2YW2

Crystal structure of GAR synthetase from Aquifex aeolicus in complex with ATP


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 0.227 
  • R-Value Work: 0.203 
  • R-Value Observed: 0.203 

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This is version 1.2 of the entry. See complete history


Literature

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


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Phosphoribosylamine--glycine ligase
A, B
424Aquifex aeolicusMutation(s): 0 
EC: 6.3.4.13
UniProt
Find proteins for O66949 (Aquifex aeolicus (strain VF5))
Explore O66949 
Go to UniProtKB:  O66949
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO66949
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 0.227 
  • R-Value Work: 0.203 
  • R-Value Observed: 0.203 
  • Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 45.797α = 97.65
b = 61.623β = 102.98
c = 89.963γ = 106.65
Software Package:
Software NamePurpose
CNSrefinement
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing

Structure Validation

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Entry History 

Revision History  (Full details and data files)

  • Version 1.0: 2007-10-23
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2023-10-25
    Changes: Data collection, Database references, Derived calculations, Refinement description