ID A2TC90_SPHYA Unreviewed; 888 AA.
AC A2TC90;
DT 06-MAR-2007, integrated into UniProtKB/TrEMBL.
DT 06-MAR-2007, sequence version 1.
DT 27-MAR-2024, entry version 92.
DE RecName: Full=Pyruvate, phosphate dikinase {ECO:0000256|ARBA:ARBA00020138, ECO:0000256|PIRNR:PIRNR000853};
DE EC=2.7.9.1 {ECO:0000256|ARBA:ARBA00011994, ECO:0000256|PIRNR:PIRNR000853};
GN Name=ppdK {ECO:0000313|EMBL:ABM91743.1};
GN ORFNames=IH86_11445 {ECO:0000313|EMBL:KFD28034.1};
OS Sphingobium yanoikuyae (Sphingomonas yanoikuyae).
OC Bacteria; Pseudomonadota; Alphaproteobacteria; Sphingomonadales;
OC Sphingomonadaceae; Sphingobium.
OX NCBI_TaxID=13690 {ECO:0000313|EMBL:ABM91743.1};
RN [1] {ECO:0000313|EMBL:ABM91743.1}
RP NUCLEOTIDE SEQUENCE.
RC STRAIN=B1 {ECO:0000313|EMBL:ABM91743.1};
RA Ni Chadhain S.M., Moritz E., Kim E., Zylstra G.J.;
RL Submitted (NOV-2006) to the EMBL/GenBank/DDBJ databases.
RN [2] {ECO:0000313|EMBL:ABM91743.1}
RP NUCLEOTIDE SEQUENCE.
RC STRAIN=B1 {ECO:0000313|EMBL:ABM91743.1};
RX PubMed=17647036; DOI=10.1007/s10295-007-0235-3;
RA Chadhain S.M., Moritz E.M., Kim E., Zylstra G.J.;
RT "Identification, cloning, and characterization of a multicomponent biphenyl
RT dioxygenase from Sphingobium yanoikuyae B1.";
RL J. Ind. Microbiol. Biotechnol. 34:605-613(2007).
RN [3] {ECO:0000313|EMBL:KFD28034.1, ECO:0000313|Proteomes:UP000029230}
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=B1 {ECO:0000313|EMBL:KFD28034.1,
RC ECO:0000313|Proteomes:UP000029230};
RA Zhao Q., Zhang X., Wang W., Peng H., Hu H.;
RT "Genome Sequence of Sphingobium yanoikuyae B1, a Polycyclic Aromatic
RT Hydrocarbon Degrading Strain.";
RL Submitted (JUL-2014) to the EMBL/GenBank/DDBJ databases.
CC -!- FUNCTION: Catalyzes the reversible phosphorylation of pyruvate and
CC phosphate. {ECO:0000256|ARBA:ARBA00003144}.
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:0000256|PIRNR:PIRNR000853};
CC -!- COFACTOR:
CC Name=Mg(2+); Xref=ChEBI:CHEBI:18420;
CC Evidence={ECO:0000256|ARBA:ARBA00001946,
CC ECO:0000256|PIRNR:PIRNR000853, ECO:0000256|PIRSR:PIRSR000853-3};
CC -!- SIMILARITY: Belongs to the PEP-utilizing enzyme family.
CC {ECO:0000256|ARBA:ARBA00007837, ECO:0000256|PIRNR:PIRNR000853}.
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DR EMBL; EF152282; ABM91743.1; -; Genomic_DNA.
DR EMBL; JPOU01000022; KFD28034.1; -; Genomic_DNA.
DR RefSeq; WP_037508587.1; NZ_KL662202.1.
DR AlphaFoldDB; A2TC90; -.
DR PATRIC; fig|13690.11.peg.2312; -.
DR Proteomes; UP000029230; Unassembled WGS sequence.
DR GO; GO:0005524; F:ATP binding; IEA:UniProtKB-UniRule.
DR GO; GO:0016301; F:kinase activity; IEA:UniProtKB-KW.
DR GO; GO:0046872; F:metal ion binding; IEA:UniProtKB-UniRule.
DR GO; GO:0050242; F:pyruvate, phosphate dikinase activity; IEA:UniProtKB-UniRule.
DR GO; GO:0016310; P:phosphorylation; IEA:UniProtKB-KW.
DR GO; GO:0006090; P:pyruvate metabolic process; IEA:UniProtKB-UniRule.
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; 3.
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 {ECO:0000256|ARBA:ARBA00022840};
KW Kinase {ECO:0000313|EMBL:ABM91743.1};
KW Magnesium {ECO:0000256|ARBA:ARBA00022842, ECO:0000256|PIRSR:PIRSR000853-3};
KW Metal-binding {ECO:0000256|ARBA:ARBA00022723,
KW ECO:0000256|PIRSR:PIRSR000853-3};
KW Nucleotide-binding {ECO:0000256|ARBA:ARBA00022741};
KW Pyruvate {ECO:0000313|EMBL:ABM91743.1};
KW Transferase {ECO:0000256|ARBA:ARBA00022679, ECO:0000313|EMBL:KFD28034.1}.
