolite-mediated recruitment of PurQ and PurS. The flexibility of the PurS dimer is proposed to play a role in the activation of the complex and the formation of the ammonia channel. A potential path for the ammonia channel is identified.
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Affiliation(s)
- Mariya Morar
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, New York 14853, USA
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Axelrod HL, McMullan D, Krishna SS, Miller MD, Elsliger MA, Abdubek P, Ambing E, Astakhova T, Carlton D, Chiu HJ, Clayton T, Duan L, Feuerhelm J, Grzechnik SK, Hale J, Han GW, Haugen J, Jaroszewski L, Jin KK, Klock HE, Knuth MW, Koesema E, Morse AT, Nigoghossian E, Okach L, Oommachen S, Paulsen J, Quijano K, Reyes R, Rife CL, van den Bedem H, Weekes D, White A, Wolf G, Xu Q, Hodgson KO, Wooley J, Deacon AM, Godzik A, Lesley SA, Wilson IA. Crystal structure of AICAR transformylase IMP cyclohydrolase (TM1249) fromThermotoga maritima at 1.88 Å resolution. Proteins 2008; 71:1042-9. [DOI: 10.1002/prot.21967] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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