PPDK_FLABI
ID PPDK_FLABI Reviewed; 953 AA.
AC Q39735;
DT 15-JUL-1998, integrated into UniProtKB/Swiss-Prot.
DT 01-NOV-1996, sequence version 1.
DT 03-AUG-2022, entry version 122.
DE RecName: Full=Pyruvate, phosphate dikinase, chloroplastic;
DE EC=2.7.9.1;
DE AltName: Full=Cold-sensitive pyruvate, orthophosphate dikinase;
DE AltName: Full=Pyruvate, orthophosphate dikinase;
DE Flags: Precursor;
OS Flaveria bidentis (Coastal plain yellowtops) (Ethulia bidentis).
OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta;
OC Spermatophyta; Magnoliopsida; eudicotyledons; Gunneridae; Pentapetalae;
OC asterids; campanulids; Asterales; Asteraceae; Asteroideae;
OC Heliantheae alliance; Tageteae; Flaveria.
OX NCBI_TaxID=4224;
RN [1]
RP NUCLEOTIDE SEQUENCE [MRNA], AND PROTEIN SEQUENCE OF 78-86.
RC TISSUE=Leaf;
RX PubMed=7766886; DOI=10.1007/bf00037024;
RA Usami S., Ohta S., Komari T., Burnell J.N.;
RT "Cold stability of pyruvate, orthophosphate dikinase of Flaveria brownii.";
RL Plant Mol. Biol. 27:969-980(1995).
RN [2]
RP BIOPHYSICOCHEMICAL PROPERTIES, ACTIVITY REGULATION, AND MUTAGENESIS OF
RP GLN-869; ALA-873; ILE-885 AND ILE-952.
RX PubMed=9038349; DOI=10.1016/s0014-5793(97)00015-x;
RA Ohta S., Usami S., Ueki J., Kumashiro T., Komari T., Burnell J.N.;
RT "Identification of the amino acid residues responsible for cold tolerance
RT in Flaveria brownii pyruvate,orthophosphate dikinase.";
RL FEBS Lett. 403:5-9(1997).
CC -!- FUNCTION: Formation of phosphoenolpyruvate, which is the primary
CC acceptor of CO(2) in C4 and some Crassulacean acid metabolism plants.
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 -!- 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). Inactivated by cold due to the dissociation
CC of the homotetramer. {ECO:0000250, ECO:0000269|PubMed:9038349}.
CC -!- BIOPHYSICOCHEMICAL PROPERTIES:
CC Kinetic parameters:
CC KM=73 uM for pyruvate {ECO:0000269|PubMed:9038349};
CC KM=25 uM for ATP {ECO:0000269|PubMed:9038349};
CC KM=118 uM for phosphate {ECO:0000269|PubMed:9038349};
CC Temperature dependence:
CC Loss of activity below 10 degrees Celsius.
CC {ECO:0000269|PubMed:9038349};
CC -!- PATHWAY: Photosynthesis; C4 acid pathway.
CC -!- SUBUNIT: Homotetramer.
CC -!- SUBCELLULAR LOCATION: Plastid, chloroplast.
CC -!- DOMAIN: The N-terminal domain contains the ATP/Pi binding site, the
CC central domain the pyrophosphate/phosphate carrier histidine, and the
CC C-terminal domain the pyruvate binding site. {ECO:0000250}.
CC -!- DOMAIN: The C-terminal domain (829-953) is involved in cold
CC sensitivity.
CC -!- PTM: Phosphorylation of Thr-533 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, mediated by a
CC phosphocarrier 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 (By
CC similarity). {ECO:0000250}.
CC -!- MISCELLANEOUS: A short cytoplasmic isoform may be produced by
CC alternative promoter usage. {ECO:0000250}.
CC -!- SIMILARITY: Belongs to the PEP-utilizing enzyme family. {ECO:0000305}.
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DR EMBL; U08400; AAA86941.1; -; mRNA.
DR PIR; S56650; S56650.
DR AlphaFoldDB; Q39735; -.
DR SMR; Q39735; -.
DR BRENDA; 2.7.9.1; 2264.
DR SABIO-RK; Q39735; -.
DR UniPathway; UPA00322; -.
DR GO; GO:0009507; C:chloroplast; IEA:UniProtKB-SubCell.
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:0015979; P:photosynthesis; 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 1: Evidence at protein level;
KW ATP-binding; Chloroplast; Direct protein sequencing; Kinase; Magnesium;
KW Metal-binding; Nucleotide-binding; Phosphoprotein; Photosynthesis; Plastid;
KW Transferase; Transit peptide.
