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- EMDB-19820: Glucose-6-phosphate dehydrogenase (G6PDH) in complex with protein... -

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Basic information

Entry
Database: EMDB / ID: EMD-19820
TitleGlucose-6-phosphate dehydrogenase (G6PDH) in complex with protein OpcA from Synechocystis sp. PCC 6803
Map dataOpcA-G6PDH complex, local refinement map
Sample
  • Complex: glucose-6-phosphate dehydrogenase in complex with OpcA
    • Protein or peptide: Glucose-6-phosphate 1-dehydrogenase
    • Protein or peptide: Putative OxPP cycle protein OpcA
KeywordsGlucose-6-phosphate dehydrogenase / OpcA / pentose phosphate pathway / OPP shunt / cyanobacteria / OXIDOREDUCTASE
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. PCC 6803 (bacteria) / Synechocystis sp. (strain PCC 6803 / Kazusa) (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.7 Å
AuthorsShvarev D
Funding support Germany, 3 items
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, 2024-
Header (metadata) releaseDec 18, 2024-
Map releaseDec 18, 2024-
UpdateDec 18, 2024-
Current statusDec 18, 2024Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_19820.png

Downloads & links

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Map

FileDownload / File: emd_19820.map.gz / Format: CCP4 / Size: 144.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationOpcA-G6PDH complex, local refinement map
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.92 Å/pix.
x 336 pix.
= 310.464 Å		0.92 Å/pix.
x 336 pix.
= 310.464 Å		0.92 Å/pix.
x 336 pix.
= 310.464 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.924 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.11
Minimum - Maximum-0.5960368 - 0.9343779
Average (Standard dev.)0.00006115799 (±0.021408482)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions336336336
Spacing336336336
CellA=B=C: 310.46402 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: OpcA-G6PDH complex, local refinement, half map A

Fileemd_19820_half_map_1.map
AnnotationOpcA-G6PDH complex, local refinement, half map A
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: OpcA-G6PDH complex, local refinement, half map B

Fileemd_19820_half_map_2.map
AnnotationOpcA-G6PDH complex, local refinement, half map B
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : glucose-6-phosphate dehydrogenase in complex with OpcA

EntireName: glucose-6-phosphate dehydrogenase in complex with OpcA
Components
  • Complex: glucose-6-phosphate dehydrogenase in complex with OpcA
    • Protein or peptide: Glucose-6-phosphate 1-dehydrogenase
    • Protein or peptide: Putative OxPP cycle protein OpcA

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Supramolecule #1: glucose-6-phosphate dehydrogenase in complex with OpcA

SupramoleculeName: glucose-6-phosphate dehydrogenase in complex with OpcA
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Synechocystis sp. PCC 6803 (bacteria)

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Macromolecule #1: Glucose-6-phosphate 1-dehydrogenase

MacromoleculeName: Glucose-6-phosphate 1-dehydrogenase / type: protein_or_peptide / ID: 1 / Number of copies: 4 / Enantiomer: LEVO / EC number: glucose-6-phosphate dehydrogenase (NADP+)
Source (natural)Organism: Synechocystis sp. (strain PCC 6803 / Kazusa) (bacteria)
Strain: PCC 6803 / Kazusa
Molecular weightTheoretical: 60.499789 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MGSSHHHHHH SSGLVPRGSH MLEMVTLLEN PFRTGLRQER TPEPLILTIF GASGDLTQRK LVPAIYQMKR ERRLPPELTV VGFARRDWS HDHFREQMRK GIEEFSTGIG SEDLWNEFAQ GLFYCSGNMD DPESYLKLKN FLGELDEKRN TRGNRVFYLA V SPNFFPPG ...String:
MGSSHHHHHH SSGLVPRGSH MLEMVTLLEN PFRTGLRQER TPEPLILTIF GASGDLTQRK LVPAIYQMKR ERRLPPELTV VGFARRDWS HDHFREQMRK GIEEFSTGIG SEDLWNEFAQ GLFYCSGNMD DPESYLKLKN FLGELDEKRN TRGNRVFYLA V SPNFFPPG IKQLGAAGML SDPVKSRIVI EKPFGRDLSS AQSLNRVVQS VCKENQVYRI DHYLGKETVQ NLMVFRFANA IF EPLWNRQ FVDHVQITVA ETVGVEERAG YYESAGALRD MVQNHLMQLF CLTAMDPPNA IDADSIRNEK VKVLQATRLA DIN NLENAG IRGQYKAGWM GGKPVPGYRE EPGVDPSSTT PTFAALKLMV DNWRWQGVPF YLRTGKRMPK KVSEIAIQFR QVPL LIFQS VAHQANPNVL SLRIQPNEGI SLRFEAKMPG SELRTRTVDM DFSYGSSFGV AAADAYHRLL LDCMLGDQTL FTRAD EVEE AWRVVTPVLS AWDAPSDPLS MPLYEAGTWE PAEAEWLINK DGRRWRRL

UniProtKB: Glucose-6-phosphate 1-dehydrogenase

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Macromolecule #2: Putative OxPP cycle protein OpcA

MacromoleculeName: Putative OxPP cycle protein OpcA / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Synechocystis sp. (strain PCC 6803 / Kazusa) (bacteria)
Strain: PCC 6803 / Kazusa
Molecular weightTheoretical: 54.621602 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MGSSHHHHHH SSGLVPRGSH MLEMGGKYQR HCPVRFHWSH CMSTTQAPPL VSLQAPKDVS LEAIESELAQ IWQTSAQKEE GLIATRATT FSFLVYEPDR VQSLLAALGY YTGPIDGITG PRMTAAIKSA QKALGVTATG LSSPEFKQAL QTAFETAHRE G NLLSTAER ...String:
MGSSHHHHHH SSGLVPRGSH MLEMGGKYQR HCPVRFHWSH CMSTTQAPPL VSLQAPKDVS LEAIESELAQ IWQTSAQKEE GLIATRATT FSFLVYEPDR VQSLLAALGY YTGPIDGITG PRMTAAIKSA QKALGVTATG LSSPEFKQAL QTAFETAHRE G NLLSTAER ITKPYSPDLE GSGIADTIAA SNPCRIITLC PTAEDDQGVQ AQLSAYCPIQ KTHQNTLICC EYITLRGTSD AL ERIGGVI TELMLPTLPK YVWWKASPEA EYGLFQRLLS HADMIIVDSS IFNNPEQDLL QLAQLVNKPE AIADLNWSRL APW QELTAE AFDPPERRSA VGEIDQISID YEKGNHAQAL MYLGWVASRL QWTPVSYSYQ PGVYEIHKIQ FCAPNQRPIE AELA GLPLA DTGQVLGDLI SLKLGSTNTQ AQCGTVLCSG TVGCMRMEAG GGAQNYRVQQ VTALDDQNTE QLLGRQLQRW GRDAL YDES MAIVLAILQL SQAG

UniProtKB: Putative OxPP cycle protein OpcA

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 7.5
VitrificationCryogen name: ETHANE / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeTFS GLACIOS
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 1.8 µm / Nominal defocus min: 0.8 µm
Sample stageCooling holder cryogen: NITROGEN

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Image processing

Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.7 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 128652
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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