Crystal structures of glycinamide ribonucleotide synthetase, PurD, from thermophilic eubacteria.
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.
Sampei
Gen-Ichi
G
Department of Applied Physics and Chemistry, Faculty of Electro-Communications, The University of Electro-Communications, 1-5-1 Chofugaoka, Chofu-shi, Tokyo, Japan. sampei@pc.uec.ac.jp
Baba
Seiki
S
Kanagawa
Mayumi
M
Yanai
Hisaaki
H
Ishii
Takeshi
T
Kawai
Hiroya
H
Fukai
Yoko
Y
Ebihara
Akio
A
Nakagawa
Noriko
N
Kawai
Gota
G
D001426:Bacterial Proteins / Q000737:chemistry* / Q000378:metabolism; D019731:Carbon-Nitrogen Ligases / Q000737:chemistry* / Q000378:metabolism; D018360:Crystallography, X-Ray; D056506:Geobacillus / Q000201:enzymology*; D008958:Models, Molecular; D008969:Molecular Sequence Data; D015394:Molecular Structure; D011487:Protein Conformation; D012265:Ribonucleotides / Q000737:chemistry* / Q000378:metabolism; D016963:Thermus thermophilus / Q000201:enzymology*
D001426:Bacterial Proteins; D012265:Ribonucleotides; C014978:glycineamide ribonucleotide; D019731:Carbon-Nitrogen Ligases; C022387:phosphoribosylamine-glycine ligase