FT TRANSIT 1..77
FT /note="Chloroplast"
FT /evidence="ECO:0000269|PubMed:7766886"
FT CHAIN 78..953
FT /note="Pyruvate, phosphate dikinase, chloroplastic"
FT /id="PRO_0000023559"
FT REGION 55..74
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT ACT_SITE 535
FT /note="Tele-phosphohistidine intermediate"
FT /evidence="ECO:0000250|UniProtKB:P11155"
FT ACT_SITE 913
FT /note="Proton donor"
FT /evidence="ECO:0000250|UniProtKB:P11155"
FT BINDING 641
FT /ligand="substrate"
FT /evidence="ECO:0000250|UniProtKB:P11155"
FT BINDING 698
FT /ligand="substrate"
FT /evidence="ECO:0000250|UniProtKB:P11155"
FT BINDING 827
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /evidence="ECO:0000250|UniProtKB:P11155"
FT BINDING 827
FT /ligand="substrate"
FT /evidence="ECO:0000250|UniProtKB:P11155"
FT BINDING 848
FT /ligand="substrate"
FT /evidence="ECO:0000250|UniProtKB:P11155"
FT BINDING 849
FT /ligand="substrate"
FT /evidence="ECO:0000250|UniProtKB:P11155"
FT BINDING 850
FT /ligand="substrate"
FT /evidence="ECO:0000250|UniProtKB:P11155"
FT BINDING 851
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /evidence="ECO:0000250|UniProtKB:P11155"
FT BINDING 851
FT /ligand="substrate"
FT /evidence="ECO:0000250|UniProtKB:P11155"
FT MOD_RES 533
FT /note="Phosphothreonine; by PDRP1"
FT /evidence="ECO:0000250"
FT MUTAGEN 869
FT /note="Q->P: 60% activity in the cold. 60% activity in the
FT cold; when associated with S-873."
FT /evidence="ECO:0000269|PubMed:9038349"
FT MUTAGEN 873
FT /note="A->S: 10% activity in the cold. 60% activity in the
FT cold; when associated with P-869."
FT /evidence="ECO:0000269|PubMed:9038349"
FT MUTAGEN 885
FT /note="I->L: 50% activity in the cold. 65% activity in the
FT cold; when associated with V-952."
FT /evidence="ECO:0000269|PubMed:9038349"
FT MUTAGEN 952
FT /note="I->V: 25% activity in the cold. 65% activity in the
FT cold; when associated with L-885."
FT /evidence="ECO:0000269|PubMed:9038349"
SQ SEQUENCE 953 AA; 104002 MW; 7BEC5276C1C1DC4C CRC64;
MMSSLSVEGM LLKSARESCL PARVNQRRNG DLRRLNHHRQ SSFVRCLTPA RVSRPELRSS
GLTPPRAVLN PVSPPVTTAK KRVFTFGKGR SEGNRDMKSL LGGKGANLAE MSSIGLSVPP
GLTISTEACE EYQQNGKSLP PGLWDEISEG LDYVQKEMSA SLGDPSKPLP LSVRSGAAIS
MPGMMDTVLN LGLNDEVVAG LAGKSGARFA YDSYRRFLDM FGNVVMGIPH SLFDEKLEQM
KAEKGIHLDT DLTAADLKDL VEKYKNVYVE AKGEKFPTDP KKQLELAVNA VFDSWDSPRA
NKYRSINQIT GLKGTAVNIQ SMVFGNMGNT SGTGVLFTRN PSTGEKKLYG EFLINAQGED
VVAGIRTPED LGTMETCMPD AYKELVENCE ILEGHYKDMM DIEFTVQENR LWMLQCRTGK
RTGKGAVRIA VDMVNEWLID TRTAIKRVET QHLDQLLHPQ FEDPSAYKSH VVATGLPASP
GAAVGQVCFS AEDAETWHAQ GKSAILVRTE TSPEDVGGMH AAAGILTARG GMTSHAAVVA
RGWGKCCVSG CADIRVNDDM KIFTIGDRVI KEGDWLSLNG TTGEVILGKQ LLAPPAMSND
LEIFMSWADQ ARRLKVMANA DTPNDALTAR NNGAQGIGLC RTEHMFFASD ERIKAVRKMI
MAVTPEQRKV ALDLLLPYQR SDFEGIFRAM DGLPVTIRLL DPPLHEFLPE GDLEHIVNEL
AVDTGMSADE IYSKIENLSE VNPMLGFRGC RLGISYPELT EMQVRAIFQA AVSMTNQGVT
VIPEIMVPLV GTPQELRHQI SVIRGVAANV FAEMGVTLEY KVGTMIEIPR AALIAEEIGK
EADFFSFGTN DLTQMTFGYS RDDVGKFLQI YLAQGILQHD PFEVIDQKGV GQLIKMATEK
GRAANPNLKV GICGEHGGEP SSVAFFDGVG LDYVSCSPFR VPIARLAAAQ VIV
