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P00349

- 6PGD_SHEEP

UniProt

P00349 - 6PGD_SHEEP

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Protein

6-phosphogluconate dehydrogenase, decarboxylating

Gene

PGD

Organism
Ovis aries (Sheep)
Status
Reviewed - Annotation score: 5 out of 5- Experimental evidence at protein leveli

Functioni

Catalyzes the oxidative decarboxylation of 6-phosphogluconate to ribulose 5-phosphate and CO2, with concomitant reduction of NADP to NADPH.

Catalytic activityi

6-phospho-D-gluconate + NADP+ = D-ribulose 5-phosphate + CO2 + NADPH.

Pathwayi

Sites

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Binding sitei103 – 1031NADP
Binding sitei103 – 1031Substrate
Binding sitei129 – 1291Substrate
Active sitei184 – 1841Proton acceptor
Active sitei191 – 1911Proton donor
Binding sitei192 – 1921Substrate
Binding sitei261 – 2611Substrate; via amide nitrogen
Binding sitei288 – 2881Substrate
Binding sitei447 – 4471Substrate; shared with dimeric partnerBy similarity
Binding sitei453 – 4531Substrate; shared with dimeric partnerBy similarity

Regions

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Nucleotide bindingi10 – 156NADP
Nucleotide bindingi33 – 353NADP
Nucleotide bindingi75 – 773NADP
Nucleotide bindingi478 – 4814NADP; shared with dimeric partnerBy similarity

GO - Molecular functioni

  1. NADP binding Source: InterPro
  2. phosphogluconate dehydrogenase (decarboxylating) activity Source: UniProtKB

GO - Biological processi

  1. D-gluconate metabolic process Source: UniProtKB-KW
  2. pentose biosynthetic process Source: Ensembl
  3. pentose-phosphate shunt Source: UniProtKB
  4. pentose-phosphate shunt, oxidative branch Source: Ensembl
Complete GO annotation...

Keywords - Molecular functioni

Oxidoreductase

Keywords - Biological processi

Gluconate utilization, Pentose shunt

Keywords - Ligandi

NADP

Enzyme and pathway databases

SABIO-RKP00349.
UniPathwayiUPA00115; UER00410.

Names & Taxonomyi

Protein namesi
Recommended name:
6-phosphogluconate dehydrogenase, decarboxylating (EC:1.1.1.44)
Gene namesi
Name:PGD
OrganismiOvis aries (Sheep)
Taxonomic identifieri9940 [NCBI]
Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaLaurasiatheriaCetartiodactylaRuminantiaPecoraBovidaeCaprinaeOvis
ProteomesiUP000002356: Unplaced

Subcellular locationi

Cytoplasm By similarity

GO - Cellular componenti

  1. cytoplasm Source: UniProtKB-KW
  2. extracellular vesicular exosome Source: Ensembl
  3. nucleus Source: Ensembl
Complete GO annotation...

Keywords - Cellular componenti

Cytoplasm

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Initiator methioninei1 – 11Removed1 Publication
Chaini2 – 4834826-phosphogluconate dehydrogenase, decarboxylatingPRO_0000090066Add
BLAST

Amino acid modifications

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Modified residuei38 – 381N6-acetyllysineBy similarity
Modified residuei257 – 2571PhosphoserineBy similarity
Modified residuei263 – 2631PhosphothreonineBy similarity
Modified residuei267 – 2671PhosphothreonineBy similarity
Modified residuei270 – 2701PhosphoserineBy similarity

Keywords - PTMi

Acetylation, Phosphoprotein

Proteomic databases

PRIDEiP00349.

Interactioni

Subunit structurei

Homodimer.2 Publications

Structurei

Secondary structure

1
483
Legend: HelixTurnBeta strand
Show more details
Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Beta strandi4 – 96Combined sources
Helixi13 – 2412Combined sources
Beta strandi29 – 324Combined sources
Helixi37 – 448Combined sources
Turni45 – 495Combined sources
Helixi58 – 647Combined sources
Beta strandi70 – 734Combined sources
Helixi79 – 9113Combined sources
Beta strandi97 – 1004Combined sources
Helixi106 – 11813Combined sources
Beta strandi122 – 1309Combined sources
Helixi131 – 1377Combined sources
Beta strandi140 – 1456Combined sources
Turni147 – 1493Combined sources
Helixi150 – 16011Combined sources
Turni165 – 1673Combined sources
Beta strandi168 – 1703Combined sources
Helixi179 – 20729Combined sources
Helixi213 – 22311Combined sources
Turni224 – 2285Combined sources
Helixi231 – 24111Combined sources
Beta strandi247 – 2504Combined sources
Helixi251 – 2533Combined sources
Helixi263 – 27412Combined sources
Helixi279 – 29214Combined sources
Helixi294 – 30310Combined sources
Helixi316 – 34934Combined sources
Helixi355 – 3617Combined sources
Beta strandi364 – 3663Combined sources
Helixi372 – 38211Combined sources
Helixi389 – 3913Combined sources
Helixi393 – 41624Combined sources
Helixi421 – 43414Combined sources
Helixi440 – 45112Combined sources
Beta strandi458 – 4603Combined sources

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
1PGNX-ray2.30A2-483[»]
1PGOX-ray2.50A2-483[»]
1PGPX-ray2.50A2-483[»]
1PGQX-ray3.17A2-483[»]
2PGDX-ray2.00A2-483[»]
ProteinModelPortaliP00349.
SMRiP00349. Positions 2-474.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiP00349.

