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P22983

- PPDK_CLOSY

UniProt

P22983 - PPDK_CLOSY

Protein

Pyruvate, phosphate dikinase

Gene

ppdK

Organism
Clostridium symbiosum (Bacteroides symbiosus)
Status
Reviewed - Annotation score: 5 out of 5- Experimental evidence at protein leveli
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    • History
      Entry version 110 (01 Oct 2014)
      Sequence version 5 (23 Jan 2007)
      Previous versions | rss
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    Functioni

    Catalyzes the reversible phosphorylation of pyruvate and phosphate. In E.histolytica and C.symbiosus, PPDK functions in the direction of ATP synthesis.

    Catalytic activityi

    ATP + pyruvate + phosphate = AMP + phosphoenolpyruvate + diphosphate.

    Cofactori

    Magnesium.

    Enzyme regulationi

    Activated by light-induced dephosphorylation. Inhibited by dark-induced phosphorylation. Both reactions are catalyzed by PDRP1 By similarity.By similarity

    Sites

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Binding sitei92 – 921ATPSequence Analysis
    Active sitei455 – 4551Tele-phosphohistidine intermediate1 Publication
    Binding sitei561 – 5611Substrate
    Binding sitei617 – 6171Substrate
    Metal bindingi745 – 7451Magnesium
    Binding sitei745 – 7451Substrate
    Binding sitei766 – 7661Substrate; via carbonyl oxygen
    Binding sitei767 – 7671Substrate; via amide nitrogen
    Binding sitei768 – 7681Substrate
    Metal bindingi769 – 7691Magnesium
    Binding sitei769 – 7691Substrate; via amide nitrogen
    Active sitei831 – 8311Proton donor2 Publications

    GO - Molecular functioni

    1. ATP binding Source: UniProtKB-KW
    2. kinase activity Source: UniProtKB-KW
    3. metal ion binding Source: UniProtKB-KW
    4. pyruvate, phosphate dikinase activity Source: UniProtKB-EC

    GO - Biological processi

    1. pyruvate metabolic process Source: InterPro

    Keywords - Molecular functioni

    Kinase, Transferase

    Keywords - Ligandi

    ATP-binding, Magnesium, Metal-binding, Nucleotide-binding

    Enzyme and pathway databases

    BioCyciRETL1328306-WGS:GSTH-1025-MONOMER.
    SABIO-RKP22983.

    Names & Taxonomyi

    Protein namesi
    Recommended name:
    Pyruvate, phosphate dikinase (EC:2.7.9.1)
    Alternative name(s):
    Pyruvate, orthophosphate dikinase
    Gene namesi
    Name:ppdK
    OrganismiClostridium symbiosum (Bacteroides symbiosus)
    Taxonomic identifieri1512 [NCBI]
    Taxonomic lineageiBacteriaFirmicutesClostridiaClostridialesLachnospiraceae

    Pathology & Biotechi

    Mutagenesis

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Mutagenesisi831 – 8311C → A: Lack of phosphotransfer activity. 1 Publication

    PTM / Processingi

    Molecule processing

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Initiator methioninei1 – 11Removed1 Publication
    Chaini2 – 874873Pyruvate, phosphate dikinasePRO_0000147046Add
    BLAST

    Amino acid modifications

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Modified residuei453 – 4531Phosphothreonine; by PDRP1By similarity

    Post-translational modificationi

    Phosphorylation of Thr-453 in the dark inactivates the enzyme. Dephosphorylation upon light stimulation reactivates the enzyme By similarity.By similarity

