8HRS

Experimental Data Snapshot

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.0 of the entry. See complete history.

Literature

(2023) J Agric Food Chem 71: 17852-17859

PubMed Abstract:
Since the discovery of l-glutamate-producing Corynebacterium glutamicum , it has evolved to be an industrial workhorse. For biobased chemical production, suppling sufficient amounts of the NADPH cofactor is crucial. Glyceraldehyde-3-phosphate dehydrogenase (GAPDH), a glycolytic enzyme that converts glyceraldehyde-3-phosphate (G3P) to 1,3-bisphosphoglycerate and produces NADH, is a major prospective solution for the cofactor imbalance issue. In this study, we determined the crystal structure of GAPDH from C. glutamicum ATCC13032 ( Cg GAPDH). Based on the structural information, we generated six Cg GAPDH variants, Cg GAPDH ^L36S, Cg GAPDH ^L36S/T37K, Cg GAPDH ^{L36S/T37K/P192S}, Cg GAPDH ^{L36S/T37K/F100V/P192S}, Cg GAPDH ^{L36S/T37K/F100L/P192S}, and Cg GAPDH ^{L36S/T37K/F100I/P192S}, that can produce both NADH and NAPDH. The final Cg GAPDH ^{L36S/T37K/F100V/P192S} variant showed a 212-fold increase in enzyme activity for NADP as well as 200% and 30% increased activity for the G3P substrate under NAD and NADP cofactor conditions, respectively. In addition, crystal structures of Cg GAPDH variants in complex with NAD(P) permit the elucidation of differences between wild-type Cg GAPDH and variants in relation to cofactor stabilization.

Organizational Affiliation

Clean Energy Research Center, Korea Institute of Science and Technology, Seoul 02792, Republic of Korea.

Macromolecule Content

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Glyceraldehyde-3-phosphate dehydrogenase	A, B, C, D	342	Corynebacterium glutamicum ATCC 13032	Mutation(s): 3 Gene Names: gap, Cgl1588, cg1791 EC: 1.2.1.12
UniProt
Find proteins for Q01651 (Corynebacterium glutamicum (strain ATCC 13032 / DSM 20300 / BCRC 11384 / JCM 1318 / LMG 3730 / NCIMB 10025)) Explore Q01651 Go to UniProtKB: Q01651
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q01651
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NAP (Subject of Investigation/LOI) Query on NAP Download Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain G [auth B] SDF format, chain I [auth C] SDF format, chain K [auth D] MOL2 format, chain E [auth A] MOL2 format, chain G [auth B] MOL2 format, chain I [auth C] MOL2 format, chain K [auth D]	E [auth A], G [auth B], I [auth C], K [auth D]	NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE C₂₁ H₂₈ N₇ O₁₇ P₃ XJLXINKUBYWONI-NNYOXOHSSA-N		Interactions Focus chain E [auth A] Focus chain G [auth B] Focus chain I [auth C] Focus chain K [auth D] Interactions & Density Focus chain E [auth A] Focus chain G [auth B] Focus chain I [auth C] Focus chain K [auth D]
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain F [auth B] SDF format, chain H [auth B] SDF format, chain J [auth C] MOL2 format, chain F [auth B] MOL2 format, chain H [auth B] MOL2 format, chain J [auth C]	F [auth B], H [auth B], J [auth C]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain F [auth B] Focus chain H [auth B] Focus chain J [auth C] Interactions & Density Focus chain F [auth B] Focus chain H [auth B] Focus chain J [auth C]