8I4N

Crystal strcuture of 6-phosphogluconate dehydrogenase from Corynebacterium glutamicum


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.41 Å
  • R-Value Free: 0.267 
  • R-Value Work: 0.200 
  • R-Value Observed: 0.203 

wwPDB Validation   3D Report Full Report


This is version 1.0 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

  • 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.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
6-phosphogluconate dehydrogenase, decarboxylating
A, B
492Corynebacterium glutamicum ATCC 13032Mutation(s): 0 
Gene Names: Cgl1452
UniProt
Find proteins for Q8NQI2 (Corynebacterium glutamicum (strain ATCC 13032 / DSM 20300 / BCRC 11384 / JCM 1318 / LMG 3730 / NCIMB 10025))
Explore Q8NQI2 
Go to UniProtKB:  Q8NQI2
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ8NQI2
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.41 Å
  • R-Value Free: 0.267 
  • R-Value Work: 0.200 
  • R-Value Observed: 0.203 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 63.897α = 90
b = 120.297β = 90
c = 152.6γ = 90
Software Package:
Software NamePurpose
HKL-2000data scaling
MOLREPphasing
REFMACrefinement
HKL-2000data reduction

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Not funded--

Revision History  (Full details and data files)

  • Version 1.0: 2023-07-26
    Type: Initial release