PUMPK_ARATH
ID PUMPK_ARATH Reviewed; 339 AA.
AC Q9LSA9;
DT 23-FEB-2022, integrated into UniProtKB/Swiss-Prot.
DT 01-OCT-2000, sequence version 1.
DT 03-AUG-2022, entry version 164.
DE RecName: Full=Uridylate kinase PUMPKIN, chloroplastic {ECO:0000305|PubMed:30409856};
DE EC=2.7.4.22 {ECO:0000269|PubMed:30409856};
DE AltName: Full=Plastid UMP kinase {ECO:0000303|PubMed:30409856};
DE AltName: Full=Protein DEFECT IN PSAA/B TRANSCRIPT ACCUMULATION 1 {ECO:0000303|PubMed:19037728};
DE AltName: Full=Uridine monophosphate kinase {ECO:0000250|UniProtKB:P0A7E9};
DE Short=UMP kinase {ECO:0000250|UniProtKB:P0A7E9};
DE Short=UMPK {ECO:0000250|UniProtKB:P0A7E9};
DE Flags: Precursor;
GN Name=PUMPKIN {ECO:0000303|PubMed:30409856};
GN Synonyms=DPT1 {ECO:0000303|PubMed:19037728};
GN OrderedLocusNames=At3g18680 {ECO:0000312|EMBL:AEE76131.1};
OS Arabidopsis thaliana (Mouse-ear cress).
OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta;
OC Spermatophyta; Magnoliopsida; eudicotyledons; Gunneridae; Pentapetalae;
OC rosids; malvids; Brassicales; Brassicaceae; Camelineae; Arabidopsis.
OX NCBI_TaxID=3702;
RN [1]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=cv. Columbia;
RX PubMed=10819329; DOI=10.1093/dnares/7.2.131;
RA Sato S., Nakamura Y., Kaneko T., Katoh T., Asamizu E., Tabata S.;
RT "Structural analysis of Arabidopsis thaliana chromosome 3. I. Sequence
RT features of the regions of 4,504,864 bp covered by sixty P1 and TAC
RT clones.";
RL DNA Res. 7:131-135(2000).
RN [2]
RP GENOME REANNOTATION.
RC STRAIN=cv. Columbia;
RX PubMed=27862469; DOI=10.1111/tpj.13415;
RA Cheng C.Y., Krishnakumar V., Chan A.P., Thibaud-Nissen F., Schobel S.,
RA Town C.D.;
RT "Araport11: a complete reannotation of the Arabidopsis thaliana reference
RT genome.";
RL Plant J. 89:789-804(2017).
RN [3]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
RC STRAIN=cv. Columbia;
RX PubMed=14593172; DOI=10.1126/science.1088305;
RA Yamada K., Lim J., Dale J.M., Chen H., Shinn P., Palm C.J., Southwick A.M.,
RA Wu H.C., Kim C.J., Nguyen M., Pham P.K., Cheuk R.F., Karlin-Newmann G.,
RA Liu S.X., Lam B., Sakano H., Wu T., Yu G., Miranda M., Quach H.L.,
RA Tripp M., Chang C.H., Lee J.M., Toriumi M.J., Chan M.M., Tang C.C.,
RA Onodera C.S., Deng J.M., Akiyama K., Ansari Y., Arakawa T., Banh J.,
RA Banno F., Bowser L., Brooks S.Y., Carninci P., Chao Q., Choy N., Enju A.,
RA Goldsmith A.D., Gurjal M., Hansen N.F., Hayashizaki Y., Johnson-Hopson C.,
RA Hsuan V.W., Iida K., Karnes M., Khan S., Koesema E., Ishida J., Jiang P.X.,
RA Jones T., Kawai J., Kamiya A., Meyers C., Nakajima M., Narusaka M.,
RA Seki M., Sakurai T., Satou M., Tamse R., Vaysberg M., Wallender E.K.,
RA Wong C., Yamamura Y., Yuan S., Shinozaki K., Davis R.W., Theologis A.,
RA Ecker J.R.;
RT "Empirical analysis of transcriptional activity in the Arabidopsis
RT genome.";
RL Science 302:842-846(2003).
