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P96789

- 6PGD_LACLM

UniProt

P96789 - 6PGD_LACLM

Protein

6-phosphogluconate dehydrogenase, decarboxylating

Gene

gnd

Organism
Lactococcus lactis subsp. cremoris (strain MG1363)
Status
Reviewed - Annotation score: 4 out of 5- Experimental evidence at protein leveli
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    • History
      Entry version 98 (01 Oct 2014)
      Sequence version 3 (01 May 2007)
      Previous versions | rss
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    • Comment

    Functioni

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

    Catalytic activityi

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

    Pathwayi

    Sites

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Binding sitei102 – 1021NADPBy similarity
    Binding sitei102 – 1021Substrate
    Active sitei184 – 1841Proton acceptor1 Publication
    Active sitei191 – 1911Proton donor1 Publication
    Binding sitei192 – 1921Substrate
    Binding sitei262 – 2621Substrate; via amide nitrogen
    Binding sitei289 – 2891Substrate
    Binding sitei447 – 4471Substrate; shared with dimeric partner
    Binding sitei453 – 4531Substrate; shared with dimeric partner

    Regions

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Nucleotide bindingi10 – 156NADP
    Nucleotide bindingi33 – 353NADP
    Nucleotide bindingi74 – 763NADP

    GO - Molecular functioni

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

    GO - Biological processi

    1. D-gluconate metabolic process Source: UniProtKB-KW
    2. pentose-phosphate shunt Source: UniProtKB-UniPathway

    Keywords - Molecular functioni

    Oxidoreductase

    Keywords - Biological processi

    Gluconate utilization, Pentose shunt

    Keywords - Ligandi

    NADP

    Enzyme and pathway databases

    BioCyciLLAC416870:GCDT-613-MONOMER.
    SABIO-RKP96789.
    UniPathwayiUPA00115; UER00410.

    Names & Taxonomyi

    Protein namesi
    Recommended name:
    6-phosphogluconate dehydrogenase, decarboxylating (EC:1.1.1.44)
    Gene namesi
    Name:gnd
    Ordered Locus Names:llmg_0586
    OrganismiLactococcus lactis subsp. cremoris (strain MG1363)
    Taxonomic identifieri416870 [NCBI]
    Taxonomic lineageiBacteriaFirmicutesBacilliLactobacillalesStreptococcaceaeLactococcus
    ProteomesiUP000000364: Chromosome

    PTM / Processingi

    Molecule processing

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Chaini1 – 4724726-phosphogluconate dehydrogenase, decarboxylatingPRO_0000090046Add
    BLAST

    Interactioni

    Subunit structurei

    Homodimer.By similarity

    Protein-protein interaction databases

    STRINGi416870.llmg_0586.

    Structurei

    Secondary structure

    1
    472
    Legend: HelixTurnBeta strand
    Show more details
    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Beta strandi4 – 96
    Helixi13 – 2412
    Beta strandi29 – 324
    Helixi36 – 4510
    Turni46 – 483
    Beta strandi51 – 533
    Helixi57 – 626
    Beta strandi69 – 724
    Helixi78 – 8710
    Helixi88 – 903
    Beta strandi96 – 994
    Helixi105 – 11410
    Turni115 – 1173
    Beta strandi121 – 1277
    Helixi130 – 1367
    Beta strandi140 – 1445
    Helixi146 – 15914
    Turni164 – 1663
    Beta strandi169 – 1713
    Helixi179 – 20729
    Helixi213 – 22311
    Turni224 – 2285
    Helixi231 – 2399
    Beta strandi245 – 2506
    Helixi251 – 2544
    Helixi264 – 27512
    Helixi280 – 29314
    Helixi295 – 30410
    Helixi316 – 34934
    Helixi355 – 3617
    Beta strandi363 – 3653
    Helixi373 – 38210
    Helixi389 – 3913
    Helixi393 – 41624
    Helixi421 – 43313
    Helixi440 – 45112
    Beta strandi457 – 4626

    3D structure databases

    Select the link destinations:
    PDBe
    RCSB PDB
    PDBj
    Links Updated
    EntryMethodResolution (Å)ChainPositionsPDBsum
    2IYOX-ray2.40A1-472[»]
    2IYPX-ray2.79A/B/C1-472[»]
    2IZ0X-ray2.60A/B/C1-472[»]
    2IZ1X-ray2.30A/B/C1-472[»]
    ProteinModelPortaliP96789.
    SMRiP96789. Positions 1-470.
    ModBaseiSearch...
    MobiDBiSearch...

    Miscellaneous databases

    EvolutionaryTraceiP96789.

    Family & Domainsi

    Region

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Regioni128 – 1303Substrate binding
    Regioni187 – 1882Substrate binding

    Sequence similaritiesi

    Phylogenomic databases

    eggNOGiCOG0362.
    HOGENOMiHOG000255147.
    KOiK00033.
    OMAiDKDGVFH.
    OrthoDBiEOG6MSS4W.

    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.

