MVD2_ARATH
ID MVD2_ARATH Reviewed; 419 AA.
AC F4JCU3; Q8LAR8; Q9M381;
DT 17-FEB-2016, integrated into UniProtKB/Swiss-Prot.
DT 28-JUN-2011, sequence version 1.
DT 03-AUG-2022, entry version 72.
DE RecName: Full=Diphosphomevalonate decarboxylase MVD2, peroxisomal {ECO:0000305};
DE EC=4.1.1.33 {ECO:0000269|PubMed:26216978};
DE AltName: Full=Mevalonate 5-diphosphate decarboxylase 2 {ECO:0000303|PubMed:26216978};
DE Short=AtMDD2 {ECO:0000303|PubMed:26216978};
DE Short=AtMVD2 {ECO:0000305};
GN Name=MVD2 {ECO:0000305}; Synonyms=MDD2 {ECO:0000303|PubMed:26216978};
GN OrderedLocusNames=At3g54250 {ECO:0000312|Araport:AT3G54250};
GN ORFNames=F24B22.210 {ECO:0000312|EMBL:CAB70999.1};
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=11130713; DOI=10.1038/35048706;
RA Salanoubat M., Lemcke K., Rieger M., Ansorge W., Unseld M., Fartmann B.,
RA Valle G., Bloecker H., Perez-Alonso M., Obermaier B., Delseny M.,
RA Boutry M., Grivell L.A., Mache R., Puigdomenech P., De Simone V.,
RA Choisne N., Artiguenave F., Robert C., Brottier P., Wincker P.,
RA Cattolico L., Weissenbach J., Saurin W., Quetier F., Schaefer M.,
RA Mueller-Auer S., Gabel C., Fuchs M., Benes V., Wurmbach E., Drzonek H.,
RA Erfle H., Jordan N., Bangert S., Wiedelmann R., Kranz H., Voss H.,
RA Holland R., Brandt P., Nyakatura G., Vezzi A., D'Angelo M., Pallavicini A.,
RA Toppo S., Simionati B., Conrad A., Hornischer K., Kauer G., Loehnert T.-H.,
RA Nordsiek G., Reichelt J., Scharfe M., Schoen O., Bargues M., Terol J.,
RA Climent J., Navarro P., Collado C., Perez-Perez A., Ottenwaelder B.,
RA Duchemin D., Cooke R., Laudie M., Berger-Llauro C., Purnelle B., Masuy D.,
RA de Haan M., Maarse A.C., Alcaraz J.-P., Cottet A., Casacuberta E.,
RA Monfort A., Argiriou A., Flores M., Liguori R., Vitale D., Mannhaupt G.,
RA Haase D., Schoof H., Rudd S., Zaccaria P., Mewes H.-W., Mayer K.F.X.,
RA Kaul S., Town C.D., Koo H.L., Tallon L.J., Jenkins J., Rooney T., Rizzo M.,
RA Walts A., Utterback T., Fujii C.Y., Shea T.P., Creasy T.H., Haas B.,
RA Maiti R., Wu D., Peterson J., Van Aken S., Pai G., Militscher J.,
RA Sellers P., Gill J.E., Feldblyum T.V., Preuss D., Lin X., Nierman W.C.,
RA Salzberg S.L., White O., Venter J.C., Fraser C.M., Kaneko T., Nakamura Y.,
RA Sato S., Kato T., Asamizu E., Sasamoto S., Kimura T., Idesawa K.,
RA Kawashima K., Kishida Y., Kiyokawa C., Kohara M., Matsumoto M., Matsuno A.,
RA Muraki A., Nakayama S., Nakazaki N., Shinpo S., Takeuchi C., Wada T.,
RA Watanabe A., Yamada M., Yasuda M., Tabata S.;
RT "Sequence and analysis of chromosome 3 of the plant Arabidopsis thaliana.";
RL Nature 408:820-822(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].
RA Brover V.V., Troukhan M.E., Alexandrov N.A., Lu Y.-P., Flavell R.B.,
RA Feldmann K.A.;
RT "Full-length cDNA from Arabidopsis thaliana.";
RL Submitted (MAR-2002) to the EMBL/GenBank/DDBJ databases.