FT DOMAIN 23..59
FT /note="Pyruvate phosphate dikinase AMP/ATP-binding"
FT /evidence="ECO:0000259|Pfam:PF01326"
FT DOMAIN 63..302
FT /note="Pyruvate phosphate dikinase AMP/ATP-binding"
FT /evidence="ECO:0000259|Pfam:PF01326"
FT DOMAIN 319..372
FT /note="Pyruvate phosphate dikinase AMP/ATP-binding"
FT /evidence="ECO:0000259|Pfam:PF01326"
FT DOMAIN 435..517
FT /note="PEP-utilising enzyme mobile"
FT /evidence="ECO:0000259|Pfam:PF00391"
FT DOMAIN 533..883
FT /note="PEP-utilising enzyme C-terminal"
FT /evidence="ECO:0000259|Pfam:PF02896"
FT ACT_SITE 469
FT /note="Tele-phosphohistidine intermediate"
FT /evidence="ECO:0000256|PIRSR:PIRSR000853-1"
FT ACT_SITE 845
FT /note="Proton donor"
FT /evidence="ECO:0000256|PIRSR:PIRSR000853-1"
FT BINDING 575
FT /ligand="substrate"
FT /evidence="ECO:0000256|PIRSR:PIRSR000853-2"
FT BINDING 631
FT /ligand="substrate"
FT /evidence="ECO:0000256|PIRSR:PIRSR000853-2"
FT BINDING 759
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /evidence="ECO:0000256|PIRSR:PIRSR000853-3"
FT BINDING 759
FT /ligand="substrate"
FT /evidence="ECO:0000256|PIRSR:PIRSR000853-2"
FT BINDING 780
FT /ligand="substrate"
FT /evidence="ECO:0000256|PIRSR:PIRSR000853-2"
FT BINDING 781
FT /ligand="substrate"
FT /evidence="ECO:0000256|PIRSR:PIRSR000853-2"
FT BINDING 782
FT /ligand="substrate"
FT /evidence="ECO:0000256|PIRSR:PIRSR000853-2"
FT BINDING 783
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /evidence="ECO:0000256|PIRSR:PIRSR000853-3"
FT BINDING 783
FT /ligand="substrate"
FT /evidence="ECO:0000256|PIRSR:PIRSR000853-2"
SQ SEQUENCE 888 AA; 96003 MW; 0FC475A5AF0B134A CRC64;
MKTVYTFGPG IAHDDSRARD KAVVGGKGAN LGEMARIGLP VPPGFTITTE ECLHFLRDRH
SQSARLDGEV RSALTHIERT VGKRFGDRHD PLLVSVRSGA RVSMPGMMDT ILNLGLNDQT
VRGLAASSGD ERFAWDSYRR FVQMYASVVL GIDHARFEDA LEKAKEDRGV SQDVDLSATD
LRDLIGEFFG IVEAERGAPF PQDVDEQLAS AIAAVFESWE SDRAKVYRRL NGIPGEWGTA
VNVQAMVFGN LGETSATGVA FTRNPATGDK AYYGEWLVNA QGEDVVAGIR TPQYLTLAAR
TAAGAKLPSM EEALPAVFTE LARLFELLEL HYQDMQDIEF TVERGKLYIL QTRSGKRTAK
AALKIAVDMV EEGLIAEEAA IRRIDPASLD QLLHPTLDPD APRTLLGSGL PASPGAASGA
VVFDADTAAV RAELGENVIL VRQETSPDDI HGMHVARGIL TAKGGMTSHA AVVARGMGRP
CVSGASSLSI DYQARSAEIG GVHIAEGDLI TIDGSTGEIF QGALPTVMPE LDREFATVMA
WADRHRRMNV RTNAETPADC EVARQFGAEG IGLCRTEHMF FDGERINFMR QMILAANVAE
RLVALDRLLP EQRSDFARIF EIMQGLPVTV RLLDPPLHEF LPHSESEFTE LSAAVGIGVD
QLRRRAEELA ESNPMLGHRG CRLGVVYPEI YEMQARAIFE AACAVSRETG QPVVPEIMIP
LVGTARELDM LKRIVIGVSE AVFAEQGLTV EFTVGTMIEL PRAALVADEI AKVGEFFSFG
TNDLTQTTLG ISRDDAGRFL GSYIDKGIFA TDPFVSIDVE GVGKLIAMAA RLGREARPDI
KLGICGEHGG DPASIAFCDR VGLDYVSASP FRVPIARLAA AQSALAAT
//