RN [4]
RP FUNCTION, DISRUPTION PHENOTYPE, SUBCELLULAR LOCATION, TISSUE SPECIFICITY,
RP AND INDUCTION BY LIGHT.
RC STRAIN=cv. Columbia, and cv. Landsberg erecta;
RX PubMed=19037728; DOI=10.1007/s11103-008-9433-2;
RA Hein P., Stoeckel J., Bennewitz S., Oelmueller R.;
RT "A protein related to prokaryotic UMP kinases is involved in psaA/B
RT transcript accumulation in Arabidopsis.";
RL Plant Mol. Biol. 69:517-528(2009).
RN [5]
RP IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
RX PubMed=19376835; DOI=10.1104/pp.109.138677;
RA Reiland S., Messerli G., Baerenfaller K., Gerrits B., Endler A.,
RA Grossmann J., Gruissem W., Baginsky S.;
RT "Large-scale Arabidopsis phosphoproteome profiling reveals novel
RT chloroplast kinase substrates and phosphorylation networks.";
RL Plant Physiol. 150:889-903(2009).
RN [6]
RP FUNCTION, DISRUPTION PHENOTYPE, SUBCELLULAR LOCATION, SUBUNIT, CATALYTIC
RP ACTIVITY, PATHWAY, AND BIOPHYSICOCHEMICAL PROPERTIES.
RC STRAIN=cv. Columbia;
RX PubMed=30409856; DOI=10.1104/pp.18.00687;
RA Schmid L.M., Ohler L., Moehlmann T., Brachmann A., Muino J.M., Leister D.,
RA Meurer J., Manavski N.;
RT "PUMPKIN, the sole plastid UMP kinase, associates with group II introns and
RT alters their metabolism.";
RL Plant Physiol. 179:248-264(2019).
CC -!- FUNCTION: Catalyzes the reversible phosphorylation of UMP to UDP
CC (PubMed:30409856). Required for specific post-transcriptional processes
CC of many plastid transcripts (e.g. PSI (PsaA, PsaF), PSII (D1, CP43,
CC CP47), Cytochrome b(6)f (Cytb(6)), ATP synthase (AtpC), LHCs (LHCa3,
CC LHCb2), and NDH (NdhH)), thus being essential for retaining
CC photosynthetic activity in chloroplasts (PubMed:19037728,
CC PubMed:30409856). Associates with group II introns of the plastid
CC transcripts trnG-UCC, trnV-UAC, petB, petD and ndhA to stabilize
CC corresponding precursor RNAs (PubMed:30409856).
CC {ECO:0000269|PubMed:19037728, ECO:0000269|PubMed:30409856}.
CC -!- CATALYTIC ACTIVITY:
CC Reaction=ATP + UMP = ADP + UDP; Xref=Rhea:RHEA:24400,
CC ChEBI:CHEBI:30616, ChEBI:CHEBI:57865, ChEBI:CHEBI:58223,
CC ChEBI:CHEBI:456216; EC=2.7.4.22;
CC Evidence={ECO:0000269|PubMed:30409856};
CC PhysiologicalDirection=left-to-right; Xref=Rhea:RHEA:24401;
CC Evidence={ECO:0000269|PubMed:30409856};
CC -!- BIOPHYSICOCHEMICAL PROPERTIES:
CC Kinetic parameters:
CC KM=0.03 mM for UMP {ECO:0000269|PubMed:30409856};
CC KM=0.17 mM for ATP {ECO:0000269|PubMed:30409856};
CC -!- PATHWAY: Pyrimidine metabolism; CTP biosynthesis via de novo pathway;
CC UDP from UMP (UMPK route): step 1/1. {ECO:0000269|PubMed:30409856}.
CC -!- SUBUNIT: Homomultimer (PubMed:30409856). Homohexamer (By similarity).
