5AOV

Ternary Crystal Structure of Pyrococcus furiosus Glyoxylate Hydroxypyruvate Reductase in presence of glyoxylate

PDB DOI: https://doi.org/10.2210/pdb5AOV/pdb

Classification: OXIDOREDUCTASE
Organism(s): Pyrococcus furiosus
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2015-09-12 Released: 2016-03-02
Deposition Author(s): Lassalle, L., Girard, E.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.40 Å
R-Value Free: 0.143
R-Value Work: 0.131
R-Value Observed: 0.132

wwPDB Validation 3D Report Full Report

This is version 2.0 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

PubMed: 26865263 Search on PubMedSearch on PubMed Central
DOI: https://doi.org/10.1038/srep20629
Primary Citation of Related Structures:
5AOV, 6BII

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). 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.

Organizational Affiliation

CNRS, IBS, F-38044 Grenoble, France.

Macromolecule Content

Total Structure Weight: 43.29 kDa
Atom Count: 3,521
Modelled Residue Count: 334
Deposited Residue Count: 336
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
GLYOXYLATE REDUCTASE	A	336	Pyrococcus furiosus	Mutation(s): 0 EC: 1.1.1.26 (PDB Primary Data), 1.1.1.81 (PDB Primary Data), 1.1.1.79 (PDB Primary Data)
UniProt
Find proteins for Q8U3Y2 (Pyrococcus furiosus (strain ATCC 43587 / DSM 3638 / JCM 8422 / Vc1)) Explore Q8U3Y2 Go to UniProtKB: Q8U3Y2
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q8U3Y2
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NAP Query on NAP Download Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A]	B [auth A]	NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE C₂₁ H₂₈ N₇ O₁₇ P₃ XJLXINKUBYWONI-NNYOXOHSSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]
1PE Query on 1PE Download Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain E [auth A] SDF format, chain F [auth A] SDF format, chain G [auth A] SDF format, chain H [auth A] SDF format, chain I [auth A] SDF format, chain J [auth A] SDF format, chain K [auth A] SDF format, chain L [auth A] SDF format, chain M [auth A] SDF format, chain N [auth A] SDF format, chain O [auth A] SDF format, chain P [auth A] SDF format, chain V [auth A] SDF format, chain Z [auth A] MOL2 format, chain D [auth A] MOL2 format, chain E [auth A] MOL2 format, chain F [auth A] MOL2 format, chain G [auth A] MOL2 format, chain H [auth A] MOL2 format, chain I [auth A] MOL2 format, chain J [auth A] MOL2 format, chain K [auth A] MOL2 format, chain L [auth A] MOL2 format, chain M [auth A] MOL2 format, chain N [auth A] MOL2 format, chain O [auth A] MOL2 format, chain P [auth A] MOL2 format, chain V [auth A] MOL2 format, chain Z [auth A]	D [auth A] E [auth A] F [auth A] G [auth A] H [auth A] D [auth A], E [auth A], F [auth A], G [auth A], H [auth A], I [auth A], J [auth A], K [auth A], L [auth A], M [auth A], N [auth A], O [auth A], P [auth A], V [auth A], Z [auth A]	PENTAETHYLENE GLYCOL C₁₀ H₂₂ O₆ JLFNLZLINWHATN-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A] Focus chain L [auth A] Focus chain M [auth A] Focus chain N [auth A] Focus chain O [auth A] Focus chain P [auth A] Focus chain V [auth A] Focus chain Z [auth A] Interactions & Density Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A] Focus chain L [auth A] Focus chain M [auth A] Focus chain N [auth A] Focus chain O [auth A] Focus chain P [auth A] Focus chain V [auth A] Focus chain Z [auth A]
GLV Query on GLV Download Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain W [auth A] MOL2 format, chain C [auth A] MOL2 format, chain W [auth A]	C [auth A], W [auth A]	GLYOXYLIC ACID C₂ H₂ O₃ HHLFWLYXYJOTON-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain W [auth A] Interactions & Density Focus chain C [auth A] Focus chain W [auth A]
EDO Query on EDO Download Ideal Coordinates CCD File SDF format, chain Q [auth A] SDF format, chain R [auth A] SDF format, chain S [auth A] SDF format, chain T [auth A] SDF format, chain U [auth A] MOL2 format, chain Q [auth A] MOL2 format, chain R [auth A] MOL2 format, chain S [auth A] MOL2 format, chain T [auth A] MOL2 format, chain U [auth A]	Q [auth A], R [auth A], S [auth A], T [auth A], U [auth A]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain Q [auth A] Focus chain R [auth A] Focus chain S [auth A] Focus chain T [auth A] Focus chain U [auth A] Interactions & Density Focus chain Q [auth A] Focus chain R [auth A] Focus chain S [auth A] Focus chain T [auth A] Focus chain U [auth A]
ACY Query on ACY Download Ideal Coordinates CCD File SDF format, chain X [auth A] SDF format, chain Y [auth A] MOL2 format, chain X [auth A] MOL2 format, chain Y [auth A]	X [auth A], Y [auth A]	ACETIC ACID C₂ H₄ O₂ QTBSBXVTEAMEQO-UHFFFAOYSA-N		Interactions Focus chain X [auth A] Focus chain Y [auth A] Interactions & Density Focus chain X [auth A] Focus chain Y [auth A]