2IP4

Crystal Structure of Glycinamide Ribonucleotide Synthetase from Thermus thermophilus HB8

Summary for 2IP4

• Entry DOI: 10.2210/pdb2ip4/pdb
• Descriptor: Phosphoribosylamine--glycine ligase, SULFATE ION (3 entities in total)
• Functional Keywords: gar synthetase, purd, thermus thermophilus, purine nucleotide, structural genomics, nppsfa, national project on protein structural and functional analyses, riken structural genomics/proteomics initiative, rsgi, ligase
• Biological source: Thermus thermophilus
• Total number of polymer chains: 2
• Total formula weight: 90160.83

Authors

Sampei, G.,Baba, S.,Kanagawa, M.,Yanai, H.,Ishii, T.,Kawai, H.,Fukai, Y.,Ebihara, A.,Nakagawa, N.,Kawai, G.,RIKEN Structural Genomics/Proteomics Initiative (RSGI) (deposition date: 2006-10-11, release date: 2007-10-30, Last modification date: 2023-11-15)

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

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: 20716513
DOI: 10.1093/jb/mvq088

Experimental method

X-RAY DIFFRACTION (2.8 Å)