8HRQ

Crystal structure of glyceraldehyde-3-phosphate dehydrogenase from Corynebacterium glutamicum ATCC13032 (L36S/T37K) in complex with NAD

PDB DOI: https://doi.org/10.2210/pdb8HRQ/pdb

Classification: STRUCTURAL PROTEIN
Organism(s): Corynebacterium glutamicum ATCC 13032
Expression System: Escherichia coli
Mutation(s): Yes

Deposited: 2022-12-15 Released: 2023-12-06
Deposition Author(s): Son, H.F., Kim, K.J.
Funding Organization(s): National Research Foundation (NRF, Korea)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.09 Å
R-Value Free: 0.245
R-Value Work: 0.177
R-Value Observed: 0.180

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

Structure-Guided Protein Engineering of Glyceraldehyde-3-phosphate Dehydrogenase from Corynebacterium glutamicum for Dual NAD/NADP Cofactor Specificity.

Son, H.F., Yu, H., Hong, J., Lee, D., Kim, I.K., Kim, K.J.

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

PubMed: 37935620 Search on PubMed
DOI: https://doi.org/10.1021/acs.jafc.3c06176
Primary Citation of Related Structures:
8HRO, 8HRP, 8HRQ, 8HRR, 8HRS, 8HRT

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

Total Structure Weight: 76.41 kDa
Atom Count: 5,454
Modelled Residue Count: 670
Deposited Residue Count: 684
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Glyceraldehyde-3-phosphate dehydrogenase	A, B	342	Corynebacterium glutamicum ATCC 13032	Mutation(s): 2 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 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NAD (Subject of Investigation/LOI) Query on NAD Download Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain J [auth B] MOL2 format, chain D [auth A] MOL2 format, chain J [auth B]	D [auth A], J [auth B]	NICOTINAMIDE-ADENINE-DINUCLEOTIDE C₂₁ H₂₇ N₇ O₁₄ P₂ BAWFJGJZGIEFAR-NNYOXOHSSA-N		Interactions Focus chain D [auth A] Focus chain J [auth B] Interactions & Density Focus chain D [auth A] Focus chain J [auth B]
CS Query on CS Download Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain I [auth B] MOL2 format, chain C [auth A] MOL2 format, chain I [auth B]	C [auth A], I [auth B]	CESIUM ION Cs NCMHKCKGHRPLCM-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain I [auth B] Interactions & Density Focus chain C [auth A] Focus chain I [auth B]
PO4 Query on PO4 Download Ideal Coordinates CCD File SDF format, chain H [auth A] SDF format, chain L [auth B] MOL2 format, chain H [auth A] MOL2 format, chain L [auth B]	H [auth A], L [auth B]	PHOSPHATE ION O₄ P NBIIXXVUZAFLBC-UHFFFAOYSA-K		Interactions Focus chain H [auth A] Focus chain L [auth B] Interactions & Density Focus chain H [auth A] Focus chain L [auth B]
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain K [auth B] MOL2 format, chain G [auth A] MOL2 format, chain K [auth B]	G [auth A], K [auth B]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain G [auth A] Focus chain K [auth B] Interactions & Density Focus chain G [auth A] Focus chain K [auth B]
EDO Query on EDO Download Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain F [auth A] MOL2 format, chain E [auth A] MOL2 format, chain F [auth A]	E [auth A], F [auth A]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain F [auth A] Interactions & Density Focus chain E [auth A] Focus chain F [auth A]