2BZN

Crystal structure of human guanosine monophosphate reductase 2 GMPR2 in complex with IMP


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.15 Å
  • R-Value Free: 0.210 
  • R-Value Work: 0.158 
  • R-Value Observed: 0.161 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


Literature

Cofactor Mobility Determines Reaction Outcome in the Impdh and Gmpr (Beta-Alpha)(8) Barrel Enzymes.

Patton, G.C.Stenmark, P.Gollapalli, D.R.Sevastik, R.Kursula, P.Flodin, S.Schuler, H.Swales, C.T.Eklund, H.Himo, F.Nordlund, P.Hedstrom, L.

(2011) Nat Chem Biol 7: 950

  • DOI: https://doi.org/10.1038/nchembio.693
  • Primary Citation of Related Structures:  
    2BZN, 2C6Q

  • PubMed Abstract: 

    Inosine monophosphate dehydrogenase (IMPDH) and guanosine monophosphate reductase (GMPR) belong to the same structural family, share a common set of catalytic residues and bind the same ligands. The structural and mechanistic features that determine reaction outcome in the IMPDH and GMPR family have not been identified. Here we show that the GMPR reaction uses the same intermediate E-XMP* as IMPDH, but in this reaction the intermediate reacts with ammonia instead of water. A single crystal structure of human GMPR type 2 with IMP and NADPH fortuitously captures three different states, each of which mimics a distinct step in the catalytic cycle of GMPR. The cofactor is found in two conformations: an 'in' conformation poised for hydride transfer and an 'out' conformation in which the cofactor is 6 Å from IMP. Mutagenesis along with substrate and cofactor analog experiments demonstrate that the out conformation is required for the deamination of GMP. Remarkably, the cofactor is part of the catalytic machinery that activates ammonia.


  • Organizational Affiliation

    Department of Biology, Brandeis University, Waltham, Massachusetts, USA.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
GMP REDUCTASE 2
A, B, C, D, E
A, B, C, D, E, F, G, H
351Homo 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
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.15 Å
  • R-Value Free: 0.210 
  • R-Value Work: 0.158 
  • R-Value Observed: 0.161 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 131.291α = 90
b = 141.35β = 90
c = 164.895γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling
MOLREPphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Revision History  (Full details and data files)

  • Version 1.0: 2005-09-02
    Type: Initial release
  • Version 1.1: 2011-11-30
    Changes: Database references, Derived calculations, Non-polymer description, Other, Version format compliance
  • Version 1.2: 2023-12-13
    Changes: Data collection, Database references, Derived calculations, Other, Refinement description