PPDK_RICBR
ID PPDK_RICBR Reviewed; 878 AA.
AC Q1RH78;
DT 29-MAY-2007, integrated into UniProtKB/Swiss-Prot.
DT 16-MAY-2006, sequence version 1.
DT 03-AUG-2022, entry version 99.
DE RecName: Full=Pyruvate, phosphate dikinase;
DE EC=2.7.9.1 {ECO:0000250|UniProtKB:P22983};
DE AltName: Full=Pyruvate, orthophosphate dikinase;
GN Name=ppdK; OrderedLocusNames=RBE_1205;
OS Rickettsia bellii (strain RML369-C).
OC Bacteria; Proteobacteria; Alphaproteobacteria; Rickettsiales;
OC Rickettsiaceae; Rickettsieae; Rickettsia; belli group.
OX NCBI_TaxID=336407;
RN [1]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=RML369-C;
RX PubMed=16703114; DOI=10.1371/journal.pgen.0020076;
RA Ogata H., La Scola B., Audic S., Renesto P., Blanc G., Robert C.,
RA Fournier P.-E., Claverie J.-M., Raoult D.;
RT "Genome sequence of Rickettsia bellii illuminates the role of amoebae in
RT gene exchanges between intracellular pathogens.";
RL PLoS Genet. 2:733-744(2006).
CC -!- FUNCTION: Catalyzes the reversible phosphorylation of pyruvate and
CC phosphate. {ECO:0000250|UniProtKB:P22983}.
CC -!- CATALYTIC ACTIVITY:
CC Reaction=ATP + phosphate + pyruvate = AMP + diphosphate + H(+) +
CC phosphoenolpyruvate; Xref=Rhea:RHEA:10756, ChEBI:CHEBI:15361,
CC ChEBI:CHEBI:15378, ChEBI:CHEBI:30616, ChEBI:CHEBI:33019,
CC ChEBI:CHEBI:43474, ChEBI:CHEBI:58702, ChEBI:CHEBI:456215; EC=2.7.9.1;
CC Evidence={ECO:0000250|UniProtKB:P22983};
CC -!- COFACTOR:
CC Name=Mg(2+); Xref=ChEBI:CHEBI:18420;
CC Evidence={ECO:0000250|UniProtKB:P11155};
CC -!- ACTIVITY REGULATION: Activated by light-induced dephosphorylation.
CC Inhibited by dark-induced phosphorylation. Both reactions are catalyzed
CC by PDRP1 (By similarity). {ECO:0000250}.
CC -!- SUBUNIT: Homodimer. {ECO:0000250}.
CC -!- DOMAIN: The N-terminal domain contains the ATP/Pi active site, the
CC central domain the pyrophosphate/phosphate carrier histidine, and the
CC C-terminal domain the pyruvate active site. {ECO:0000250}.
CC -!- PTM: Phosphorylation of Thr-457 in the dark inactivates the enzyme.
CC Dephosphorylation upon light stimulation reactivates the enzyme (By
CC similarity). {ECO:0000250}.
CC -!- MISCELLANEOUS: The reaction takes place in three steps, each mediated
CC by a carrier histidine residue located on the surface of the central
CC domain. The two first partial reactions are catalyzed at an active site
CC located on the N-terminal domain, and the third partial reaction is
CC catalyzed at an active site located on the C-terminal domain. For
CC catalytic turnover, the central domain swivels from the concave surface
CC of the N-terminal domain to that of the C-terminal domain.
CC -!- SIMILARITY: Belongs to the PEP-utilizing enzyme family. {ECO:0000305}.
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DR EMBL; CP000087; ABE05286.1; -; Genomic_DNA.
DR RefSeq; WP_011477864.1; NC_007940.1.
DR AlphaFoldDB; Q1RH78; -.
DR SMR; Q1RH78; -.
DR STRING; 336407.RBE_1205; -.
DR EnsemblBacteria; ABE05286; ABE05286; RBE_1205.
DR KEGG; rbe:RBE_1205; -.
DR eggNOG; COG0574; Bacteria.
DR eggNOG; COG1080; Bacteria.
DR HOGENOM; CLU_015345_0_2_5; -.
DR OMA; RRFVQMY; -.
DR OrthoDB; 997616at2; -.
DR Proteomes; UP000001951; Chromosome.
DR GO; GO:0005524; F:ATP binding; IEA:UniProtKB-KW.
DR GO; GO:0016301; F:kinase activity; IEA:UniProtKB-KW.
DR GO; GO:0046872; F:metal ion binding; IEA:UniProtKB-KW.
DR GO; GO:0050242; F:pyruvate, phosphate dikinase activity; IEA:UniProtKB-EC.
DR GO; GO:0016310; P:phosphorylation; IEA:UniProtKB-KW.
DR GO; GO:0006090; P:pyruvate metabolic process; IEA:InterPro.
DR Gene3D; 3.20.20.60; -; 1.
DR Gene3D; 3.30.1490.20; -; 1.
DR InterPro; IPR013815; ATP_grasp_subdomain_1.
DR InterPro; IPR008279; PEP-util_enz_mobile_dom.
DR InterPro; IPR018274; PEP_util_AS.
DR InterPro; IPR000121; PEP_util_C.
DR InterPro; IPR023151; PEP_util_CS.
DR InterPro; IPR036637; Phosphohistidine_dom_sf.
