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 Å
  • R-Value Free: 0.176 
  • R-Value Work: 0.148 

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:  

  • 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 reduct ...

    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

    Univ. Grenoble Alpes, IBS, F-38044 Grenoble, France.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Glyoxylate reductase
A, B
333Pyrococcus yayanosii (strain CH1 / JCM 16557)Mutation(s): 0 
Gene Names: gyaR
EC: 1.1.1.26
Find proteins for F8AEA4 (Pyrococcus yayanosii (strain CH1 / JCM 16557))
Go to UniProtKB:  F8AEA4
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MLI
Query on MLI

Download SDF File 
Download CCD File 
A, B
MALONATE ION
C3 H2 O4
OFOBLEOULBTSOW-UHFFFAOYSA-L
 Ligand Interaction
GOL
Query on GOL

Download SDF File 
Download CCD File 
A, B
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
NAP
Query on NAP

Download SDF File 
Download CCD File 
A, B
NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE
2'-MONOPHOSPHOADENOSINE 5'-DIPHOSPHORIBOSE
C21 H28 N7 O17 P3
XJLXINKUBYWONI-NNYOXOHSSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2 Å
  • R-Value Free: 0.176 
  • R-Value Work: 0.148 
  • Space Group: P 62 2 2
Unit Cell:
Length (Å)Angle (°)
a = 141.063α = 90.00
b = 141.063β = 90.00
c = 260.792γ = 120.00
Software Package:
Software NamePurpose
XDSdata reduction
SCALAdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
PHASERphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of HealthUnited States--

Revision History 

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