2C6Q

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.70 Å
  • R-Value Free: 0.206 
  • R-Value Work: 0.163 
  • R-Value Observed: 0.165 

wwPDB Validation   3D Report Full Report


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: 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 ...

    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
MoleculeChainsSequence LengthOrganismDetailsImage
GMP REDUCTASE 2
A, B, C, D, E, F, G, H
A, B, C, D, E, F, G, H
351Homo sapiensMutation(s): 0 
Gene Names: GMPR2
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
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NDP
Query on NDP

Download Ideal Coordinates CCD File 
J [auth A],
L [auth B],
N [auth C],
P [auth D],
R [auth E],
J [auth A],
L [auth B],
N [auth C],
P [auth D],
R [auth E],
T [auth F],
W [auth H]
NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE
C21 H30 N7 O17 P3
ACFIXJIJDZMPPO-NNYOXOHSSA-N
 Ligand Interaction
IMP
Query on IMP

Download Ideal Coordinates CCD File 
I [auth A],
K [auth B],
M [auth C],
O [auth D],
Q [auth E],
I [auth A],
K [auth B],
M [auth C],
O [auth D],
Q [auth E],
S [auth F],
U [auth G],
V [auth H]
INOSINIC ACID
C10 H13 N4 O8 P
GRSZFWQUAKGDAV-KQYNXXCUSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.70 Å
  • R-Value Free: 0.206 
  • R-Value Work: 0.163 
  • R-Value Observed: 0.165 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 131.676α = 90
b = 141.366β = 90
c = 164.318γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
XSCALEdata scaling

Structure Validation

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Ligand Structure Quality Assessment 



Entry History 

Revision History  (Full details and data files)

  • Version 1.0: 2005-11-30
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Advisory, Refinement description, Version format compliance
  • Version 1.2: 2011-11-30
    Changes: Database references, Derived calculations, Non-polymer description, Other