RN [4]
RP FUNCTION, CATALYTIC ACTIVITY, AND BIOPHYSICOCHEMICAL PROPERTIES.
RX PubMed=26216978; DOI=10.1073/pnas.1504798112;
RA Henry L.K., Gutensohn M., Thomas S.T., Noel J.P., Dudareva N.;
RT "Orthologs of the archaeal isopentenyl phosphate kinase regulate terpenoid
RT production in plants.";
RL Proc. Natl. Acad. Sci. U.S.A. 112:10050-10055(2015).
CC -!- FUNCTION: Performs the first committed step in the biosynthesis of
CC isoprene-containing compounds such as sterols and terpenoids. Is
CC specific for (R)-5-diphosphomevalonate (MVAPP). The catalytic
CC efficiency with (R)-5-phosphomevalonate (MVAP) as substrate is 10000-
CC fold lower than for MVAPP. {ECO:0000269|PubMed:26216978}.
CC -!- CATALYTIC ACTIVITY:
CC Reaction=(R)-5-diphosphomevalonate + ATP = ADP + CO2 + isopentenyl
CC diphosphate + phosphate; Xref=Rhea:RHEA:23732, ChEBI:CHEBI:16526,
CC ChEBI:CHEBI:30616, ChEBI:CHEBI:43474, ChEBI:CHEBI:57557,
CC ChEBI:CHEBI:128769, ChEBI:CHEBI:456216; EC=4.1.1.33;
CC Evidence={ECO:0000269|PubMed:26216978};
CC -!- BIOPHYSICOCHEMICAL PROPERTIES:
CC Kinetic parameters:
CC KM=26 uM for (R)-5-diphosphomevalonate {ECO:0000269|PubMed:26216978};
CC KM=4600 uM for (R)-5-phosphomevalonate {ECO:0000269|PubMed:26216978};
CC Note=kcat is 3.2 sec(-1) with (R)-5-diphosphomevalonate as substrate.
CC kcat is 0.034 sec(-1) with (R)-5-phosphomevalonate as substrate.
CC {ECO:0000269|PubMed:26216978};
CC -!- PATHWAY: Isoprenoid biosynthesis; isopentenyl diphosphate biosynthesis
CC via mevalonate pathway; isopentenyl diphosphate from (R)-mevalonate:
CC step 3/3. {ECO:0000305}.
CC -!- SUBUNIT: Homodimer. {ECO:0000250|UniProtKB:O23722}.
CC -!- SUBCELLULAR LOCATION: Peroxisome {ECO:0000250|UniProtKB:O23722}.
CC -!- SIMILARITY: Belongs to the diphosphomevalonate decarboxylase family.
CC {ECO:0000305}.
CC -!- SEQUENCE CAUTION:
CC Sequence=CAB70999.1; Type=Erroneous gene model prediction; Evidence={ECO:0000305};
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DR EMBL; AL132957; CAB70999.1; ALT_SEQ; Genomic_DNA.
DR EMBL; CP002686; AEE79204.1; -; Genomic_DNA.
DR EMBL; AY087654; AAM65192.1; -; mRNA.
DR PIR; T47584; T47584.
DR RefSeq; NP_566995.1; NM_115285.3.
DR AlphaFoldDB; F4JCU3; -.
DR SMR; F4JCU3; -.
DR STRING; 3702.AT3G54250.1; -.
DR PaxDb; F4JCU3; -.
DR PRIDE; F4JCU3; -.
DR ProteomicsDB; 251381; -.
DR EnsemblPlants; AT3G54250.1; AT3G54250.1; AT3G54250.
DR GeneID; 824592; -.
DR Gramene; AT3G54250.1; AT3G54250.1; AT3G54250.
DR KEGG; ath:AT3G54250; -.
DR Araport; AT3G54250; -.
DR TAIR; locus:2080265; AT3G54250.
DR eggNOG; KOG2833; Eukaryota.
DR HOGENOM; CLU_040369_4_4_1; -.
DR InParanoid; F4JCU3; -.
DR OrthoDB; 1065019at2759; -.
DR UniPathway; UPA00057; UER00100.
DR PRO; PR:F4JCU3; -.
DR Proteomes; UP000006548; Chromosome 3.
