PMK_ARATH
ID PMK_ARATH Reviewed; 505 AA.
AC Q9C6T1; Q681V6; Q682Q9;
DT 17-FEB-2016, integrated into UniProtKB/Swiss-Prot.
DT 01-JUN-2001, sequence version 1.
DT 03-AUG-2022, entry version 155.
DE RecName: Full=Phosphomevalonate kinase, peroxisomal {ECO:0000305};
DE EC=2.7.4.2 {ECO:0000269|PubMed:24327557};
DE AltName: Full=5-phosphomevalonate kinase {ECO:0000303|PubMed:21655959};
DE Short=AtPMK {ECO:0000303|PubMed:21655959};
GN Name=PMK {ECO:0000303|PubMed:21655959};
GN OrderedLocusNames=At1g31910 {ECO:0000312|Araport:AT1G31910};
GN ORFNames=F5M6.9 {ECO:0000312|EMBL:AAG50716.1};
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=11130712; DOI=10.1038/35048500;
RA Theologis A., Ecker J.R., Palm C.J., Federspiel N.A., Kaul S., White O.,
RA Alonso J., Altafi H., Araujo R., Bowman C.L., Brooks S.Y., Buehler E.,
RA Chan A., Chao Q., Chen H., Cheuk R.F., Chin C.W., Chung M.K., Conn L.,
RA Conway A.B., Conway A.R., Creasy T.H., Dewar K., Dunn P., Etgu P.,
RA Feldblyum T.V., Feng J.-D., Fong B., Fujii C.Y., Gill J.E., Goldsmith A.D.,
RA Haas B., Hansen N.F., Hughes B., Huizar L., Hunter J.L., Jenkins J.,
RA Johnson-Hopson C., Khan S., Khaykin E., Kim C.J., Koo H.L.,
RA Kremenetskaia I., Kurtz D.B., Kwan A., Lam B., Langin-Hooper S., Lee A.,
RA Lee J.M., Lenz C.A., Li J.H., Li Y.-P., Lin X., Liu S.X., Liu Z.A.,
RA Luros J.S., Maiti R., Marziali A., Militscher J., Miranda M., Nguyen M.,
RA Nierman W.C., Osborne B.I., Pai G., Peterson J., Pham P.K., Rizzo M.,
RA Rooney T., Rowley D., Sakano H., Salzberg S.L., Schwartz J.R., Shinn P.,
RA Southwick A.M., Sun H., Tallon L.J., Tambunga G., Toriumi M.J., Town C.D.,
RA Utterback T., Van Aken S., Vaysberg M., Vysotskaia V.S., Walker M., Wu D.,
RA Yu G., Fraser C.M., Venter J.C., Davis R.W.;
RT "Sequence and analysis of chromosome 1 of the plant Arabidopsis thaliana.";
RL Nature 408:816-820(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] (ISOFORMS 1 AND 2).
RC STRAIN=cv. Columbia;
RA Totoki Y., Seki M., Ishida J., Nakajima M., Enju A., Kamiya A.,
RA Narusaka M., Shin-i T., Nakagawa M., Sakamoto N., Oishi K., Kohara Y.,
RA Kobayashi M., Toyoda A., Sakaki Y., Sakurai T., Iida K., Akiyama K.,
RA Satou M., Toyoda T., Konagaya A., Carninci P., Kawai J., Hayashizaki Y.,
RA Shinozaki K.;
RT "Large-scale analysis of RIKEN Arabidopsis full-length (RAFL) cDNAs.";
RL Submitted (SEP-2004) to the EMBL/GenBank/DDBJ databases.
RN [4]
RP SUBCELLULAR LOCATION.
RX PubMed=21655959; DOI=10.1007/s00425-011-1444-6;
RA Simkin A.J., Guirimand G., Papon N., Courdavault V., Thabet I., Ginis O.,
RA Bouzid S., Giglioli-Guivarc'h N., Clastre M.;
RT "Peroxisomal localisation of the final steps of the mevalonic acid pathway
RT in planta.";
RL Planta 234:903-914(2011).
RN [5]
RP ACETYLATION [LARGE SCALE ANALYSIS] AT ALA-2, CLEAVAGE OF INITIATOR
RP METHIONINE [LARGE SCALE ANALYSIS], AND IDENTIFICATION BY MASS SPECTROMETRY
RP [LARGE SCALE ANALYSIS].
RX PubMed=22223895; DOI=10.1074/mcp.m111.015131;
RA Bienvenut W.V., Sumpton D., Martinez A., Lilla S., Espagne C., Meinnel T.,
RA Giglione C.;
RT "Comparative large-scale characterisation of plant vs. mammal proteins
RT reveals similar and idiosyncratic N-alpha acetylation features.";
RL Mol. Cell. Proteomics 11:M111.015131-M111.015131(2012).
