PPDK_RHIME
ID PPDK_RHIME Reviewed; 898 AA.
AC Q59754; Q59755; Q59756;
DT 30-MAY-2000, integrated into UniProtKB/Swiss-Prot.
DT 30-MAY-2000, sequence version 2.
DT 03-AUG-2022, entry version 145.
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; Synonyms=podA; OrderedLocusNames=R00932; ORFNames=SMc00025;
OS Rhizobium meliloti (strain 1021) (Ensifer meliloti) (Sinorhizobium
OS meliloti).
OC Bacteria; Proteobacteria; Alphaproteobacteria; Hyphomicrobiales;
OC Rhizobiaceae; Sinorhizobium/Ensifer group; Sinorhizobium.
OX NCBI_TaxID=266834;
RN [1]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=1021;
RX PubMed=11481430; DOI=10.1073/pnas.161294398;
RA Capela D., Barloy-Hubler F., Gouzy J., Bothe G., Ampe F., Batut J.,
RA Boistard P., Becker A., Boutry M., Cadieu E., Dreano S., Gloux S.,
RA Godrie T., Goffeau A., Kahn D., Kiss E., Lelaure V., Masuy D., Pohl T.,
RA Portetelle D., Puehler A., Purnelle B., Ramsperger U., Renard C.,
RA Thebault P., Vandenbol M., Weidner S., Galibert F.;
RT "Analysis of the chromosome sequence of the legume symbiont Sinorhizobium
RT meliloti strain 1021.";
RL Proc. Natl. Acad. Sci. U.S.A. 98:9877-9882(2001).
RN [2]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=1021;
RX PubMed=11474104; DOI=10.1126/science.1060966;
RA Galibert F., Finan T.M., Long S.R., Puehler A., Abola P., Ampe F.,
RA Barloy-Hubler F., Barnett M.J., Becker A., Boistard P., Bothe G.,
RA Boutry M., Bowser L., Buhrmester J., Cadieu E., Capela D., Chain P.,
RA Cowie A., Davis R.W., Dreano S., Federspiel N.A., Fisher R.F., Gloux S.,
RA Godrie T., Goffeau A., Golding B., Gouzy J., Gurjal M., Hernandez-Lucas I.,
RA Hong A., Huizar L., Hyman R.W., Jones T., Kahn D., Kahn M.L., Kalman S.,
RA Keating D.H., Kiss E., Komp C., Lelaure V., Masuy D., Palm C., Peck M.C.,
RA Pohl T.M., Portetelle D., Purnelle B., Ramsperger U., Surzycki R.,
RA Thebault P., Vandenbol M., Vorhoelter F.J., Weidner S., Wells D.H.,
RA Wong K., Yeh K.-C., Batut J.;
RT "The composite genome of the legume symbiont Sinorhizobium meliloti.";
RL Science 293:668-672(2001).
RN [3]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA] OF 77-190; 202-266 AND 711-758.
RC STRAIN=RCR2011 / SU47;
RX PubMed=9168612; DOI=10.1099/00221287-143-5-1639;
RA Oesteraas M., Driscoll B.T., Finan T.M.;
RT "Increased pyruvate orthophosphate dikinase activity results in an
RT alternative gluconeogenic pathway in Rhizobium (Sinorhizobium) meliloti.";
RL Microbiology 143:1639-1648(1997).
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-466 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; AL591688; CAC45504.1; -; Genomic_DNA.
DR EMBL; U61376; AAB58818.1; -; Genomic_DNA.
DR EMBL; U61377; AAB58820.1; -; Genomic_DNA.
DR EMBL; U61378; AAB58819.1; -; Genomic_DNA.
DR RefSeq; NP_385038.1; NC_003047.1.
DR RefSeq; WP_010968929.1; NC_003047.1.
DR AlphaFoldDB; Q59754; -.
DR SMR; Q59754; -.
DR STRING; 266834.SMc00025; -.
DR PRIDE; Q59754; -.
DR EnsemblBacteria; CAC45504; CAC45504; SMc00025.
DR GeneID; 61602397; -.
DR KEGG; sme:SMc00025; -.
DR PATRIC; fig|266834.11.peg.2330; -.
DR eggNOG; COG0574; Bacteria.
DR eggNOG; COG1080; Bacteria.
DR HOGENOM; CLU_015345_0_2_5; -.
DR OMA; RRFVQMY; -.
DR Proteomes; UP000001976; 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; Reference proteome; Transferase.