Family & Domainsi

Region

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Regioni129 – 1313Substrate binding
Regioni187 – 1882Substrate binding

Sequence similaritiesi

Phylogenomic databases

HOVERGENiHBG000029.
KOiK00033.

Family and domain databases

Gene3Di1.10.1040.10. 1 hit.
1.20.5.320. 1 hit.
3.40.50.720. 1 hit.
InterProiIPR008927. 6-PGluconate_DH_C-like.
IPR006114. 6PGDH_C.
IPR006113. 6PGDH_decarbox.
IPR006115. 6PGDH_NADP-bd.
IPR006184. 6PGdom_BS.
IPR013328. DH_multihelical.
IPR012284. Fibritin/6PGD_C-extension.
IPR016040. NAD(P)-bd_dom.
[Graphical view]
PfamiPF00393. 6PGD. 1 hit.
PF03446. NAD_binding_2. 1 hit.
[Graphical view]
PIRSFiPIRSF000109. 6PGD. 1 hit.
SUPFAMiSSF48179. SSF48179. 1 hit.
TIGRFAMsiTIGR00873. gnd. 1 hit.
PROSITEiPS00461. 6PGD. 1 hit.
[Graphical view]

Sequencei

Sequence statusi: Complete.

Sequence processingi: The displayed sequence is further processed into a mature form.

P00349-1 [UniParc]FASTAAdd to Basket

« Hide

        10         20         30         40         50
MAQADIALIG LAVMGQNLIL NMNDHGFVVC AFNRTVSKVD DFLANEAKGT
60 70 80 90 100
KVLGAHSLEE MVSKLKKPRR IILLVKAGQA VDNFIEKLVP LLDIGDIIID
110 120 130 140 150
GGNSEYRDTM RRCRDLKDKG ILFVGSGVSG GEDGARYGPS LMPGGNKEAW
160 170 180 190 200
PHIKAIFQGI AAKVGTGEPC CDWVGDDGAG HFVKMVHNGI EYGDMQLICE
210 220 230 240 250
AYHLMKDVLG LGHKEMAKAF EEWNKTELDS FLIEITASIL KFQDADGKHL
260 270 280 290 300
LPKIRDSAGQ KGTGKWTAIS ALEYGVPVTL IGEAVFARCL SSLKDERIQA
310 320 330 340 350
SKKLKGPQNI PFEGDKKSFL EDIRKALYAS KIISYAQGFM LLRQAATEFG
360 370 380 390 400
WTLNYGGIAL MWRGGCIIRS VFLGKIKDAF DRNPGLQNLL LDDFFKSAVE
410 420 430 440 450
NCQDSWRRAI STGVQAGIPM PCFTTALSFY DGYRHAMLPA NLIQAQRDYF
460 470 480
GAHTYELLAK PGQFIHTNWT GHGGSVSSSS YNA
Length:483
Mass (Da):52,970
Last modified:January 23, 2007 - v4
Checksum:iF4AC5DB414385F11
GO

Sequence cautioni

The sequence described in 1 Publication differs from that shown. Reason: Incorrect CNBR peptide order. Many sequencing errors.Curated

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
X60195 mRNA. Translation: CAA42751.1.
PIRiS15280.
S27359. DESHGC.
RefSeqiNP_001009467.1. NM_001009467.2.
UniGeneiOar.419.

Genome annotation databases

GeneIDi443541.
KEGGioas:443541.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
X60195 mRNA. Translation: CAA42751.1 .
PIRi S15280.
S27359. DESHGC.
RefSeqi NP_001009467.1. NM_001009467.2.
UniGenei Oar.419.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
Entry Method Resolution (Å) Chain Positions PDBsum
1PGN X-ray 2.30 A 2-483 [» ]
1PGO X-ray 2.50 A 2-483 [» ]
1PGP X-ray 2.50 A 2-483 [» ]
1PGQ X-ray 3.17 A 2-483 [» ]
2PGD X-ray 2.00 A 2-483 [» ]
ProteinModelPortali P00349.
SMRi P00349. Positions 2-474.
ModBasei Search...
MobiDBi Search...