RN [6]
RP CATALYTIC ACTIVITY, AND BIOPHYSICOCHEMICAL PROPERTIES.
RX PubMed=24327557; DOI=10.7554/elife.00672;
RA Dellas N., Thomas S.T., Manning G., Noel J.P.;
RT "Discovery of a metabolic alternative to the classical mevalonate
RT pathway.";
RL Elife 2:E00672-E00672(2013).
CC -!- CATALYTIC ACTIVITY:
CC Reaction=(R)-5-phosphomevalonate + ATP = (R)-5-diphosphomevalonate +
CC ADP; Xref=Rhea:RHEA:16341, ChEBI:CHEBI:30616, ChEBI:CHEBI:57557,
CC ChEBI:CHEBI:58146, ChEBI:CHEBI:456216; EC=2.7.4.2;
CC Evidence={ECO:0000269|PubMed:24327557};
CC -!- BIOPHYSICOCHEMICAL PROPERTIES:
CC Kinetic parameters:
CC KM=11.8 uM for (R)-5-phosphomevalonate {ECO:0000269|PubMed:24327557};
CC Note=kcat is 20.9 sec(-1) with (R)-5-phosphomevalonate.
CC {ECO:0000269|PubMed:24327557};
CC -!- PATHWAY: Isoprenoid biosynthesis; isopentenyl diphosphate biosynthesis
CC via mevalonate pathway; isopentenyl diphosphate from (R)-mevalonate:
CC step 2/3. {ECO:0000305}.
CC -!- SUBCELLULAR LOCATION: Peroxisome {ECO:0000269|PubMed:21655959}.
CC -!- ALTERNATIVE PRODUCTS:
CC Event=Alternative splicing; Named isoforms=2;
CC Name=1;
CC IsoId=Q9C6T1-1; Sequence=Displayed;
CC Name=2;
CC IsoId=Q9C6T1-2; Sequence=VSP_058117, VSP_058118;
CC -!- SIMILARITY: Belongs to the GHMP kinase family. Mevalonate kinase
CC subfamily. {ECO:0000305}.
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DR EMBL; AC079041; AAG50716.1; -; Genomic_DNA.
DR EMBL; CP002684; AEE31414.1; -; Genomic_DNA.
DR EMBL; CP002684; AEE31415.1; -; Genomic_DNA.
DR EMBL; AK175299; BAD43062.1; -; mRNA.
DR EMBL; AK175308; BAD43071.1; -; mRNA.
DR EMBL; AK175511; BAD43274.1; -; mRNA.
DR EMBL; AK176723; BAD44486.1; -; mRNA.
DR EMBL; AK176889; BAD44652.1; -; mRNA.
DR EMBL; AK221797; BAD93949.1; -; mRNA.
DR PIR; C86443; C86443.
DR RefSeq; NP_001185124.1; NM_001198195.1. [Q9C6T1-2]
DR RefSeq; NP_174473.1; NM_102927.3. [Q9C6T1-1]
DR AlphaFoldDB; Q9C6T1; -.
DR STRING; 3702.AT1G31910.1; -.
DR iPTMnet; Q9C6T1; -.
DR PaxDb; Q9C6T1; -.
DR PRIDE; Q9C6T1; -.
DR ProteomicsDB; 234854; -. [Q9C6T1-1]
DR EnsemblPlants; AT1G31910.1; AT1G31910.1; AT1G31910. [Q9C6T1-1]
DR EnsemblPlants; AT1G31910.2; AT1G31910.2; AT1G31910. [Q9C6T1-2]
DR GeneID; 840081; -.
DR Gramene; AT1G31910.1; AT1G31910.1; AT1G31910. [Q9C6T1-1]
DR Gramene; AT1G31910.2; AT1G31910.2; AT1G31910. [Q9C6T1-2]
DR KEGG; ath:AT1G31910; -.
DR Araport; AT1G31910; -.
DR TAIR; locus:2034466; AT1G31910.
DR eggNOG; KOG4519; Eukaryota.
DR HOGENOM; CLU_022059_1_0_1; -.
DR InParanoid; Q9C6T1; -.
DR OMA; LVIHRTM; -.
DR OrthoDB; 1165296at2759; -.
DR PhylomeDB; Q9C6T1; -.
DR BioCyc; ARA:AT1G31910-MON; -.
DR UniPathway; UPA00057; UER00099.
DR PRO; PR:Q9C6T1; -.
DR Proteomes; UP000006548; Chromosome 1.
DR ExpressionAtlas; Q9C6T1; baseline and differential.