    Keywords - PTMi

    Phosphoprotein

    Interactioni

    Subunit structurei

    Homodimer.1 Publication

    Structurei

    Secondary structure

    1
    874
    Legend: HelixTurnBeta strand
    Show more details
    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Beta strandi5 – 73
    Helixi8 – 103
    Helixi13 – 153
    Helixi16 – 3116
    Beta strandi39 – 424
    Helixi44 – 518
    Turni52 – 543
    Helixi59 – 7618
    Beta strandi78 – 803
    Beta strandi83 – 853
    Beta strandi89 – 946
    Turni100 – 1023
    Beta strandi105 – 1095
    Helixi115 – 1239
    Helixi126 – 14419
    Helixi149 – 16214
    Helixi168 – 1703
    Helixi173 – 18816
    Turni189 – 1935
    Helixi200 – 21415
    Helixi218 – 2269
    Helixi231 – 2333
    Beta strandi236 – 2416
    Beta strandi252 – 2598
    Turni261 – 2633
    Beta strandi266 – 27510
    Helixi278 – 2836
    Beta strandi284 – 2863
    Helixi291 – 2933
    Helixi294 – 2974
    Helixi299 – 31618
    Beta strandi320 – 3278
    Beta strandi330 – 3389
    Helixi343 – 35513
    Beta strandi357 – 3593
    Helixi361 – 3677
    Helixi370 – 3778
    Helixi383 – 3886
    Beta strandi391 – 3944
    Beta strandi396 – 3994
    Beta strandi401 – 41010
    Helixi411 – 4199
    Beta strandi424 – 4307
    Helixi433 – 4353
    Helixi436 – 4416
    Beta strandi443 – 4497
    Beta strandi452 – 4543
    Helixi455 – 4639
    Beta strandi466 – 4694
    Beta strandi475 – 4773
    Turni478 – 4814
    Beta strandi482 – 4854
    Beta strandi488 – 4914
    Beta strandi495 – 4995
    Turni500 – 5023
    Beta strandi504 – 5085
    Helixi519 – 53113
    Beta strandi534 – 5396
    Helixi543 – 5519
    Beta strandi556 – 5605
    Helixi564 – 5674
    Helixi569 – 58012
    Helixi584 – 5929
    Helixi595 – 60915
    Beta strandi614 – 6174
    Helixi623 – 6264
    Helixi631 – 64111
    Helixi645 – 65511
    Helixi660 – 6623
    Helixi667 – 6726
    Helixi674 – 69522
    Beta strandi702 – 7054
    Helixi711 – 73222
    Beta strandi739 – 7446
    Helixi747 – 7515
    Helixi753 – 7564
    Turni757 – 7593
    Beta strandi761 – 7655
    Helixi767 – 7759
    Helixi779 – 79113
    Turni799 – 8013
    Turni805 – 8073
    Helixi808 – 82215
    Beta strandi827 – 8304
    Helixi833 – 8364
    Helixi838 – 8469
    Beta strandi850 – 8545
    Helixi856 – 8583
    Helixi859 – 87214

    3D structure databases

    Select the link destinations:
    PDBe
    RCSB PDB
    PDBj
    Links Updated
    EntryMethodResolution (Å)ChainPositionsPDBsum
    1DIKX-ray2.30A1-874[»]
    1GGOX-ray2.60A2-874[»]
    1JDEX-ray2.80A2-874[»]
    1KBLX-ray1.94A2-874[»]
    1KC7X-ray2.20A2-874[»]
    2DIKX-ray2.50A2-874[»]
    2FM4NMR-A384-511[»]
    2R82X-ray3.60A1-874[»]
    ProteinModelPortaliP22983.
    SMRiP22983. Positions 2-873.
    ModBaseiSearch...
    MobiDBiSearch...

    Miscellaneous databases

    EvolutionaryTraceiP22983.

    Family & Domainsi

    Region

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Regioni2 – 340339N-terminalAdd
    BLAST
    Regioni340 – 39960Linker 1Add
    BLAST
    Regioni400 – 49899CentralAdd
    BLAST
    Regioni499 – 53335Linker 2Add
    BLAST
    Regioni534 – 874341C-terminalAdd
    BLAST

    Domaini

    The N-terminal domain contains the ATP/Pi binding site, the central domain the pyrophosphate/phosphate carrier histidine, and the C-terminal domain the pyruvate binding site.

