2A7R

Crystal structure of human Guanosine Monophosphate reductase 2 (GMPR2)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.00 Å
  • R-Value Free: 0.276 
  • R-Value Work: 0.228 
  • R-Value Observed: 0.228 

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This is version 1.2 of the entry. See complete history


Literature

Crystal Structure of Human Guanosine Monophosphate Reductase 2 (GMPR2) in Complex with GMP

Li, J.Wei, Z.Zheng, M.Gu, X.Deng, Y.Qiu, R.Chen, F.Ji, C.Gong, W.Xie, Y.Mao, Y.

(2006) J Mol Biol 355: 980-988

  • DOI: https://doi.org/10.1016/j.jmb.2005.11.047
  • Primary Citation of Related Structures:  
    2A7R

  • PubMed Abstract: 

    Guanosine monophosphate reductase (GMPR) catalyzes the irreversible and NADPH-dependent reductive deamination of GMP to IMP, and plays a critical role in re-utilization of free intracellular bases and purine nucleosides. Here, we report the first crystal structure of human GMP reductase 2 (hGMPR2) in complex with GMP at 3.0 A resolution. The protein forms a tetramer composed of subunits adopting the ubiquitous (alpha/beta)8 barrel fold. Interestingly, the substrate GMP is bound to hGMPR2 through interactions with Met269, Ser270, Arg286, Ser288, and Gly290; this makes the conformation of the adjacent flexible binding region (residues 268-289) fixed, much like a door on a hinge. Structure comparison and sequence alignment analyses show that the conformation of the active site loop (residues 179-187) is similar to those of hGMPR1 and inosine monophosphate dehydrogenases (IMPDHs). We propose that Cys186 is the potential active site, and that the conformation of the loop (residues 129-133) suggests a preference for the coenzyme NADPH over NADH. This structure provides important information towards understanding the functions of members of the GMPR family.


  • Organizational Affiliation

    State Key Laboratory of Genetic Engineering, Institute of Genetics, School of Life Sciences, Fudan University, Shanghai 200433, People's Republic of China.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
GMP reductase 2
A, B, C, D
366Homo sapiensMutation(s): 0 
EC: 1.7.1.7
UniProt & NIH Common Fund Data Resources
Find proteins for Q9P2T1 (Homo sapiens)
Explore Q9P2T1 
Go to UniProtKB:  Q9P2T1
PHAROS:  Q9P2T1
GTEx:  ENSG00000100938 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9P2T1
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
5GP
Query on 5GP

Download Ideal Coordinates CCD File 
G [auth A],
J [auth B],
M [auth C]
GUANOSINE-5'-MONOPHOSPHATE
C10 H14 N5 O8 P
RQFCJASXJCIDSX-UUOKFMHZSA-N
SO4
Query on SO4

Download Ideal Coordinates CCD File 
E [auth A]
F [auth A]
H [auth B]
I [auth B]
K [auth C]
E [auth A],
F [auth A],
H [auth B],
I [auth B],
K [auth C],
L [auth C],
N [auth D],
O [auth D]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.00 Å
  • R-Value Free: 0.276 
  • R-Value Work: 0.228 
  • R-Value Observed: 0.228 
  • Space Group: P 32 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 110.56α = 90
b = 110.56β = 90
c = 209.75γ = 120
Software Package:
Software NamePurpose
CNSrefinement
MOSFLMdata reduction
ADDREFdata scaling
CNSphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2006-01-31
    Type: Initial release
  • Version 1.1: 2008-04-30
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance