PPDK_RICTY
ID PPDK_RICTY Reviewed; 880 AA.
AC Q68WP2;
DT 29-MAY-2007, integrated into UniProtKB/Swiss-Prot.
DT 11-OCT-2004, sequence version 1.
DT 03-AUG-2022, entry version 100.
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=RT0478;
OS Rickettsia typhi (strain ATCC VR-144 / Wilmington).
OC Bacteria; Proteobacteria; Alphaproteobacteria; Rickettsiales;
OC Rickettsiaceae; Rickettsieae; Rickettsia; typhus group.
OX NCBI_TaxID=257363;
RN [1]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=ATCC VR-144 / Wilmington;
RX PubMed=15317790; DOI=10.1128/jb.186.17.5842-5855.2004;
RA McLeod M.P., Qin X., Karpathy S.E., Gioia J., Highlander S.K., Fox G.E.,
RA McNeill T.Z., Jiang H., Muzny D., Jacob L.S., Hawes A.C., Sodergren E.,
RA Gill R., Hume J., Morgan M., Fan G., Amin A.G., Gibbs R.A., Hong C.,
RA Yu X.-J., Walker D.H., Weinstock G.M.;
RT "Complete genome sequence of Rickettsia typhi and comparison with sequences
RT of other Rickettsiae.";
RL J. Bacteriol. 186:5842-5855(2004).
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; AE017197; AAU03950.1; -; Genomic_DNA.
DR RefSeq; WP_011190933.1; NC_006142.1.
DR AlphaFoldDB; Q68WP2; -.
DR SMR; Q68WP2; -.
DR STRING; 257363.RT0478; -.
DR EnsemblBacteria; AAU03950; AAU03950; RT0478.
DR KEGG; rty:RT0478; -.
DR eggNOG; COG0574; Bacteria.
DR eggNOG; COG1080; Bacteria.
DR HOGENOM; CLU_015345_0_2_5; -.
DR OMA; RRFVQMY; -.
DR OrthoDB; 997616at2; -.
DR Proteomes; UP000000604; 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; 2.
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..880
FT /note="Pyruvate, phosphate dikinase"
FT /id="PRO_0000289279"
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..879
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; 98165 MW; FFFE55AEEA138B34 CRC64;
MNKLIYYFGN NGSDGNASMK NILGNKGAGL AEMSNLKLPI PNGFTITTEL CNYFYKHNNN
LPKNFQNELQ QAITKLEITT GKIFGSTTSN PLLLSVRSGS TVSMPGMMDT ILNLGMNNEV
CNALADSCGN KLFALDSYRR FLEMYGSTVL SIPSDLFEQI YEKHKVQADI YKDSDITVEL
LEKIIDDFKR LHIKYTKQLI KDPYEQLESA IKAVLYSWKN NRAIVYRKLN NISEDFGTAI
NIQEMVFGNL GKTSATGVVF TRSPSTGEKK LFGEFLINAQ GEDIVSGTRT PMPIIANDSN
SMQAMMPEVF TKLSQIAKKL EEHYLDMQDI EFTIENNKLY ILQTRTAKRT AIAAINIAVQ
MVEEKLISKE QALMRIDPES LNQLLHTRID YSKKLTAIAE GLPASPGAAT GIVVFSPYDA
EKLSHHHKVI LVRHDTSPED INGMHVASGI LTIRGGMTSH AAVVARGMGK PCVCGTNNLS
IDEQKQILIA GDIVIKQGDI ITIDGGSGKI FLGEMPLIQP TFSEESTLIL DWADEISSLK
VRANAETVND ALVSIKFGAQ GIGLCRSEHM FFDKNKIPLV REMIIAPDIE RRQCALQKLL
PLQTEDFKAL FRVMKNKPVN IRLLDPPLHE FLPTTDEDKK NLAHSLNLPL SMIHQRLHAM
HEVNPMLGHR GCRLGICLPE IYQMQIEAIL TAIFELHKKE HIESNLELMI PLISNVAEIK
KLKMDIYAVV KKLEQRYSYK FSFTLGTMIE LPRAALGSKK IAKEVDYFSF GTNDLTQTTY
GISRDDIASF LPYYLEEKIF ESDPFTTLDE EGVGELIKIA IKRGKSSNAN LKLGACGEHA
GNPTSIAFFH KMNLNYVSCS PYRIPIARIA AAQAKIKQGS