    Sequence similaritiesi

    Belongs to the PEP-utilizing enzyme family.Curated

    Family and domain databases

    Gene3Di3.20.20.60. 1 hit.
    3.30.1490.20. 2 hits.
    3.30.470.20. 1 hit.
    3.50.30.10. 1 hit.
    InterProiIPR013815. ATP_grasp_subdomain_1.
    IPR013816. ATP_grasp_subdomain_2.
    IPR008279. PEP-util_enz_mobile_dom.
    IPR018274. PEP_util_AS.
    IPR000121. PEP_util_C.
    IPR023151. PEP_util_CS.
    IPR002192. PPDK_PEP-bd.
    IPR010121. Pyruvate_phosphate_dikinase.
    IPR015813. Pyrv/PenolPyrv_Kinase-like_dom.
    [Graphical view]
    PANTHERiPTHR22931:SF9. PTHR22931:SF9. 1 hit.
    PfamiPF00391. PEP-utilizers. 1 hit.
    PF02896. PEP-utilizers_C. 1 hit.
    PF01326. PPDK_N. 1 hit.
    [Graphical view]
    PIRSFiPIRSF000853. PPDK. 1 hit.
    SUPFAMiSSF51621. SSF51621. 1 hit.
    SSF52009. SSF52009. 1 hit.
    TIGRFAMsiTIGR01828. pyru_phos_dikin. 1 hit.
    PROSITEiPS00742. PEP_ENZYMES_2. 1 hit.
    PS00370. PEP_ENZYMES_PHOS_SITE. 1 hit.
    [Graphical view]

    Sequencei

    Sequence statusi: Complete.

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

    P22983-1 [UniParc]FASTAAdd to Basket

    « Hide

    MAKWVYKFEE GNASMRNLLG GKGCNLAEMT ILGMPIPQGF TVTTEACTEY    50
    YNSGKQITQE IQDQIFEAIT WLEELNGKKF GDTEDPLLVS VRSGARASMP 100
    GMMDTILNLG LNDVAVEGFA KKTGNPRFAY DSYRRFIQMY SDVVMEVPKS 150
    HFEKIIDAMK EEKGVHFDTD LTADDLKELA EKFKAVYKEA MNGEEFPQEP 200
    KDQLMGAVKA VFRSWDNPRA IVYRRMNDIP GDWGTAVNVQ TMVFGNKGET 250
    SGTGVAFTRN PSTGEKGIYG EYLINAQGED VVAGVRTPQP ITQLENDMPD 300
    CYKQFMDLAM KLEKHFRDMQ DMEFTIEEGK LYFLQTRNGK RTAPAALQIA 350
    CDLVDEGMIT EEEAVVRIEA KSLDQLLHPT FNPAALKAGE VIGSALPASP 400
    GAAAGKVYFT ADEAKAAHEK GERVILVRLE TSPEDIEGMH AAEGILTVRG 450
    GMTSHAAVVA RGMGTCCVSG CGEIKINEEA KTFELGGHTF AEGDYISLDG 500
    STGKIYKGDI ETQEASVSGS FERIMVWADK FRTLKVRTNA DTPEDTLNAV 550
    KLGAEGIGLC RTEHMFFEAD RIMKIRKMIL SDSVEAREEA LNELIPFQKG 600
    DFKAMYKALE GRPMTVRYLD PPLHEFVPHT EEEQAELAKN MGLTLAEVKA 650
    KVDELHEFNP MMGHRGCRLA VTYPEIAKMQ TRAVMEAAIE VKEETGIDIV 700
    PEIMIPLVGE KKELKFVKDV VVEVAEQVKK EKGSDMQYHI GTMIEIPRAA 750
    LTADAIAEEA EFFSFGTNDL TQMTFGFSRD DAGKFLDSYY KAKIYESDPF 800
    ARLDQTGVGQ LVEMAVKKGR QTRPGLKCGI CGEHGGDPSS VEFCHKVGLN 850
    YVSCSPFRVP IARLAAAQAA LNNK 874
    Length:874
    Mass (Da):96,654
    Last modified:January 23, 2007 - v5
    Checksum:i13C1918807DEA36C
    GO

    Experimental Info

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Sequence conflicti94 – 941G → A in AAA22917. (PubMed:2176881)Curated
    Sequence conflicti515 – 5151A → R in AAA22917. (PubMed:2176881)Curated
    Sequence conflicti836 – 87439GDPSS…ALNNK → EILLP in AAA22917. (PubMed:2176881)CuratedAdd
    BLAST

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    M60920 mRNA. Translation: AAA22917.1.
    PIRiA36231. KIQAPO.