DR GO; GO:0005777; C:peroxisome; IDA:UniProtKB.
DR GO; GO:0005524; F:ATP binding; IEA:UniProtKB-KW.
DR GO; GO:0004631; F:phosphomevalonate kinase activity; IDA:UniProtKB.
DR GO; GO:0010142; P:farnesyl diphosphate biosynthetic process, mevalonate pathway; IBA:GO_Central.
DR GO; GO:0019287; P:isopentenyl diphosphate biosynthetic process, mevalonate pathway; IDA:UniProtKB.
DR GO; GO:0016310; P:phosphorylation; IEA:UniProtKB-KW.
DR GO; GO:0016126; P:sterol biosynthetic process; IEA:UniProtKB-KW.
DR Gene3D; 3.30.230.10; -; 1.
DR Gene3D; 3.30.70.890; -; 1.
DR InterPro; IPR016005; Erg8.
DR InterPro; IPR013750; GHMP_kinase_C_dom.
DR InterPro; IPR036554; GHMP_kinase_C_sf.
DR InterPro; IPR006204; GHMP_kinase_N_dom.
DR InterPro; IPR035102; Phosphomevalonate_kinase.
DR InterPro; IPR020568; Ribosomal_S5_D2-typ_fold.
DR InterPro; IPR014721; Ribosomal_S5_D2-typ_fold_subgr.
DR PANTHER; PTHR31814; PTHR31814; 1.
DR Pfam; PF08544; GHMP_kinases_C; 1.
DR Pfam; PF00288; GHMP_kinases_N; 1.
DR PIRSF; PIRSF017288; PMK_GHMP_euk; 1.
DR SUPFAM; SSF54211; SSF54211; 1.
DR TIGRFAMs; TIGR01219; Pmev_kin_ERG8; 1.
PE 1: Evidence at protein level;
KW Acetylation; Alternative splicing; ATP-binding; Kinase; Lipid biosynthesis;
KW Lipid metabolism; Nucleotide-binding; Peroxisome; Reference proteome;
KW Steroid biosynthesis; Steroid metabolism; Sterol biosynthesis;
KW Sterol metabolism; Transferase.
FT INIT_MET 1
FT /note="Removed"
FT /evidence="ECO:0007744|PubMed:22223895"
FT CHAIN 2..505
FT /note="Phosphomevalonate kinase, peroxisomal"
FT /id="PRO_0000435609"
FT MOTIF 57..65
FT /note="Peroxisomal targeting signal PTS2"
FT /evidence="ECO:0000305|PubMed:21655959"
FT BINDING 177..187
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /evidence="ECO:0000255"
FT MOD_RES 2
FT /note="N-acetylalanine"
FT /evidence="ECO:0007744|PubMed:22223895"
FT VAR_SEQ 418..450
FT /note="IEPESQTQLLDSTMSAEGVLLAGVPGAGGFDAI -> NLNSIHDIRVPQIPH
FT LEQIDFIIIDLEGPWNCR (in isoform 2)"
FT /id="VSP_058117"
FT VAR_SEQ 451..505
FT /note="Missing (in isoform 2)"
FT /id="VSP_058118"
FT CONFLICT 44
FT /note="E -> G (in Ref. 3; BAD43274)"
FT /evidence="ECO:0000305"
FT CONFLICT 54
FT /note="K -> N (in Ref. 3; BAD43274)"
FT /evidence="ECO:0000305"
SQ SEQUENCE 505 AA; 54409 MW; B1CBA6CA338B3D63 CRC64;
MAVVASAPGK VLMTGGYLVL EKPNAGLVLS TNARFYAIVK PINEEVKPES WAWKWTDVKL
TSPQLSRESM YKLSLNHLTL QSVSASDSRN PFVEHAIQYA IAAAHLATEK DKESLHKLLL
QGLDITILGS NDFYSYRNQI ESAGLPLTPE SLGTLAPFAS ITFNAAESNG ANSKPEVAKT
GLGSSAAMTT AVVAALLHYL GVVDLSDPCK EGKFGCSDLD VIHMIAQTSH CLAQGKVGSG
FDVSCAVYGS QRYVRFSPEV LSFAQVAVTG LPLNEVIGTI LKGKWDNKRT EFSLPPLMNL
FLGEPGSGGS STPSMVGAVK KWQMSDPEKA RENWQNLSDA NLELETKLND LSKLAKDHWD
VYLRVIKSCS VLTSEKWVLH ATEPINEAII KELLEAREAM LRIRILMRQM GEAASVPIEP
ESQTQLLDST MSAEGVLLAG VPGAGGFDAI FAITLGDSGT KLTQAWSSHN VLALLVREDP
HGVCLESGDP RTTCITSGVS SIHLE
