6BII image
Deposition Date 2017-11-02
Release Date 2018-01-17
Last Version Date 2023-10-04
Entry Detail
PDB ID:
6BII
Keywords:
Title:
Crystal Structure of Pyrococcus yayanosii Glyoxylate Hydroxypyruvate Reductase in complex with NADP and malonate (re-refinement of 5AOW)
Biological Source:
Host Organism:
Method Details:
Experimental Method:
Resolution:
2.00 Å
R-Value Free:
0.17
R-Value Work:
0.14
R-Value Observed:
0.14
Space Group:
P 62 2 2
Macromolecular Entities
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Glyoxylate reductase
Gene (Uniprot):gyaR
Chain IDs:A, B
Chain Length:333
Number of Molecules:2
Biological Source:Pyrococcus yayanosii (strain CH1 / JCM 16557)
Primary Citation
New insights into the mechanism of substrates trafficking in Glyoxylate/Hydroxypyruvate reductases.
Sci Rep 6 20629 20629 (2016)
PMID: 26865263 DOI: 10.1038/srep20629

Abstact

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.

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