6VPB

A novel membrane-bound 6-phosphogluconate dehydrogenase from the acetic acid bacteria Gluconacetobacter diazotrophicus (Gd6PGD)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.87 Å
  • R-Value Free: 0.222 
  • R-Value Work: 0.183 
  • R-Value Observed: 0.184 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

The structure of a novel membrane-associated 6-phosphogluconate dehydrogenase from Gluconacetobacter diazotrophicus (Gd6PGD) reveals a subfamily of short-chain 6PGDs.

Sarmiento-Pavia, P.D.Rodriguez-Hernandez, A.Rodriguez-Romero, A.Sosa-Torres, M.E.

(2021) FEBS J 288: 1286-1304

  • DOI: https://doi.org/10.1111/febs.15472
  • Primary Citation of Related Structures:  
    6VPB

  • PubMed Abstract: 

    The enzyme 6-phosphogluconate dehydrogenase catalyzes the conversion of 6-phosphogluconate to ribulose-5-phosphate. It represents an important reaction in the oxidative pentose phosphate pathway, producing a ribose precursor essential for nucleotide and nucleic acid synthesis. We succeeded, for the first time, to determine the three-dimensional structure of this enzyme from an acetic acid bacterium, Gluconacetobacter diazotrophicus (Gd6PGD). Active Gd6PGD, a homodimer (70 kDa), was present in both the soluble and the membrane fractions of the nitrogen-fixing microorganism. The Gd6PGD belongs to the newly described subfamily of short-chain (333 AA) 6PGDs, compared to the long-chain subfamily (480 AA; e.g., Ovis aries, Homo sapiens). The shorter amino acid sequence in Gd6PGD induces the exposition of hydrophobic residues in the C-terminal domain. This distinct structural feature is key for the protein to associate with the membrane. Furthermore, in terms of function, the short-chain 6PGD seems to prefer NAD + over NADP + , delivering NADH to the membrane-bound NADH dehydrogenase of the microorganisms required by the terminal oxidases to reduce dioxygen to water for energy conservation. ENZYME: ECnonbreakingspace1.1.1.343. DATABASE: Structural data are available in PDB database under the accession number 6VPB.


  • Organizational Affiliation

    Facultad de Química, Universidad Nacional Autónoma de México, Coyoacán, Mexico.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
6-phosphogluconate dehydrogenase
A, B
332Gluconacetobacter diazotrophicus PA1 5Mutation(s): 0 
UniProt
Find proteins for A9H324 (Gluconacetobacter diazotrophicus (strain ATCC 49037 / DSM 5601 / CCUG 37298 / CIP 103539 / LMG 7603 / PAl5))
Explore A9H324 
Go to UniProtKB:  A9H324
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA9H324
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.87 Å
  • R-Value Free: 0.222 
  • R-Value Work: 0.183 
  • R-Value Observed: 0.184 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 91.76α = 90
b = 82.097β = 103.407
c = 81.831γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
PHENIXrefinement
HKL-3000data reduction
HKL-3000data scaling
AutoSolphasing

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Consejo Nacional de Ciencia y Tecnologia (CONACYT)Mexico299048

Revision History  (Full details and data files)

  • Version 1.0: 2020-07-22
    Type: Initial release
  • Version 1.1: 2021-03-10
    Changes: Database references
  • Version 1.2: 2024-03-06
    Changes: Data collection, Database references, Refinement description