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- EMDB-25226: Structure of G6PD-D200N tetramer bound to NADP+ -

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Basic information

Entry
Database: EMDB / ID: EMD-25226
TitleStructure of G6PD-D200N tetramer bound to NADP+
Map data
Sample
  • Organelle or cellular component: G6PD protein
    • Protein or peptide: Glucose-6-phosphate 1-dehydrogenase
  • Ligand: NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE
Keywordsapo protein / OXIDOREDUCTASE
Function / homology
Function and homology information


negative regulation of protein glutathionylation / pentose biosynthetic process / ribose phosphate biosynthetic process / positive regulation of calcium ion transmembrane transport via high voltage-gated calcium channel / glucose-6-phosphate dehydrogenase (NADP+) / pentose-phosphate shunt, oxidative branch / glucose-6-phosphate dehydrogenase activity / response to iron(III) ion / Pentose phosphate pathway / NADPH regeneration ...negative regulation of protein glutathionylation / pentose biosynthetic process / ribose phosphate biosynthetic process / positive regulation of calcium ion transmembrane transport via high voltage-gated calcium channel / glucose-6-phosphate dehydrogenase (NADP+) / pentose-phosphate shunt, oxidative branch / glucose-6-phosphate dehydrogenase activity / response to iron(III) ion / Pentose phosphate pathway / NADPH regeneration / negative regulation of cell growth involved in cardiac muscle cell development / glucose 6-phosphate metabolic process / NADP metabolic process / pentose-phosphate shunt / D-glucose binding / NFE2L2 regulates pentose phosphate pathway genes / response to food / cholesterol biosynthetic process / erythrocyte maturation / centriolar satellite / negative regulation of reactive oxygen species metabolic process / regulation of neuron apoptotic process / substantia nigra development / glutathione metabolic process / TP53 Regulates Metabolic Genes / lipid metabolic process / response to organic cyclic compound / cytoplasmic side of plasma membrane / glucose metabolic process / NADP binding / cellular response to oxidative stress / response to ethanol / intracellular membrane-bounded organelle / protein homodimerization activity / extracellular exosome / identical protein binding / membrane / cytosol / cytoplasm
Similarity search - Function
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 / NAD(P)-binding domain superfamily
Similarity search - Domain/homology
Glucose-6-phosphate 1-dehydrogenase
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.2 Å
AuthorsWei X / Marmorstein R
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS) United States
CitationJournal: Proc Natl Acad Sci U S A / Year: 2022
Title: Allosteric role of a structural NADP molecule in glucose-6-phosphate dehydrogenase activity.
Authors: Xuepeng Wei / Kathryn Kixmoeller / Elana Baltrusaitis / Xiaolu Yang / Ronen Marmorstein /
Abstract: Human glucose-6-phosphate dehydrogenase (G6PD) is the main cellular source of NADPH, and thus plays a key role in maintaining reduced glutathione to protect cells from oxidative stress disorders such ...Human glucose-6-phosphate dehydrogenase (G6PD) is the main cellular source of NADPH, and thus plays a key role in maintaining reduced glutathione to protect cells from oxidative stress disorders such as hemolytic anemia. G6PD is a multimeric enzyme that uses the cofactors β-D-glucose 6-phosphate (G6P) and "catalytic" NADP (NADPc), as well as a "structural" NADP (NADPs) located ∼25 Å from the active site, to generate NADPH. While X-ray crystallographic and biochemical studies have revealed a role for NADPs in maintaining the catalytic activity by stabilizing the multimeric G6PD conformation, other potential roles for NADPs have not been evaluated. Here, we determined the high resolution cryo-electron microscopy structures of human wild-type G6PD in the absence of bound ligands and a catalytic G6PD-D200N mutant bound to NADPc and NADPs in the absence or presence of G6P. A comparison of these structures, together with previously reported structures, reveals that the unliganded human G6PD forms a mixture of dimers and tetramers with similar overall folds, and binding of NADPs induces a structural ordering of a C-terminal extension region and allosterically regulates G6P binding and catalysis. These studies have implications for understanding G6PD deficiencies and for therapy of G6PD-mediated disorders.
History
DepositionOct 28, 2021-
Header (metadata) releaseJul 13, 2022-
Map releaseJul 13, 2022-
UpdateJun 5, 2024-
Current statusJun 5, 2024Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_25226.png

Downloads & links

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Map

FileDownload / File: emd_25226.map.gz / Format: CCP4 / Size: 22.2 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.83 Å/pix.
x 180 pix.
= 149.4 Å		0.83 Å/pix.
x 180 pix.
= 149.4 Å		0.83 Å/pix.
x 180 pix.
= 149.4 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.83 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.4
Minimum - Maximum-2.6357706 - 4.5659347
Average (Standard dev.)0.00878374 (±0.23401786)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions180180180
Spacing180180180
CellA=B=C: 149.4 Å
α=β=γ: 90.0 °

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Supplemental data

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Sample components

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Entire : G6PD protein

EntireName: G6PD protein
Components
  • Organelle or cellular component: G6PD protein
    • Protein or peptide: Glucose-6-phosphate 1-dehydrogenase
  • Ligand: NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE

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Supramolecule #1: G6PD protein

SupramoleculeName: G6PD protein / type: organelle_or_cellular_component / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 200 KDa

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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: Homo sapiens (human)
Molecular weightTheoretical: 60.403754 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MAEQVALSRT QVCGILREEL FQGDAFHQSD THIFIIMGAS GDLAKKKIYP TIWWLFRDGL LPENTFIVGY ARSRLTVADI RKQSEPFFK ATPEEKLKLE DFFARNSYVA GQYDDAASYQ RLNSHMNALH LGSQANRLFY LALPPTVYEA VTKNIHESCM S QIGWNRII ...String:
MAEQVALSRT QVCGILREEL FQGDAFHQSD THIFIIMGAS GDLAKKKIYP TIWWLFRDGL LPENTFIVGY ARSRLTVADI RKQSEPFFK ATPEEKLKLE DFFARNSYVA GQYDDAASYQ RLNSHMNALH LGSQANRLFY LALPPTVYEA VTKNIHESCM S QIGWNRII VEKPFGRDLQ SSDRLSNHIS SLFREDQIYR IDHYLGKEMV QNLMVLRFAN RIFGPIWNRD NIACVILTFK EP FGTEGRG GYFDEFGIIR DVMQNHLLQM LCLVAMEKPA STNSDDVRDE KVKVLKCISE VQANNVVLGQ YVGNPDGEGE ATK GYLDDP TVPRGSTTAT FAAVVLYVEN ERWDGVPFIL RCGKALNERK AEVRLQFHDV AGDIFHQQCK RNELVIRVQP NEAV YTKMM TKKPGMFFNP EESELDLTYG NRYKNVKLPD AYERLILDVF CGSQMHFVRS DELREAWRIF TPLLHQIELE KPKPI PYIY GSRGPTEADE LMKRVGFQYE GTYKWVNPHK LLEHHHHHH

UniProtKB: Glucose-6-phosphate 1-dehydrogenase

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Macromolecule #2: NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE

MacromoleculeName: NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / type: ligand / ID: 2 / Number of copies: 8 / Formula: NAP
Molecular weightTheoretical: 743.405 Da
Chemical component information

ChemComp-NAP:
NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE

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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

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 40.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.0 µm / Nominal defocus min: 1.0 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

2bh9

Final reconstructionApplied symmetry - Point group: D2 (2x2 fold dihedral) / Resolution.type: BY AUTHOR / Resolution: 2.2 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 243562
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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