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P00349

- 6PGD_SHEEP

UniProt

P00349 - 6PGD_SHEEP

Protein

6-phosphogluconate dehydrogenase, decarboxylating

Gene

PGD

Organism
Ovis aries (Sheep)
Status
Reviewed - Annotation score: 5 out of 5- Experimental evidence at protein leveli
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    • History
      Entry version 122 (01 Oct 2014)
      Sequence version 4 (23 Jan 2007)
      Previous versions | rss
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    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

    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-SubCell

    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 – 96
    Helixi13 – 2412
    Beta strandi29 – 324
    Helixi37 – 448
    Turni45 – 495
    Helixi58 – 647
    Beta strandi70 – 734
    Helixi79 – 9113
    Beta strandi97 – 1004
    Helixi106 – 11813
    Beta strandi122 – 1309
    Helixi131 – 1377
    Beta strandi140 – 1456
    Turni147 – 1493
    Helixi150 – 16011
    Turni165 – 1673
    Beta strandi168 – 1703
    Helixi179 – 20729
    Helixi213 – 22311
    Turni224 – 2285
    Helixi231 – 24111
    Beta strandi247 – 2504
    Helixi251 – 2533
    Helixi263 – 27412
    Helixi279 – 29214
    Helixi294 – 30310
    Helixi316 – 34934
    Helixi355 – 3617
    Beta strandi364 – 3663
    Helixi372 – 38211
    Helixi389 – 3913
    Helixi393 – 41624
    Helixi421 – 43414
    Helixi440 – 45112
    Beta strandi458 – 4603

    3D structure databases

    Select the link destinations:
    PDBe
    RCSB PDB
    PDBj
    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.

    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

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    MAQADIALIG LAVMGQNLIL NMNDHGFVVC AFNRTVSKVD DFLANEAKGT    50
    KVLGAHSLEE MVSKLKKPRR IILLVKAGQA VDNFIEKLVP LLDIGDIIID 100
    GGNSEYRDTM RRCRDLKDKG ILFVGSGVSG GEDGARYGPS LMPGGNKEAW 150
    PHIKAIFQGI AAKVGTGEPC CDWVGDDGAG HFVKMVHNGI EYGDMQLICE 200
    AYHLMKDVLG LGHKEMAKAF EEWNKTELDS FLIEITASIL KFQDADGKHL 250
    LPKIRDSAGQ KGTGKWTAIS ALEYGVPVTL IGEAVFARCL SSLKDERIQA 300
    SKKLKGPQNI PFEGDKKSFL EDIRKALYAS KIISYAQGFM LLRQAATEFG 350
    WTLNYGGIAL MWRGGCIIRS VFLGKIKDAF DRNPGLQNLL LDDFFKSAVE 400
    NCQDSWRRAI STGVQAGIPM PCFTTALSFY DGYRHAMLPA NLIQAQRDYF 450
    GAHTYELLAK PGQFIHTNWT GHGGSVSSSS YNA 483
    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.

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    X60195 mRNA. Translation: CAA42751.1.
    PIRiS15280.
    S27359. DESHGC.
    RefSeqiNP_001009467.1. NM_001009467.2.
    UniGeneiOar.419.

    Genome annotation databases

    GeneIDi443541.

    Cross-referencesi

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    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:
    PDBe
    RCSB PDB
    PDBj
    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.

    Organism-specific databases

    CTDi 5226.

    Phylogenomic databases

    HOVERGENi HBG000029.

    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: October 1, 2014
    This is version 122 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