    P96789-1 [UniParc]FASTAAdd to Basket

    « Hide

    MAQANFGVVG MAVMGKNLAL NVESRGYTVA IYNRTTSKTE EVYKEHQDKN    50
    LVFTKTLEEF VGSLEKPRRI MLMVQAGAAT DATIKSLLPL LDIGDILIDG 100
    GNTHFPDTMR RNAELADSGI NFIGTGVSGG EKGALLGPSM MPGGQKEAYD 150
    LVAPIFEQIA AKAPQDGKPC VAYMGANGAG HYVKMVHNGI EYGDMQLIAE 200
    SYDLLKRILG LSNAEIQAIF EEWNEGELDS YLIEITKEVL KRKDDEGEGY 250
    IVDKILDKAG NKGTGKWTSE SALDLGVPLP LITESVFARY ISTYKDERVK 300
    ASKVLSGPAL DFSGDKKEVI EKIRKALYFS KIMSYAQGFA QLRKASEEFD 350
    WDLPYGTIAQ IWRAGCIIRA EFLQNITDAF DKDSELENLL LDDYFVDITK 400
    RYQEAVRDVV SLAVQAGTPI PTFTSAISYY DSYRSENLPA NLIQAQRDYF 450
    GAHTYERTDK AGIFHYDWYT ED 472
    Length:472
    Mass (Da):52,460
    Last modified:May 1, 2007 - v3
    Checksum:iA0075C9F46171F1C
    GO

    Experimental Info

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Sequence conflicti43 – 431Y → F in AAC12804. (PubMed:9931298)Curated

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    U74322 Genomic DNA. Translation: AAC12804.1.
    AM406671 Genomic DNA. Translation: CAL97186.1.
    RefSeqiYP_001031931.1. NC_009004.1.

    Genome annotation databases

    EnsemblBacteriaiCAL97186; CAL97186; llmg_0586.
    GeneIDi4798708.
    KEGGillm:llmg_0586.
    PATRICi22282257. VBILacLac4574_0596.

    Cross-referencesi

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    U74322 Genomic DNA. Translation: AAC12804.1 .
    AM406671 Genomic DNA. Translation: CAL97186.1 .
    RefSeqi YP_001031931.1. NC_009004.1.

    3D structure databases

    Select the link destinations:
    PDBe
    RCSB PDB
    PDBj
    Links Updated
    Entry Method Resolution (Å) Chain Positions PDBsum
    2IYO X-ray 2.40 A 1-472 [» ]
    2IYP X-ray 2.79 A/B/C 1-472 [» ]
    2IZ0 X-ray 2.60 A/B/C 1-472 [» ]
    2IZ1 X-ray 2.30 A/B/C 1-472 [» ]
    ProteinModelPortali P96789.
    SMRi P96789. Positions 1-470.
    ModBasei Search...
    MobiDBi Search...

    Protein-protein interaction databases

    STRINGi 416870.llmg_0586.

    Protocols and materials databases

    Structural Biology Knowledgebase Search...

    Genome annotation databases

    EnsemblBacteriai CAL97186 ; CAL97186 ; llmg_0586 .
    GeneIDi 4798708.
    KEGGi llm:llmg_0586.
    PATRICi 22282257. VBILacLac4574_0596.

    Phylogenomic databases

    eggNOGi COG0362.
    HOGENOMi HOG000255147.
    KOi K00033.
    OMAi DKDGVFH.
    OrthoDBi EOG6MSS4W.

    Enzyme and pathway databases

    UniPathwayi UPA00115 ; UER00410 .
    BioCyci LLAC416870:GCDT-613-MONOMER.
    SABIO-RK P96789.

    Miscellaneous databases

    EvolutionaryTracei P96789.

    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. "6-phosphogluconate dehydrogenase from Lactococcus lactis: a role for arginine residues in binding substrate and coenzyme."
      Tetaud E., Hanau S., Wells J.M., Le Page R.W.F., Adams M.J., Arkison S., Barrett M.P.
      Biochem. J. 338:55-60(1999) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
    2. "The complete genome sequence of the lactic acid bacterial paradigm Lactococcus lactis subsp. cremoris MG1363."
      Wegmann U., O'Connell-Motherway M., Zomer A., Buist G., Shearman C., Canchaya C., Ventura M., Goesmann A., Gasson M.J., Kuipers O.P., van Sinderen D., Kok J.
      J. Bacteriol. 189:3256-3270(2007) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
      Strain: MG1363.
    3. "Crystal structures of a bacterial 6-phosphogluconate dehydrogenase reveal aspects of specificity, mechanism and mode of inhibition by analogues of high-energy reaction intermediates."
      Sundaramoorthy R., Iulek J., Barrett M.P., Bidet O., Ruda G.F., Gilbert I.H., Hunter W.N.
      FEBS J. 274:275-286(2007) [PubMed] [Europe PMC] [Abstract]
      Cited for: X-RAY CRYSTALLOGRAPHY (2.3 ANGSTROMS) IN COMPLEXES WITH SUBSTRATE; PRODUCT; INHIBITORS AND NADP, SUBUNIT, ACTIVE SITE.

    Entry informationi

    Entry namei6PGD_LACLM
    AccessioniPrimary (citable) accession number: P96789
    Secondary accession number(s): A2RIU0
    Entry historyi
    Integrated into UniProtKB/Swiss-Prot: May 30, 2000
    Last sequence update: May 1, 2007
    Last modified: October 1, 2014
    This is version 98 of the entry and version 3 of the sequence. [Complete history]
    Entry statusiReviewed (UniProtKB/Swiss-Prot)
    Annotation programProkaryotic Protein Annotation Program

    Miscellaneousi

    Keywords - Technical termi

    3D-structure, Complete 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