FT CHAIN 1..898
FT /note="Pyruvate, phosphate dikinase"
FT /id="PRO_0000147047"
FT REGION 1..355
FT /note="N-terminal"
FT REGION 356..412
FT /note="Linker 1"
FT REGION 413..511
FT /note="Central"
FT REGION 512..546
FT /note="Linker 2"
FT REGION 547..898
FT /note="C-terminal"
FT ACT_SITE 468
FT /note="Tele-phosphohistidine intermediate"
FT /evidence="ECO:0000250|UniProtKB:P11155"
FT ACT_SITE 844
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 574
FT /ligand="substrate"
FT /evidence="ECO:0000250|UniProtKB:P11155"
FT BINDING 630
FT /ligand="substrate"
FT /evidence="ECO:0000250|UniProtKB:P11155"
FT BINDING 758
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /evidence="ECO:0000250|UniProtKB:P11155"
FT BINDING 758
FT /ligand="substrate"
FT /evidence="ECO:0000250|UniProtKB:P11155"
FT BINDING 779
FT /ligand="substrate"
FT /evidence="ECO:0000250|UniProtKB:P11155"
FT BINDING 780
FT /ligand="substrate"
FT /evidence="ECO:0000250|UniProtKB:P11155"
FT BINDING 781
FT /ligand="substrate"
FT /evidence="ECO:0000250|UniProtKB:P11155"
FT BINDING 782
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /evidence="ECO:0000250|UniProtKB:P11155"
FT BINDING 782
FT /ligand="substrate"
FT /evidence="ECO:0000250|UniProtKB:P11155"
FT MOD_RES 466
FT /note="Phosphothreonine; by PDRP1"
FT /evidence="ECO:0000250"
FT CONFLICT 88
FT /note="N -> I (in Ref. 3; AAB58818)"
FT /evidence="ECO:0000305"
FT CONFLICT 128
FT /note="G -> D (in Ref. 3; AAB58818)"
FT /evidence="ECO:0000305"
FT CONFLICT 711..712
FT /note="AV -> LL (in Ref. 3)"
FT /evidence="ECO:0000305"
FT CONFLICT 722..723
FT /note="GL -> V (in Ref. 3)"
FT /evidence="ECO:0000305"
FT CONFLICT 736..738
FT /note="AVA -> DGR (in Ref. 3; AAB58820)"
FT /evidence="ECO:0000305"
SQ SEQUENCE 898 AA; 97561 MW; D055560636388CD5 CRC64;
MAKWVYTFGA GQAEGSAEDR DRLGGKGANL AEMCNLGLPV PPGLTIVTAA CNSYLEKGRS
MPEGLREQVR EGITRMEKIT GRVFGDTNRP LLLSVRSGAR ASMPGMMDTV LNLGLNDQSV
HALGHDAGDA RFAWDSYRRF IQMYGDVVMG VDHEVFEEVL EDEKARLGHE QDTELSAVEW
QHVISRYKEA IEEVLGLPFP QDPEVQLWGA IGAVFSSWMN PRAITYRHLH GIPAGWGTAV
NVQAMVFGNL GNSSATGVAF TRNPSTGEKE LYGEFLVNAQ GEDVVAGIRT PQNITEAARI
ASGSDKPSLE KLMPEAFAEF EKICNALERH YRDMQDIEFT IERGKLWMLQ TRSGKRTAKS
ALKIAVDMAE EGLISKEEAV ARIDPASLDQ LLHPTIDPHA RRDIIGSGLP ASPGAATGEI
VFSSDEAVQA VKEGRKVILV RVETSPEDIH GMHAAEGILT TRGGMTSHAA VVARGMGTPC
VSGAGSIRVD QRNELLIAAS VTLRKGDVIT IDGSSGQVLK GEIPMLQPEL SGDFGKIMQW
ADASRRMTVR TNAETPADAR AARSFGAEGI GLCRTEHMFF EDDRINVMRE MILAEDEAGR
RTALAKLLPM QRSDFVELFS IMHGLPVTIR LLDPPLHEFL PKTDEEIAEV ARVLTIDPAE
LRQRVDALHE FNPMLGHRGC RLAISYPEIA EMQARAIFEA AVQAAHDTGA AVVPEIMVPL
VGLRAELDYV KARIEAVAKE VIGEAGVNID YLIGTMIELP RAALRADTIA ESADFFSFGT
NDLTQTTFGI SRDDAALFLA TYQQKGIIEQ DPFVSLDFEG VGELIQIAAE RGRRTKNGLK
LGICGEHGGD PASIRFCEEA GLDYVSCSPF RVPIARLAAA QATINGREVA EVQALAAS
