9EMN | pdb_00009emn

Glucose-6-phosphate dehydrogenase (G6PDH) from Synechocystis sp. PCC 6803


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.30 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.0 of the entry. See complete history


Literature

Structural basis of the allosteric regulation of cyanobacterial glucose-6-phosphate dehydrogenase by the redox sensor OpcA.

Doello, S.Shvarev, D.Theune, M.Sauerwein, J.Klon, A.Keskin, E.Boehm, M.Gutekunst, K.Forchhammer, K.

(2024) Proc Natl Acad Sci U S A 121: e2411604121-e2411604121

  • DOI: https://doi.org/10.1073/pnas.2411604121
  • Primary Citation of Related Structures:  
    9EMM, 9EMN

  • PubMed Abstract: 

    The oxidative pentose phosphate (OPP) pathway is a fundamental carbon catabolic route for generating reducing power and metabolic intermediates for biosynthetic processes. In addition, its first two reactions form the OPP shunt, which replenishes the Calvin-Benson cycle under certain conditions. Glucose-6-phosphate dehydrogenase (G6PDH) catalyzes the first and rate-limiting reaction of this metabolic route. In photosynthetic organisms, G6PDH is redox-regulated to allow fine-tuning and to prevent futile cycles while carbon is being fixed. In cyanobacteria, regulation of G6PDH requires the redox protein OpcA, but the underlying molecular mechanisms behind this allosteric activation remain elusive. Here, we used enzymatic assays and in vivo interaction analyses to show that OpcA binds G6PDH under different environmental conditions. However, complex formation enhances G6PDH activity when OpcA is oxidized and inhibits it when OpcA is reduced. To understand the molecular basis of this regulation, we used cryogenic electron microscopy to determine the structure of Synechocystis G6PDH and the G6PDH-OpcA complex. OpcA binds the G6PDH tetramer and induces conformational changes in the active site of G6PDH. The redox sensitivity of OpcA is achieved by intramolecular disulfide bridge formation, which influences the allosteric regulation of G6PDH. In vitro assays reveal that the level of G6PDH activation depends on the number of bound OpcA molecules, which implies that this mechanism allows delicate fine-tuning. Our findings unveil a unique molecular mechanism governing the regulation of the OPP in Synechocystis .


  • Organizational Affiliation
    • Interfaculty Institute for Microbiology and Infection Medicine, Microbiology and Organismic Interactions, University of Tübingen, Tübingen 72076, Germany.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Glucose-6-phosphate 1-dehydrogenase
A, B, C, D
532Synechocystis sp. PCC 6803 substr. KazusaMutation(s): 0 
Gene Names: zwfslr1843
EC: 1.1.1.49
UniProt
Find proteins for P73411 (Synechocystis sp. (strain ATCC 27184 / PCC 6803 / Kazusa))
Explore P73411 
Go to UniProtKB:  P73411
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP73411
Sequence Annotations
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.30 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX1.20_4459:

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data

  • Released Date: 2024-12-18 
  • Deposition Author(s): Shvarev, D.

Funding OrganizationLocationGrant Number
German Research Foundation (DFG)GermanyMO2752/3-6
German Research Foundation (DFG)GermanySFB 1557
German Research Foundation (DFG)GermanyINST190/196-1 FUGG

Revision History  (Full details and data files)

  • Version 1.0: 2024-12-18
    Type: Initial release