Chemistry

BindingDBi P00349.
ChEMBLi CHEMBL1169597.

Proteomic databases

PRIDEi P00349.

Protocols and materials databases

Structural Biology Knowledgebase Search...

Genome annotation databases

GeneIDi 443541.
KEGGi oas:443541.

Organism-specific databases

CTDi 5226.

Phylogenomic databases

HOVERGENi HBG000029.
KOi K00033.

Enzyme and pathway databases

UniPathwayi UPA00115 ; UER00410 .
SABIO-RK P00349.

Miscellaneous databases

EvolutionaryTracei P00349.

Family and domain databases

Gene3Di 1.10.1040.10. 1 hit.
1.20.5.320. 1 hit.
3.40.50.720. 1 hit.
InterProi IPR008927. 6-PGluconate_DH_C-like.
IPR006114. 6PGDH_C.
IPR006113. 6PGDH_decarbox.
IPR006115. 6PGDH_NADP-bd.
IPR006184. 6PGdom_BS.
IPR013328. DH_multihelical.
IPR012284. Fibritin/6PGD_C-extension.
IPR016040. NAD(P)-bd_dom.
[Graphical view ]
Pfami PF00393. 6PGD. 1 hit.
PF03446. NAD_binding_2. 1 hit.
[Graphical view ]
PIRSFi PIRSF000109. 6PGD. 1 hit.
SUPFAMi SSF48179. SSF48179. 1 hit.
TIGRFAMsi TIGR00873. gnd. 1 hit.
PROSITEi PS00461. 6PGD. 1 hit.
[Graphical view ]
ProtoNeti Search...

Publicationsi

  1. "Sheep 6-phosphogluconate dehydrogenase. Revised protein sequence based upon the sequences of cDNA clones obtained with the polymerase chain reaction."
    Somers D.O., Medd S.M., Walker J.E., Adams M.J.
    Biochem. J. 288:1061-1067(1992) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [MRNA].
    Tissue: Liver.
  2. "Amino acid sequence of ovine 6-phosphogluconate dehydrogenase."
    Carne A., Walker J.E.
    J. Biol. Chem. 258:12895-12906(1983) [PubMed] [Europe PMC] [Abstract]
    Cited for: PRELIMINARY PROTEIN SEQUENCE OF 2-483, CLEAVAGE OF INITIATOR METHIONINE.
    Tissue: Liver.
  3. "The three dimensional structure of sheep liver 6-phosphogluconate dehydrogenase at 2.6-A resolution."
    Adams M.J., Archibald I.G., Bugg C.E., Carne A., Gover S., Helliwell J.R., Pickersgill R.W., White S.W.
    EMBO J. 2:1009-1014(1983) [PubMed] [Europe PMC] [Abstract]
    Cited for: X-RAY CRYSTALLOGRAPHY (2.6 ANGSTROMS).
  4. "The structure of 6-phosphogluconate dehydrogenase refined at 2.5-A resolution."
    Adams M.J., Gover S., Leaback R., Phillips C., Somers D.O.
    Acta Crystallogr. B 47:817-820(1991) [PubMed] [Europe PMC] [Abstract]
    Cited for: X-RAY CRYSTALLOGRAPHY (2.5 ANGSTROMS).
  5. "Crystallographic study of coenzyme, coenzyme analogue and substrate binding in 6-phosphogluconate dehydrogenase: implications for NADP specificity and the enzyme mechanism."
    Adams M.J., Ellis G.H., Gover S., Naylor C.E., Phillips C.
    Structure 2:651-668(1994) [PubMed] [Europe PMC] [Abstract]
    Cited for: X-RAY CRYSTALLOGRAPHY (2.3 ANGSTROMS) OF 2-483 IN COMPLEXES WITH NADP AND SUBSTRATE, SUBUNIT.
  6. "Structure of 6-phosphogluconate dehydrogenase refined at 2-A resolution."
    Phillips C., Gover S., Adams M.J.
    Acta Crystallogr. D 51:290-304(1995) [PubMed] [Europe PMC] [Abstract]
    Cited for: X-RAY CRYSTALLOGRAPHY (2.0 ANGSTROMS) OF 2-483, SUBUNIT.

Entry informationi

Entry namei6PGD_SHEEP
AccessioniPrimary (citable) accession number: P00349
Entry historyi
Integrated into UniProtKB/Swiss-Prot: July 21, 1986
Last sequence update: January 23, 2007
Last modified: November 26, 2014
This is version 124 of the entry and version 4 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programChordata Protein Annotation Program

Miscellaneousi

Keywords - Technical termi

3D-structure, Complete proteome, Direct protein sequencing, Reference proteome

Documents

  1. PATHWAY comments
    Index of metabolic and biosynthesis pathways
  2. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
  3. SIMILARITY comments
    Index of protein domains and families

External Data

Dasty 3