DR ExpressionAtlas; F4JCU3; baseline and differential.
DR GO; GO:0005829; C:cytosol; IBA:GO_Central.
DR GO; GO:0005777; C:peroxisome; IEA:UniProtKB-SubCell.
DR GO; GO:0005524; F:ATP binding; IEA:UniProtKB-KW.
DR GO; GO:0004163; F:diphosphomevalonate decarboxylase activity; IDA:TAIR.
DR GO; GO:0019287; P:isopentenyl diphosphate biosynthetic process, mevalonate pathway; IBA:GO_Central.
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; IPR036554; GHMP_kinase_C_sf.
DR InterPro; IPR006204; GHMP_kinase_N_dom.
DR InterPro; IPR005935; Mev_decarb.
DR InterPro; IPR029765; Mev_diP_decarb.
DR InterPro; IPR041431; Mvd1_C.
DR InterPro; IPR020568; Ribosomal_S5_D2-typ_fold.
DR InterPro; IPR014721; Ribosomal_S5_D2-typ_fold_subgr.
DR Pfam; PF00288; GHMP_kinases_N; 1.
DR Pfam; PF18376; MDD_C; 1.
DR PIRSF; PIRSF015950; Mev_P_decrbx; 1.
DR SUPFAM; SSF54211; SSF54211; 1.
DR SUPFAM; SSF55060; SSF55060; 1.
DR TIGRFAMs; TIGR01240; mevDPdecarb; 1.
PE 1: Evidence at protein level;
KW ATP-binding; Lipid biosynthesis; Lipid metabolism; Lyase;
KW Nucleotide-binding; Peroxisome; Reference proteome; Steroid biosynthesis;
KW Steroid metabolism; Sterol biosynthesis; Sterol metabolism.
FT CHAIN 1..419
FT /note="Diphosphomevalonate decarboxylase MVD2, peroxisomal"
FT /id="PRO_0000435608"
FT MOTIF 40..48
FT /note="Peroxisomal targeting signal PTS2"
FT /evidence="ECO:0000250|UniProtKB:O23722"
FT BINDING 23..26
FT /ligand="(R)-5-diphosphomevalonate"
FT /ligand_id="ChEBI:CHEBI:57557"
FT /evidence="ECO:0000250|UniProtKB:O23722"
FT BINDING 78
FT /ligand="(R)-5-diphosphomevalonate"
FT /ligand_id="ChEBI:CHEBI:57557"
FT /evidence="ECO:0000250|UniProtKB:O23722"
FT BINDING 161..166
FT /ligand="(R)-5-diphosphomevalonate"
FT /ligand_id="ChEBI:CHEBI:57557"
FT /evidence="ECO:0000250|UniProtKB:O23722"
FT BINDING 217
FT /ligand="(R)-5-diphosphomevalonate"
FT /ligand_id="ChEBI:CHEBI:57557"
FT /evidence="ECO:0000250|UniProtKB:O23722"
FT CONFLICT 28
FT /note="D -> H (in Ref. 3; AAM65192)"
FT /evidence="ECO:0000305"
SQ SEQUENCE 419 AA; 46248 MW; A6380A9707C8B844 CRC64;
MATEKWVFMV TAQTPTNIAV IKYWGKRDEV RILPVNDSIS VTLDPDHLCT VTTVAVSPAF
DRDRMWLNGK EISLSGSRYQ NCLREIRGRA GDVEDMEKGI KIRKKDWEKL NLHIASHNNF
PTAAGLASSA AGFACLVFSL AKLMNVDEDP SHLSAIARQG SGSACRSLFG GFVKWTMGSK
EDGSDSVAVQ LADEKHWDDL VIIIAVVSSR QKETSSTSGM RESVETSLLL QHRAKEVVPK
RILQMEEAIK NRDFASFTQL TCTDSNQFHA VCLDTSPPIF YMNDTSHRII SLVEKWNRSE
GTPQVAYTFD AGPNAVLIAR NRKVAVQLLQ GLLYYFPPKS DTDMKSYVVG DNSILKEAGL
DGASGVENLQ PPPEIKDNIG SQDQKGEVSY FICTRPGKGP IVLHDQTQAL LDPETGLPK
