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- PDB-9emm: Glucose-6-phosphate dehydrogenase (G6PDH) in complex with protein... -

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Basic information

Entry
Database: PDB / ID: 9emm
TitleGlucose-6-phosphate dehydrogenase (G6PDH) in complex with protein OpcA from Synechocystis sp. PCC 6803
Components
  • Glucose-6-phosphate 1-dehydrogenase
  • Putative OxPP cycle protein OpcA
KeywordsOXIDOREDUCTASE / Glucose-6-phosphate dehydrogenase / OpcA / pentose phosphate pathway / OPP shunt / cyanobacteria
Function / homology
Function and homology information


glucose-6-phosphate dehydrogenase (NADP+) / glucose-6-phosphate dehydrogenase activity / pentose-phosphate shunt, oxidative branch / glucose metabolic process / NADP binding / cytosol
Similarity search - Function
Glucose-6-phosphate dehydrogenase assembly protein OpcA / Glucose-6-phosphate dehydrogenase assembly protein OpcA, N-terminal domain / Glucose-6-phosphate dehydrogenase assembly protein OpcA, C-terminal domain / Glucose-6-phosphate dehydrogenase subunit N-terminal domain / Glucose-6-phosphate dehydrogenase subunit C-terminal domain / PGBD superfamily / Glucose-6-phosphate dehydrogenase, active site / Glucose-6-phosphate dehydrogenase active site. / Glucose-6-phosphate dehydrogenase / Glucose-6-phosphate dehydrogenase, NAD-binding ...Glucose-6-phosphate dehydrogenase assembly protein OpcA / Glucose-6-phosphate dehydrogenase assembly protein OpcA, N-terminal domain / Glucose-6-phosphate dehydrogenase assembly protein OpcA, C-terminal domain / Glucose-6-phosphate dehydrogenase subunit N-terminal domain / Glucose-6-phosphate dehydrogenase subunit C-terminal domain / PGBD superfamily / Glucose-6-phosphate dehydrogenase, active site / Glucose-6-phosphate dehydrogenase active site. / Glucose-6-phosphate dehydrogenase / Glucose-6-phosphate dehydrogenase, NAD-binding / Glucose-6-phosphate dehydrogenase, C-terminal / Glucose-6-phosphate dehydrogenase, NAD binding domain / Glucose-6-phosphate dehydrogenase, C-terminal domain / Peptidoglycan binding-like / Putative peptidoglycan binding domain / PGBD-like superfamily / NAD(P)-binding domain superfamily
Similarity search - Domain/homology
Glucose-6-phosphate 1-dehydrogenase / Putative OxPP cycle protein OpcA
Similarity search - Component
Biological speciesSynechocystis sp. (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.7 Å
AuthorsShvarev, D.
Funding support Germany, 3items
OrganizationGrant numberCountry
German Research Foundation (DFG)MO2752/3-6 Germany
German Research Foundation (DFG)SFB 1557 Germany
German Research Foundation (DFG)INST190/196-1 FUGG Germany
CitationJournal: Proc Natl Acad Sci U S A / Year: 2024
Title: Structural basis of the allosteric regulation of cyanobacterial glucose-6-phosphate dehydrogenase by the redox sensor OpcA.
Authors: Sofia Doello / Dmitry Shvarev / Marius Theune / Jakob Sauerwein / Alexander Klon / Erva Keskin / Marko Boehm / Kirstin Gutekunst / Karl Forchhammer /
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 ...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 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 .
History
DepositionMar 8, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 18, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Glucose-6-phosphate 1-dehydrogenase
E: Putative OxPP cycle protein OpcA
C: Glucose-6-phosphate 1-dehydrogenase
D: Glucose-6-phosphate 1-dehydrogenase
B: Glucose-6-phosphate 1-dehydrogenase


Theoretical massNumber of molelcules
Total (without water)296,6215
Polymers296,6215
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Protein
Glucose-6-phosphate 1-dehydrogenase / G6PD


Mass: 60499.789 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Synechocystis sp. (strain PCC 6803 / Kazusa) (bacteria)
Strain: PCC 6803 / Kazusa / Gene: zwf, slr1843 / Production host: Escherichia coli (E. coli)
References: UniProt: P73411, glucose-6-phosphate dehydrogenase (NADP+)
#2: Protein Putative OxPP cycle protein OpcA


Mass: 54621.602 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Synechocystis sp. (strain PCC 6803 / Kazusa) (bacteria)
Strain: PCC 6803 / Kazusa / Gene: opcA, slr1734 / Production host: Escherichia coli (E. coli) / References: UniProt: P73720
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: glucose-6-phosphate dehydrogenase in complex with OpcA
Type: COMPLEX / Entity ID: all / Source: RECOMBINANT
Source (natural)Organism: Synechocystis sp. PCC 6803 (bacteria)
Source (recombinant)Organism: Escherichia coli (E. coli)
Buffer solutionpH: 7.5
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE

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Electron microscopy imaging

MicroscopyModel: TFS GLACIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 1800 nm / Nominal defocus min: 800 nm
Specimen holderCryogen: NITROGEN
Image recordingElectron dose: 50 e/Å2 / Film or detector model: FEI FALCON IV (4k x 4k)

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Processing

EM softwareName: PHENIX / Version: 1.20_4459: / Category: model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.7 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 128652 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00518835
ELECTRON MICROSCOPYf_angle_d0.63225541
ELECTRON MICROSCOPYf_dihedral_angle_d4.4232543
ELECTRON MICROSCOPYf_chiral_restr0.0442735
ELECTRON MICROSCOPYf_plane_restr0.0053365

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