CC Forms RNA-containing megadalton-sized complexes (PubMed:30409856).
CC {ECO:0000250|UniProtKB:P0A7E9, ECO:0000269|PubMed:30409856}.
CC -!- SUBCELLULAR LOCATION: Plastid, chloroplast stroma
CC {ECO:0000269|PubMed:19037728, ECO:0000269|PubMed:30409856}.
CC -!- TISSUE SPECIFICITY: Expressed exclusively in leaves, but not in roots.
CC {ECO:0000269|PubMed:19037728}.
CC -!- INDUCTION: Induced by light, detected at low levels in etiolated
CC seedlings. {ECO:0000269|PubMed:19037728}.
CC -!- DISRUPTION PHENOTYPE: Reduced capacity to grow photoautotrophically
CC associated with low levels of many plastid transcripts (e.g. PSI (PsaA,
CC PsaF), PSII (D1, CP43, CP47), Cytochrome b(6)f (Cytb(6)), ATP synthase
CC (AtpC), LHCs (LHCa3, LHCb2), and NDH (NdhH)) but abnormal accumulation
CC of others, altered plastid translation as well as a strongly affected
CC plastid ultrastructure (e.g. almost absent stromal lamellae and swollen
CC grana stacks) with a large number of plastoglobuli and reduced
CC photosynthetic performance due to strong defects in the major complexes
CC of the thylakoid membrane. {ECO:0000269|PubMed:19037728,
CC ECO:0000269|PubMed:30409856}.
CC -!- SIMILARITY: Belongs to the UMP kinase family. {ECO:0000305}.
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DR EMBL; AB026654; BAB01794.1; -; Genomic_DNA.
DR EMBL; CP002686; AEE76131.1; -; Genomic_DNA.
DR EMBL; AY050828; AAK92763.1; -; mRNA.
DR EMBL; AY091161; AAM14100.1; -; mRNA.
DR RefSeq; NP_188498.1; NM_112754.3.
DR SMR; Q9LSA9; -.
DR IntAct; Q9LSA9; 1.
DR STRING; 3702.AT3G18680.1; -.
DR PaxDb; Q9LSA9; -.
DR PRIDE; Q9LSA9; -.
DR ProMEX; Q9LSA9; -.
DR ProteomicsDB; 189552; -.
DR EnsemblPlants; AT3G18680.1; AT3G18680.1; AT3G18680.
DR GeneID; 821399; -.
DR Gramene; AT3G18680.1; AT3G18680.1; AT3G18680.
DR Araport; AT3G18680; -.
DR TAIR; locus:2093949; AT3G18680.
DR eggNOG; ENOG502QVYQ; Eukaryota.
DR HOGENOM; CLU_033861_4_0_1; -.
DR InParanoid; Q9LSA9; -.
DR OMA; PIIVFDM; -.
DR PhylomeDB; Q9LSA9; -.
DR UniPathway; UPA00159; UER00275.
DR Proteomes; UP000006548; Chromosome 3.
DR ExpressionAtlas; Q9LSA9; baseline and differential.
DR GO; GO:0009507; C:chloroplast; IDA:TAIR.
DR GO; GO:0009570; C:chloroplast stroma; IDA:UniProtKB.
DR GO; GO:0005524; F:ATP binding; IEA:UniProtKB-KW.
DR GO; GO:0043621; F:protein self-association; IDA:UniProtKB.
DR GO; GO:0003723; F:RNA binding; IPI:TAIR.
DR GO; GO:1990825; F:sequence-specific mRNA binding; IDA:UniProtKB.
DR GO; GO:0033862; F:UMP kinase activity; IDA:TAIR.
DR GO; GO:0044210; P:'de novo' CTP biosynthetic process; IEA:UniProtKB-UniPathway.
DR GO; GO:0009658; P:chloroplast organization; IMP:UniProtKB.
DR GO; GO:0031425; P:chloroplast RNA processing; IMP:UniProtKB.