    Cross-referencesi

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    M60920 mRNA. Translation: AAA22917.1 .
    PIRi A36231. KIQAPO.

    3D structure databases

    Select the link destinations:
    PDBe
    RCSB PDB
    PDBj
    Links Updated
    Entry Method Resolution (Å) Chain Positions PDBsum
    1DIK X-ray 2.30 A 1-874 [» ]
    1GGO X-ray 2.60 A 2-874 [» ]
    1JDE X-ray 2.80 A 2-874 [» ]
    1KBL X-ray 1.94 A 2-874 [» ]
    1KC7 X-ray 2.20 A 2-874 [» ]
    2DIK X-ray 2.50 A 2-874 [» ]
    2FM4 NMR - A 384-511 [» ]
    2R82 X-ray 3.60 A 1-874 [» ]
    ProteinModelPortali P22983.
    SMRi P22983. Positions 2-873.
    ModBasei Search...
    MobiDBi Search...

    Protocols and materials databases

    Structural Biology Knowledgebase Search...

    Enzyme and pathway databases

    BioCyci RETL1328306-WGS:GSTH-1025-MONOMER.
    SABIO-RK P22983.

    Miscellaneous databases

    EvolutionaryTracei P22983.

    Family and domain databases

    Gene3Di 3.20.20.60. 1 hit.
    3.30.1490.20. 2 hits.
    3.30.470.20. 1 hit.
    3.50.30.10. 1 hit.
    InterProi IPR013815. ATP_grasp_subdomain_1.
    IPR013816. ATP_grasp_subdomain_2.
    IPR008279. PEP-util_enz_mobile_dom.
    IPR018274. PEP_util_AS.
    IPR000121. PEP_util_C.
    IPR023151. PEP_util_CS.
    IPR002192. PPDK_PEP-bd.
    IPR010121. Pyruvate_phosphate_dikinase.
    IPR015813. Pyrv/PenolPyrv_Kinase-like_dom.
    [Graphical view ]
    PANTHERi PTHR22931:SF9. PTHR22931:SF9. 1 hit.
    Pfami PF00391. PEP-utilizers. 1 hit.
    PF02896. PEP-utilizers_C. 1 hit.
    PF01326. PPDK_N. 1 hit.
    [Graphical view ]
    PIRSFi PIRSF000853. PPDK. 1 hit.
    SUPFAMi SSF51621. SSF51621. 1 hit.
    SSF52009. SSF52009. 1 hit.
    TIGRFAMsi TIGR01828. pyru_phos_dikin. 1 hit.
    PROSITEi PS00742. PEP_ENZYMES_2. 1 hit.
    PS00370. PEP_ENZYMES_PHOS_SITE. 1 hit.
    [Graphical view ]
    ProtoNeti Search...

