6BII

Crystal Structure of Pyrococcus yayanosii Glyoxylate Hydroxypyruvate Reductase in complex with NADP and malonate (re-refinement of 5AOW)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.176 
  • R-Value Work: 0.148 
  • R-Value Observed: 0.150 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

New insights into the mechanism of substrates trafficking in Glyoxylate/Hydroxypyruvate reductases.

Lassalle, L.Engilberge, S.Madern, D.Vauclare, P.Franzetti, B.Girard, E.

(2016) Sci Rep 6: 20629-20629

  • DOI: 10.1038/srep20629
  • Primary Citation of Related Structures:  
    6BII, 5AOV

  • PubMed Abstract: 
  • Glyoxylate accumulation within cells is highly toxic. In humans, it is associated with hyperoxaluria type 2 (PH2) leading to renal failure. The glyoxylate content within cells is regulated by the NADPH/NADH dependent glyoxylate/hydroxypyruvate reductases (GRHPR) ...

    Glyoxylate accumulation within cells is highly toxic. In humans, it is associated with hyperoxaluria type 2 (PH2) leading to renal failure. The glyoxylate content within cells is regulated by the NADPH/NADH dependent glyoxylate/hydroxypyruvate reductases (GRHPR). These are highly conserved enzymes with a dual activity as they are able to reduce glyoxylate to glycolate and to convert hydroxypyruvate into D-glycerate. Despite the determination of high-resolution X-ray structures, the substrate recognition mode of this class of enzymes remains unclear. We determined the structure at 2.0 Å resolution of a thermostable GRHPR from Archaea as a ternary complex in the presence of D-glycerate and NADPH. This shows a binding mode conserved between human and archeal enzymes. We also determined the first structure of GRHPR in presence of glyoxylate at 1.40 Å resolution. This revealed the pivotal role of Leu53 and Trp138 in substrate trafficking. These residues act as gatekeepers at the entrance of a tunnel connecting the active site to protein surface. Taken together, these results allowed us to propose a general model for GRHPR mode of action.


    Related Citations: 
    • Structural, Biochemical, and Evolutionary Characterizations of Glyoxylate/Hydroxypyruvate Reductases Show Their Division into Two Distinct Subfamilies.
      Kutner, J., Shabalin, I.G., Matelska, D., Handing, K.B., Gasiorowska, O., Sroka, P., Gorna, M.W., Ginalski, K., Wozniak, K., Minor, W.
      (2018) Biochemistry 57: 963

    Organizational Affiliation

    CEA, IBS, F-38044 Grenoble, France.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Glyoxylate reductaseA, B333Pyrococcus yayanosii CH1Mutation(s): 0 
Gene Names: gyaRPYCH_09300
EC: 1.1.1.26
Find proteins for F8AEA4 (Pyrococcus yayanosii (strain CH1 / JCM 16557))
Explore F8AEA4 
Go to UniProtKB:  F8AEA4
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
NAPKi:  2000000   nM  Binding MOAD
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.176 
  • R-Value Work: 0.148 
  • R-Value Observed: 0.150 
  • Space Group: P 62 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 141.063α = 90
b = 141.063β = 90
c = 260.792γ = 120
Software Package:
Software NamePurpose
REFMACrefinement
PDB_EXTRACTdata extraction
XDSdata reduction
SCALAdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of HealthUnited States--

Revision History  (Full details and data files)

  • Version 1.0: 2018-01-17
    Type: Initial release
  • Version 1.1: 2018-01-31
    Changes: Database references
  • Version 1.2: 2018-02-28
    Changes: Database references
  • Version 1.3: 2018-05-16
    Changes: Data collection, Database references