DR GO; GO:0016310; P:phosphorylation; IEA:UniProtKB-KW.
DR GO; GO:0042548; P:regulation of photosynthesis, light reaction; IMP:UniProtKB.
DR GO; GO:0009416; P:response to light stimulus; IEP:UniProtKB.
DR CDD; cd04254; AAK_UMPK-PyrH-Ec; 1.
DR Gene3D; 3.40.1160.10; -; 1.
DR HAMAP; MF_01220_B; PyrH_B; 1.
DR InterPro; IPR036393; AceGlu_kinase-like_sf.
DR InterPro; IPR001048; Asp/Glu/Uridylate_kinase.
DR InterPro; IPR015963; Uridylate_kinase_bac.
DR Pfam; PF00696; AA_kinase; 1.
DR SUPFAM; SSF53633; SSF53633; 1.
DR TIGRFAMs; TIGR02075; pyrH_bact; 1.
PE 1: Evidence at protein level;
KW ATP-binding; Chloroplast; Kinase; Nucleotide-binding; Plastid;
KW Pyrimidine biosynthesis; Reference proteome; RNA-binding; Transferase;
KW Transit peptide.
FT TRANSIT 1..53
FT /note="Chloroplast"
FT /evidence="ECO:0000255"
FT CHAIN 54..339
FT /note="Uridylate kinase PUMPKIN, chloroplastic"
FT /id="PRO_0000454293"
FT REGION 52..89
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT REGION 110..115
FT /note="Involved in allosteric activation by GTP"
FT /evidence="ECO:0000255"
FT COMPBIAS 52..85
FT /note="Polar residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT BINDING 102..105
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /evidence="ECO:0000250|UniProtKB:P0A7E9"
FT BINDING 144
FT /ligand="UMP"
FT /ligand_id="ChEBI:CHEBI:57865"
FT /evidence="ECO:0000250|UniProtKB:P0A7E9"
FT BINDING 145
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /evidence="ECO:0000250|UniProtKB:P0A7E9"
FT BINDING 149
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /evidence="ECO:0000250|UniProtKB:P0A7E9"
FT BINDING 165
FT /ligand="UMP"
FT /ligand_id="ChEBI:CHEBI:57865"
FT /evidence="ECO:0000250|UniProtKB:P0A7E9"
FT BINDING 180..184
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /evidence="ECO:0000250|UniProtKB:P0A7E9"
FT BINDING 189..191
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /evidence="ECO:0000250|UniProtKB:P0A7E9"
FT BINDING 226..233
FT /ligand="UMP"
FT /ligand_id="ChEBI:CHEBI:57865"
FT /evidence="ECO:0000250|UniProtKB:P0A7E9"
FT BINDING 253
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /evidence="ECO:0000250|UniProtKB:P0A7E9"
FT BINDING 259
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /evidence="ECO:0000250|UniProtKB:P0A7E9"
FT BINDING 262
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /evidence="ECO:0000250|UniProtKB:P0A7E9"
SQ SEQUENCE 339 AA; 36263 MW; 6BC2300ECB38297F CRC64;
MAIPLPLTSC SPISTSSSIS RTSFVPLTLR NRTFFSNQNY SRRVLISCSS SLSSDNGSSP
DSMNGNGNGN GSSLNGQSSF PRLPSFDGTS KPPLKWRRVL LKVSGEALAG DEEQNIDPKV
TMAIAREVAA VTRLGIEVAI VVGGGNIFRG STWAGCSGLD RSSADYIGML ATVMNAIFLQ
ATMESIGIPT RVQTAFRMSE VAEPYIRRRA IRHLEKGRVV IFAAGTGNPF FTTDTAAALR
CAEINAEVVL KATNVDGVFD DDPKRNPNAR LLDSLTYQEV TSKDLSVMDM TAITLCQENN
IPVVVFNLSE PGNIAKAIKG ERVGTLIGGT WNSIVTTTS
