2YS6
Crystal structure of GAR synthetase from Geobacillus kaustophilus
Summary for 2YS6
| Entry DOI | 10.2210/pdb2ys6/pdb |
| Related | 2YRW |
| Descriptor | Phosphoribosylglycinamide synthetase, GLYCINE, ADENOSINE MONOPHOSPHATE, ... (4 entities in total) |
| Functional Keywords | glycinamide ribonucleotide synthetase, gar synthetase, atp binding, purine nucleotide biosynthetic pathway, structural genomics, nppsfa, national project on protein structural and functional analyses, riken structural genomics/proteomics initiative, rsgi, ligase |
| Biological source | Geobacillus kaustophilus |
| Total number of polymer chains | 1 |
| Total formula weight | 48651.07 |
| Authors | Baba, S.,Kanagawa, M.,Kuramitsu, S.,Yokoyama, S.,Kawai, G.,Sampei, G.,RIKEN Structural Genomics/Proteomics Initiative (RSGI) (deposition date: 2007-04-03, release date: 2007-10-09, Last modification date: 2023-10-25) |
| Primary citation | Sampei, G.,Baba, S.,Kanagawa, M.,Yanai, H.,Ishii, T.,Kawai, H.,Fukai, Y.,Ebihara, A.,Nakagawa, N.,Kawai, G. Crystal structures of glycinamide ribonucleotide synthetase, PurD, from thermophilic eubacteria J.Biochem., 148:429-438, 2010 Cited by PubMed 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. PubMed: 20716513DOI: 10.1093/jb/mvq088 PDB entries with the same primary citation |
| Experimental method | X-RAY DIFFRACTION (2.21 Å) |
Structure validation
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