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Crystal structures of glycinamide ribonucleotide synthetase, PurD, from thermophilic eubacteria.

Sampei G, Baba S, Kanagawa M, Yanai H, Ishii T, Kawai H, Fukai Y, Ebihara A, Nakagawa N, Kawai G
J Biochem 148 429-38 (2010)
Related entries: 2ip4, 2yrw, 2yrx, 2ys6, 2yw2, 2yya

Cited: 12 times
EuropePMC logo PMID: 20716513

Abstract

Glycinamide ribonucleotide synthetase (GAR-syn, PurD) catalyses the second reaction of the purine biosynthetic pathway; the conversion of phosphoribosylamine, glycine and ATP to glycinamide ribonucleotide (GAR), ADP and Pi. In the present study, crystal structures of GAR-syn's from Thermus thermophilus, Geobacillus kaustophilus and Aquifex aeolicus were determined in apo forms. Crystal structures in ligand-bound forms were also determined for G. kaustophilus and A. aeolicus proteins. In general, overall structures of GAR-syn's are similar to each other. However, the orientations of the B domains are varied among GAR-syn's and the MD simulation suggested the mobility of the B domain. Furthermore, it was demonstrated that the B loop in the B domain fixes the position of the β- and γ- phosphate groups of the bound ATP. The structures of GAR-syn's and the bound ligands were compared with each other in detail, and structures of GAR-syn's with full ligands, as well as the possible reaction mechanism, were proposed.

Articles - 2ys7 mentioned but not cited (2)

  1. Structural studies of tri-functional human GART. Welin M, Grossmann JG, Flodin S, Nyman T, Stenmark P, Trésaugues L, Kotenyova T, Johansson I, Nordlund P, Lehtiö L. Nucleic Acids Res 38 7308-7319 (2010)
  2. Rapid countermeasure discovery against Francisella tularensis based on a metabolic network reconstruction. Chaudhury S, Abdulhameed MD, Singh N, Tawa GJ, D'haeseleer PM, Zemla AT, Navid A, Zhou CE, Franklin MC, Cheung J, Rudolph MJ, Love J, Graf JF, Rozak DA, Dankmeyer JL, Amemiya K, Daefler S, Wallqvist A. PLoS One 8 e63369 (2013)


Articles citing this publication (10)

  1. Helicobacter pylori relies primarily on the purine salvage pathway for purine nucleotide biosynthesis. Liechti G, Goldberg JB. J Bacteriol 194 839-854 (2012)
  2. A peptide ligase and the ribosome cooperate to synthesize the peptide pheganomycin. Noike M, Matsui T, Ooya K, Sasaki I, Ohtaki S, Hamano Y, Maruyama C, Ishikawa J, Satoh Y, Ito H, Morita H, Dairi T. Nat Chem Biol 11 71-76 (2015)
  3. Comparative Transcriptomic Analysis Reveals Novel Insights into the Adaptive Response of Skeletonema costatum to Changing Ambient Phosphorus. Zhang SF, Yuan CJ, Chen Y, Chen XH, Li DX, Liu JL, Lin L, Wang DZ. Front Microbiol 7 1476 (2016)
  4. Comparative Investigation into Formycin A and Pyrazofurin A Biosynthesis Reveals Branch Pathways for the Construction of C-Nucleoside Scaffolds. Zhang M, Zhang P, Xu G, Zhou W, Gao Y, Gong R, Cai YS, Cong H, Deng Z, Price NPJ, Mao X, Chen W. Appl Environ Microbiol 86 (2020)
  5. Selection markers for transformation of the sequenced reference monokaryon Okayama 7/#130 and homokaryon AmutBmut of Coprinopsis cinerea. Dörnte B, Peng C, Fang Z, Kamran A, Yulvizar C, Kües U. Fungal Biol Biotechnol 7 15 (2020)
  6. Structures and reaction mechanisms of the two related enzymes, PurN and PurU. Sampei G, Kanagawa M, Baba S, Shimasaki T, Taka H, Mitsui S, Fujiwara S, Yanagida Y, Kusano M, Suzuki S, Terao K, Kawai H, Fukai Y, Nakagawa N, Ebihara A, Kuramitsu S, Yokoyama S, Kawai G. J Biochem 154 569-579 (2013)
  7. Different Ways of Doing the Same: Variations in the Two Last Steps of the Purine Biosynthetic Pathway in Prokaryotes. Costa Brandão Cruz D, Lima Santana L, Siqueira Guedes A, Teodoro de Souza J, Arthur Santos Marbach P. Genome Biol Evol 11 1235-1249 (2019)
  8. Free-Energy Profile Analysis of the Catalytic Reaction of Glycinamide Ribonucleotide Synthetase. Yamamoto N, Sampei G, Kawai G. Life (Basel) 12 281 (2022)
  9. Structural features of Cryptococcus neoformans bifunctional GAR/AIR synthetase may present novel antifungal drug targets. Chua SMH, Wizrah MSI, Luo Z, Lim BYJ, Kappler U, Kobe B, Fraser JA. J Biol Chem 297 101091 (2021)
  10. β-Strand-mediated interactions of protein domains. Bhat AS, Kinch LN, Grishin NV. Proteins 88 1513-1527 (2020)


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