    Publicationsi

    1. "Analysis of sequence homologies in plant and bacterial pyruvate phosphate dikinase, enzyme I of the bacterial phosphoenolpyruvate: sugar phosphotransferase system and other PEP-utilizing enzymes. Identification of potential catalytic and regulatory motifs."
      Pocalyko D.J., Carroll L.J., Martin B.M., Babbitt P.C., Dunaway-Mariano D.
      Biochemistry 29:10757-10765(1990) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA], PROTEIN SEQUENCE OF 2-11; 56-70; 128-134; 226-243; 372-386; 407-415; 652-664 AND 693-702.
    2. Dunaway-Mariano D., Ye D.
      Submitted (SEP-2000) to UniProtKB
      Cited for: SEQUENCE REVISION TO 94.
    3. "Pyruvate phosphate dikinase: sequence of the histidyl peptide, the pyrophosphoryl and phosphoryl carrier."
      Goss N.H., Evans C.T., Wood H.G.
      Biochemistry 19:5805-5809(1980) [PubMed] [Europe PMC] [Abstract]
      Cited for: PROTEIN SEQUENCE OF 451-462.
    4. "Location of the catalytic site for phosphoenolpyruvate formation within the primary structure of Clostridium symbiosum pyruvate phosphate dikinase. 1. Identification of an essential cysteine by chemical modification with [1-14C]bromopyruvate and site-directed mutagenesis."
      Xu Y., Yankie L., Shen L., Jung Y.S., Mariano P.S., Dunaway-Mariano D., Martin B.M.
      Biochemistry 34:2181-2187(1995) [PubMed] [Europe PMC] [Abstract]
      Cited for: ACTIVE SITE CYS-831, MUTAGENESIS OF CYS-831.
    5. "Investigation of the role of the domain linkers in separate site catalysis by Clostridium symbiosum pyruvate phosphate dikinase."
      Wei M., Ye D., Dunaway-Mariano D.
      Biochemistry 40:13466-13473(2001) [PubMed] [Europe PMC] [Abstract]
      Cited for: STRUCTURE.
    6. "Investigation of the catalytic site within the ATP-grasp domain of Clostridium symbiosum pyruvate phosphate dikinase."
      Ye D., Wei M., McGuire M., Huang K., Kapadia G., Herzberg O., Martin B.M., Dunaway-Mariano D.
      J. Biol. Chem. 276:37630-37639(2001) [PubMed] [Europe PMC] [Abstract]
      Cited for: X-RAY CRYSTALLOGRAPHY (2.8 ANGSTROMS), ACTIVE SITE HIS-455.
    7. "Swiveling-domain mechanism for enzymatic phosphotransfer between remote reaction sites."
      Herzberg O., Cheng C.C.H., Kapadia G., McGuire M., Carroll L.J., Noh S.J., Dunaway-Mariano D.
      Proc. Natl. Acad. Sci. U.S.A. 93:2652-2657(1996) [PubMed] [Europe PMC] [Abstract]
      Cited for: X-RAY CRYSTALLOGRAPHY (2.3 ANGSTROMS) IN COMPLEX WITH SUBSTRATE ANALOG, SEQUENCE REVISION, ACTIVE SITE CYS-831, SUBSTRATE BINDING AT ARG-561; ARG-617; GLU-745; GLY-766; THR-767; ASN-768 AND ASP-769, METAL BINDING AT GLU-745 AND ASP-769.
    8. "Location of the phosphate binding site within Clostridium symbiosum pyruvate phosphate dikinase."
      McGuire M., Huang K., Kapadia G., Herzberg O., Dunaway-Mariano D.
      Biochemistry 37:13463-13474(1998) [PubMed] [Europe PMC] [Abstract]
      Cited for: X-RAY CRYSTALLOGRAPHY (2.5 ANGSTROMS).
      Strain: JM101.

    Entry informationi

    Entry nameiPPDK_CLOSY
    AccessioniPrimary (citable) accession number: P22983
    Entry historyi
    Integrated into UniProtKB/Swiss-Prot: August 1, 1991
    Last sequence update: January 23, 2007
    Last modified: October 1, 2014
    This is version 110 of the entry and version 5 of the sequence. [Complete history]
    Entry statusiReviewed (UniProtKB/Swiss-Prot)
    Annotation programProkaryotic Protein Annotation Program

    Miscellaneousi

    Miscellaneous

    The reaction takes place in three steps, each mediated by a carrier histidine residue located on the surface of the central domain. The two first partial reactions are catalyzed at an active site located on the N-terminal domain, and the third partial reaction is catalyzed at an active site located on the C-terminal domain. For catalytic turnover, the central domain swivels from the concave surface of the N-terminal domain to that of the C-terminal domain.

    Keywords - Technical termi

    3D-structure, Direct protein sequencing

    Documents

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

    External Data

    Dasty 3