DR InterPro; IPR002192; PPDK_AMP/ATP-bd.
DR InterPro; IPR010121; Pyruvate_phosphate_dikinase.
DR InterPro; IPR015813; Pyrv/PenolPyrv_Kinase-like_dom.
DR InterPro; IPR040442; Pyrv_Kinase-like_dom_sf.
DR PANTHER; PTHR22931; PTHR22931; 1.
DR Pfam; PF00391; PEP-utilizers; 1.
DR Pfam; PF02896; PEP-utilizers_C; 1.
DR Pfam; PF01326; PPDK_N; 3.
DR PIRSF; PIRSF000853; PPDK; 1.
DR SUPFAM; SSF51621; SSF51621; 1.
DR SUPFAM; SSF52009; SSF52009; 1.
DR TIGRFAMs; TIGR01828; pyru_phos_dikin; 1.
DR PROSITE; PS00742; PEP_ENZYMES_2; 1.
DR PROSITE; PS00370; PEP_ENZYMES_PHOS_SITE; 1.
PE 3: Inferred from homology;
KW ATP-binding; Kinase; Magnesium; Metal-binding; Nucleotide-binding;
KW Phosphoprotein; Transferase.
FT CHAIN 1..878
FT /note="Pyruvate, phosphate dikinase"
FT /id="PRO_0000289277"
FT REGION 1..347
FT /note="N-terminal"
FT REGION 348..404
FT /note="Linker 1"
FT REGION 405..502
FT /note="Central"
FT REGION 503..537
FT /note="Linker 2"
FT REGION 538..878
FT /note="C-terminal"
FT ACT_SITE 459
FT /note="Tele-phosphohistidine intermediate"
FT /evidence="ECO:0000250|UniProtKB:P11155"
FT ACT_SITE 835
FT /note="Proton donor"
FT /evidence="ECO:0000250|UniProtKB:P11155"
FT BINDING 96
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /evidence="ECO:0000255"
FT BINDING 565
FT /ligand="substrate"
FT /evidence="ECO:0000250|UniProtKB:P11155"
FT BINDING 621
FT /ligand="substrate"
FT /evidence="ECO:0000250|UniProtKB:P11155"
FT BINDING 749
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /evidence="ECO:0000250|UniProtKB:P11155"
FT BINDING 749
FT /ligand="substrate"
FT /evidence="ECO:0000250|UniProtKB:P11155"
FT BINDING 770
FT /ligand="substrate"
FT /evidence="ECO:0000250|UniProtKB:P11155"
FT BINDING 771
FT /ligand="substrate"
FT /evidence="ECO:0000250|UniProtKB:P11155"
FT BINDING 772
FT /ligand="substrate"
FT /evidence="ECO:0000250|UniProtKB:P11155"
FT BINDING 773
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /evidence="ECO:0000250|UniProtKB:P11155"
FT BINDING 773
FT /ligand="substrate"
FT /evidence="ECO:0000250|UniProtKB:P11155"
FT MOD_RES 457
FT /note="Phosphothreonine; by PDRP1"
FT /evidence="ECO:0000250"
SQ SEQUENCE 878 AA; 97899 MW; 695C07C45EBD12C4 CRC64;
MKKLIYYFGS NGSDGNASMK DILGNKGAGL AEMSNLKLPI PDGFTITTEL CNYFYTHDNS
FPKNFRNELR TAVEKLEATT GKVFGSTKNP LLLSVRSGSI VSMPGMMDTI LNLGMNDEVC
AALGEVCKDK RFALDSYKRF LEMYGATVLS IPSDLFEQIY ERHKIQADIY RDSDVTPQLL
EKIIEDFKKL HVKYAEKLIT DPYEQLESAI KAVLNSWMSN RAVIYRKINN ISESSGTAIN
IQSMVFGNLS KTSATGVIFT RSPSTGEKKL FGEFLINAQG EDIVSGTRTP LPIISDDSNS
MKATMPKVFD ELSKISETLE KHYLDMQDIE FTIENSKLYI LQTRTAKRTA IAAIKIAVQM
VEEKLISKEQ ALMRIDPESL NQLLHTRIDY SKGLTSIADG LPASPGAATG IIVFSPYDAE
KLSHHHKVIL VRHDTSPEDI NGMHVSSGIL TIRGGMTSHA AVVARGMGKP CVCGTNNLVI
DEKKQTLIAG DLILKQDDII TIDGGTGKVF LGAVPLIQPT FSEESKLILE WADETSKLKI
RTNAETVSDA LVSVKFGAKG IGLCRSEHMF FDKNKIPLVR EMIIAPDIDR RKLAVQKLLP
LQTQDFKALF RVMGDKPVNI RLLDPPLHEF LPTTEEDKKN LASSLNLPLS MINQRLHAMH
EVNPMLGHRG CRLGICSPEI YQMQVEAIFT AIFELHKEEN IECKLELMIP LISNVNEIKK
LKGDIYEMIH ELEERYEHKF SFSLGTMIEL PRAALNSKKI AEEVDYFSFG TNDLTQTTYG
ISRDDIASFL PYYLEERIFE SDPFTTLDEE GVGELIEIAI KRGKSSNPSL KLGACGEHAG
HPASIEFFHK MNLDYVSCSP YRIPIARIAA AQAKIKHG
