8I4Q | pdb_00008i4q

Crystal structure of 6-phosphogluconate dehydrogenase from Corynebacterium glutamicum

PDB DOI: https://doi.org/10.2210/pdb8I4Q/pdb

Classification: OXIDOREDUCTASE
Organism(s): Corynebacterium glutamicum ATCC 13032
Expression System: Escherichia coli 'BL21-Gold(DE3)pLysS AG
Mutation(s): No

Deposited: 2023-01-20 Released: 2023-07-26
Deposition Author(s): Yu, H., Kim, K.-J.
Funding Organization(s): Not funded

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.90 Å
R-Value Free:
0.202 (Depositor), 0.210 (DCC)
R-Value Work:
0.164 (Depositor), 0.180 (DCC)
R-Value Observed:
0.166 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.1 of the entry. See complete history.

Literature

Crystal Structures of 6-Phosphogluconate Dehydrogenase from Corynebacterium glutamicum.

Yu, H., Hong, J., Seok, J., Seu, Y.B., Kim, I.K., Kim, K.J.

(2023) J Microbiol Biotechnol 33: 1-9

PubMed: 37417004 Search on PubMedSearch on PubMed Central
DOI: https://doi.org/10.4014/jmb.2305.05002
Primary Citation of Related Structures:
8I4N, 8I4Q

PubMed Abstract:
Corynebacterium glutamicum ( C. glutamicum ) has been considered a very important and meaningful industrial microorganism for the production of amino acids worldwide. To produce amino acids, cells require nicotinamide adenine dinucleotide phosphate (NADPH), which is a biological reducing agent. The pentose phosphate pathway (PPP) can supply NADPH in cells via the 6-phosphogluconate dehydrogenase (6PGD) enzyme, which is an oxidoreductase that converts 6-phosphogluconate (6PG) to ribulose 5-phosphate (Ru5P), to produce NADPH. In this study, we identified the crystal structure of 6PGD_apo and 6PGD_NADP from C. glutamicum ATCC 13032 ( Cg 6PGD) and reported our biological research based on this structure. We identified the substrate binding site and co-factor binding site of Cg 6PGD, which are crucial for understanding this enzyme. Based on the findings of our research, Cg 6PGD is expected to be used as a NADPH resource in the food industry and as a drug target in the pharmaceutical industry.

Organizational Affiliation

School of Life Sciences, BK21 FOUR KNU Creative BioResearch Group, Kyungpook National University, Daegu 41566, Republic of Korea.

Macromolecule Content

Total Structure Weight: 107.98 kDa
Atom Count: 8,011
Modelled Residue Count: 958
Deposited Residue Count: 984
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
6-phosphogluconate dehydrogenase, decarboxylating	A, B	492	Corynebacterium glutamicum ATCC 13032	Mutation(s): 0 Gene Names: Cgl1452 EC: 1.1.1.44
UniProt
Find proteins for Q8NQI2 (Corynebacterium glutamicum (strain ATCC 13032 / DSM 20300 / JCM 1318 / BCRC 11384 / CCUG 27702 / LMG 3730 / NBRC 12168 / NCIMB 10025 / NRRL B-2784 / 534)) Explore Q8NQI2 Go to UniProtKB: Q8NQI2
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q8NQI2
Sequence Annotations Expand
Reference Sequence LOADING

Small Molecules

Ligands 3 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 C [auth A] SDF format, chain I [auth B] MOL2 format, chain C [auth A] MOL2 format, chain I [auth B] mmCIF format, chain C [auth A] mmCIF format, chain I [auth B]	C [auth A], I [auth B]	NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE C₂₁ H₂₈ N₇ O₁₇ P₃ XJLXINKUBYWONI-NNYOXOHSSA-N		Interactions Focus chain C [auth A] Focus chain I [auth B] Interactions & Density Focus chain C [auth A] Focus chain I [auth B]
TRS Query on TRS 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 J [auth B] SDF format, chain K [auth B] MOL2 format, chain D [auth A] MOL2 format, chain E [auth A] MOL2 format, chain F [auth A] MOL2 format, chain J [auth B] MOL2 format, chain K [auth B] mmCIF format, chain D [auth A] mmCIF format, chain E [auth A] mmCIF format, chain F [auth A] mmCIF format, chain J [auth B] mmCIF format, chain K [auth B]	D [auth A], E [auth A], F [auth A], J [auth B], K [auth B]	2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL C₄ H₁₂ N O₃ LENZDBCJOHFCAS-UHFFFAOYSA-O		Interactions Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain J [auth B] Focus chain K [auth B] Interactions & Density Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain J [auth B] Focus chain K [auth B]
MG Query on MG Download Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain H [auth A] SDF format, chain L [auth B] SDF format, chain M [auth B] SDF format, chain N [auth B] SDF format, chain O [auth B] SDF format, chain P [auth B] MOL2 format, chain G [auth A] MOL2 format, chain H [auth A] MOL2 format, chain L [auth B] MOL2 format, chain M [auth B] MOL2 format, chain N [auth B] MOL2 format, chain O [auth B] MOL2 format, chain P [auth B] mmCIF format, chain G [auth A] mmCIF format, chain H [auth A] mmCIF format, chain L [auth B] mmCIF format, chain M [auth B] mmCIF format, chain N [auth B] mmCIF format, chain O [auth B] mmCIF format, chain P [auth B]	G [auth A] H [auth A] L [auth B] M [auth B] N [auth B] G [auth A], H [auth A], L [auth B], M [auth B], N [auth B], O [auth B], P [auth B]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain G [auth A] Focus chain H [auth A] Focus chain L [auth B] Focus chain M [auth B] Focus chain N [auth B] Focus chain O [auth B] Focus chain P [auth B] Interactions & Density Focus chain G [auth A] Focus chain H [auth A] Focus chain L [auth B] Focus chain M [auth B] Focus chain N [auth B] Focus chain O [auth B] Focus chain P [auth B]