ID PPDK_RICPR Reviewed; 880 AA.
AC Q9ZD55;
DT 30-MAY-2000, integrated into UniProtKB/Swiss-Prot.
DT 01-MAY-1999, sequence version 1.
DT 27-MAR-2024, entry version 134.
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=RP492;
OS Rickettsia prowazekii (strain Madrid E).
OC Bacteria; Pseudomonadota; Alphaproteobacteria; Rickettsiales;
OC Rickettsiaceae; Rickettsieae; Rickettsia; typhus group.
OX NCBI_TaxID=272947;
RN [1]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=Madrid E;
RX PubMed=9823893; DOI=10.1038/24094;
RA Andersson S.G.E., Zomorodipour A., Andersson J.O., Sicheritz-Ponten T.,
RA Alsmark U.C.M., Podowski R.M., Naeslund A.K., Eriksson A.-S., Winkler H.H.,
RA Kurland C.G.;
RT "The genome sequence of Rickettsia prowazekii and the origin of
RT mitochondria.";
RL Nature 396:133-140(1998).
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-458 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; AJ235272; CAA14944.1; -; Genomic_DNA.
DR PIR; F71652; F71652.
DR RefSeq; NP_220868.1; NC_000963.1.
DR RefSeq; WP_004597734.1; NC_000963.1.
DR AlphaFoldDB; Q9ZD55; -.
DR SMR; Q9ZD55; -.
DR STRING; 272947.gene:17555572; -.
DR EnsemblBacteria; CAA14944; CAA14944; CAA14944.
DR GeneID; 57569616; -.
DR KEGG; rpr:RP492; -.
DR PATRIC; fig|272947.5.peg.501; -.
DR eggNOG; COG0574; Bacteria.
DR eggNOG; COG1080; Bacteria.
DR HOGENOM; CLU_015345_0_2_5; -.
DR OrthoDB; 9765468at2; -.
DR Proteomes; UP000002480; 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; 1.20.80.30; -; 1.
DR Gene3D; 3.30.1490.20; ATP-grasp fold, A domain; 1.
DR Gene3D; 3.30.470.20; ATP-grasp fold, B domain; 1.
DR Gene3D; 3.20.20.60; Phosphoenolpyruvate-binding domains; 1.
DR Gene3D; 3.50.30.10; Phosphohistidine domain; 1.
DR Gene3D; 1.10.189.10; Pyruvate Phosphate Dikinase, domain 2; 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 NCBIfam; TIGR01828; pyru_phos_dikin; 1.
DR PANTHER; PTHR22931; PHOSPHOENOLPYRUVATE DIKINASE-RELATED; 1.
DR PANTHER; PTHR22931:SF9; PYRUVATE, PHOSPHATE DIKINASE 1, CHLOROPLASTIC; 1.
DR Pfam; PF00391; PEP-utilizers; 1.
DR Pfam; PF02896; PEP-utilizers_C; 1.
DR Pfam; PF01326; PPDK_N; 2.
DR PIRSF; PIRSF000853; PPDK; 1.
DR SUPFAM; SSF56059; Glutathione synthetase ATP-binding domain-like; 1.
DR SUPFAM; SSF51621; Phosphoenolpyruvate/pyruvate domain; 1.
DR SUPFAM; SSF52009; Phosphohistidine domain; 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; Reference proteome; Transferase.
FT CHAIN 1..880
FT /note="Pyruvate, phosphate dikinase"
FT /id="PRO_0000147049"
FT REGION 1..348
FT /note="N-terminal"
FT REGION 349..405
FT /note="Linker 1"
FT REGION 406..503
FT /note="Central"
FT REGION 504..538
FT /note="Linker 2"
FT REGION 539..880
FT /note="C-terminal"
FT ACT_SITE 460
FT /note="Tele-phosphohistidine intermediate"
FT /evidence="ECO:0000250|UniProtKB:P11155"
FT ACT_SITE 836
FT /note="Proton donor"
FT /evidence="ECO:0000250|UniProtKB:P11155"
FT BINDING 97
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /evidence="ECO:0000255"
FT BINDING 566
FT /ligand="substrate"
FT /evidence="ECO:0000250|UniProtKB:P11155"
FT BINDING 622
FT /ligand="substrate"
FT /evidence="ECO:0000250|UniProtKB:P11155"
FT BINDING 750
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /evidence="ECO:0000250|UniProtKB:P11155"
FT BINDING 750
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="substrate"
FT /evidence="ECO:0000250|UniProtKB:P11155"
FT BINDING 774
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /evidence="ECO:0000250|UniProtKB:P11155"
FT BINDING 774
FT /ligand="substrate"
FT /evidence="ECO:0000250|UniProtKB:P11155"
FT MOD_RES 458
FT /note="Phosphothreonine; by PDRP1"
FT /evidence="ECO:0000250"
SQ SEQUENCE 880 AA; 98302 MW; C8CB877B7EAFFAF3 CRC64;
MNKLIYYFGN NGSDGNASMN NILGNKGAGL AEMSNLKLPI PNGFTITTEL CNYFYKHNNN
FPKNFQNELQ QAISKLEVTT GKIFGSTTSN PLLLSVRSGS TVSMPGMMDT ILNLGMNNEV
CNALADACGN KLFALDSYRR FLEMYGSTVL SIPSDLFEQI YENHKIQADI YKDSDITVEL
LEKIIDDFKR LHIKYDKQLI NDPYEQLESA IKAVLYSWKN NRAIIYRKLN NISEDFGTAI
NIQEMVFGNL GKTSATGVAF TRSPSTGEKK LFGEFLINAQ GEDIVSGTRT PMPIIANDSN
SMQAMMPEVF KELSQIAKKL EEHYLDMQDI EFTIENNKLY ILQTRTAKRT AIAAINIAVQ
MVKEKLISKE QALMRIDPES LNQLLHTRID YSKGLTSIAE GLPASPGAAT GIVVFSPYDA
EKLSHHHKVI LVRHDTSPED INGMHVSSGI LTIRGGMTSH AAVVARGMGK PCVCGTNNLS
IDEQKQILIA GDIVIKQGDI ITIDGGSGKI FLGEMPLIQP TFSEESKLIL DWADEISSLK
VRANAETVND ALVSIKFGAQ GIGLCRSEHM FFDKNKIPLV REMIIAPDIE RRQCALQKLL
PLQTEDFKSL FRVMKNKPVN IRLLDPPLHE FLPTTEEDKK NLANSLNLPL SMIHQRLHAM
HEVNPMLGHR GCRLGICLPE IYQMQIEAIF TAIFELHKKE HIESNLELMI PLISNVAEIK
KLKMYIYEVV QELEQRYSYK FSFTLGTMIE LPRAALESKK IAKEVDYFSF GTNDLTQTTY
GISRDDIASF LPYYLEEKIF ESDPFTTLDE EGVGELIEIA IKRGKSSNAN LKLGACGEHA
GNPTSIAFFH KANLNYVSCS PYRIPIARIA AAQAKIKQGS
//
