Crystal structure of GAR synthetase from Geobacillus kaustophilus

Experimental Data Snapshot

  • Resolution: 2.21 Å
  • R-Value Free: 0.251 
  • R-Value Work: 0.208 
  • R-Value Observed: 0.208 

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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.

(2010) J Biochem 148: 429-438

  • DOI: https://doi.org/10.1093/jb/mvq088
  • Primary Citation of Related Structures:  
    2IP4, 2YRW, 2YRX, 2YS6, 2YS7, 2YW2, 2YYA

  • 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.

  • Organizational Affiliation

    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

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Phosphoribosylglycinamide synthetase451Geobacillus kaustophilusMutation(s): 0 
Find proteins for Q5L3C7 (Geobacillus kaustophilus (strain HTA426))
Explore Q5L3C7 
Go to UniProtKB:  Q5L3C7
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ5L3C7
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 2.21 Å
  • R-Value Free: 0.251 
  • R-Value Work: 0.208 
  • R-Value Observed: 0.208 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 51.231α = 90
b = 83.552β = 90
c = 94.726γ = 90
Software Package:
Software NamePurpose
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

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Entry History 

Revision History  (Full details and data files)

  • Version 1.0: 2007-10-09
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2023-10-25
    Changes: Data collection, Database references, Refinement description