MVD1_ARATH
ID MVD1_ARATH Reviewed; 412 AA.
AC O23722; Q8LB37;
DT 17-FEB-2016, integrated into UniProtKB/Swiss-Prot.
DT 01-JAN-1998, sequence version 1.
DT 03-AUG-2022, entry version 151.
DE RecName: Full=Diphosphomevalonate decarboxylase MVD1, peroxisomal {ECO:0000305};
DE EC=4.1.1.33 {ECO:0000269|PubMed:24327557, ECO:0000269|PubMed:26216978};
DE AltName: Full=Mevalonate 5-diphosphate decarboxylase 1 {ECO:0000303|PubMed:26216978};
DE Short=AtMDD1 {ECO:0000303|PubMed:26216978};
DE Short=AtMVD1 {ECO:0000303|PubMed:21655959};
GN Name=MVD1 {ECO:0000303|PubMed:21655959};
GN Synonyms=MDD1 {ECO:0000303|PubMed:26216978},
GN MVD {ECO:0000303|PubMed:21655959};
GN OrderedLocusNames=At2g38700 {ECO:0000312|Araport:AT2G38700};
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 [GENOMIC DNA / MRNA], FUNCTION, AND SUBUNIT.
RX PubMed=10344201; DOI=10.1023/a:1006181720100;
RA Cordier H., Karst F., Berges T.;
RT "Heterologous expression in Saccharomyces cerevisiae of an Arabidopsis
RT thaliana cDNA encoding mevalonate diphosphate decarboxylase.";
RL Plant Mol. Biol. 39:953-967(1999).
RN [2]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=cv. Columbia;
RX PubMed=10617197; DOI=10.1038/45471;
RA Lin X., Kaul S., Rounsley S.D., Shea T.P., Benito M.-I., Town C.D.,
RA Fujii C.Y., Mason T.M., Bowman C.L., Barnstead M.E., Feldblyum T.V.,
RA Buell C.R., Ketchum K.A., Lee J.J., Ronning C.M., Koo H.L., Moffat K.S.,
RA Cronin L.A., Shen M., Pai G., Van Aken S., Umayam L., Tallon L.J.,
RA Gill J.E., Adams M.D., Carrera A.J., Creasy T.H., Goodman H.M.,
RA Somerville C.R., Copenhaver G.P., Preuss D., Nierman W.C., White O.,
RA Eisen J.A., Salzberg S.L., Fraser C.M., Venter J.C.;
RT "Sequence and analysis of chromosome 2 of the plant Arabidopsis thaliana.";
RL Nature 402:761-768(1999).
RN [3]
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 [4]
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 [5]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
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 (JUL-2006) to the EMBL/GenBank/DDBJ databases.
RN [6]
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 [7]
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 [8]
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).
RN [9]
RP FUNCTION, CATALYTIC ACTIVITY, BIOPHYSICOCHEMICAL PROPERTIES, AND DISRUPTION
RP PHENOTYPE.
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).
RN [10]
RP X-RAY CRYSTALLOGRAPHY (2.30 ANGSTROMS) IN COMPLEX WITH
RP (R)-5-DIPHOSPHOMEVALONATE.
RX PubMed=31268677; DOI=10.1021/acschembio.9b00322;
RA Thomas S.T., Louie G.V., Lubin J.W., Lundblad V., Noel J.P.;
RT "Substrate specificity and engineering of mevalonate 5-phosphate
RT decarboxylase.";
RL ACS Chem. Biol. 14:1767-1779(2019).
CC -!- FUNCTION: Performs the first committed step in the biosynthesis of
CC isoprene-containing compounds such as sterols and terpenoids
CC (PubMed:10344201, PubMed:26216978). Is specific for (R)-5-
CC diphosphomevalonate (MVAPP). The catalytic efficiency with (R)-5-
CC phosphomevalonate (MVAP) as substrate is 10000-fold lower than for
CC MVAPP (PubMed:26216978). Can complement a yeast mutant defective in MVD
CC activity (PubMed:10344201). {ECO:0000269|PubMed:10344201,
CC 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:24327557, ECO:0000269|PubMed:26216978};
CC -!- BIOPHYSICOCHEMICAL PROPERTIES:
CC Kinetic parameters:
CC KM=15.7 uM for (R)-5-diphosphomevalonate
CC {ECO:0000269|PubMed:24327557};
CC KM=26 uM for (R)-5-diphosphomevalonate {ECO:0000269|PubMed:26216978};
CC KM=2800 uM for (R)-5-phosphomevalonate {ECO:0000269|PubMed:26216978};
CC Note=kcat is 2.0 sec(-1) with (R)-5-diphosphomevalonate as substrate
CC (PubMed:24327557). kcat is 3.2 sec(-1) with (R)-5-diphosphomevalonate
CC as substrate (PubMed:26216978). kcat is 0.033 sec(-1) with (R)-5-
CC phosphomevalonate as substrate (PubMed:26216978).
CC {ECO:0000269|PubMed:24327557, 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:0000269|PubMed:10344201}.
CC -!- SUBCELLULAR LOCATION: Peroxisome {ECO:0000269|PubMed:21655959}.
CC -!- DISRUPTION PHENOTYPE: Decreased contents of campesterol and sitosterol
CC (by 50% and 30%, respectively, compared with wild type). Decreased
CC emissions of beta-caryophyllene (by 35% compared with wild-type).
CC {ECO:0000269|PubMed:26216978}.
CC -!- SIMILARITY: Belongs to the diphosphomevalonate decarboxylase family.
CC {ECO:0000305}.
CC -!- SEQUENCE CAUTION:
CC Sequence=AAM64988.1; Type=Erroneous initiation; Note=Truncated N-terminus.; Evidence={ECO:0000305};
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DR EMBL; Y14325; CAA74700.1; -; mRNA.
DR EMBL; Y17593; CAA76803.1; -; Genomic_DNA.
DR EMBL; AC005499; AAC67348.1; -; Genomic_DNA.
DR EMBL; CP002685; AEC09574.1; -; Genomic_DNA.
DR EMBL; BT008769; AAP68208.1; -; mRNA.
DR EMBL; AK228357; BAF00296.1; -; mRNA.
DR EMBL; AY087442; AAM64988.1; ALT_INIT; mRNA.
DR PIR; T52625; T52625.
DR RefSeq; NP_181404.1; NM_129427.5.
DR PDB; 6N10; X-ray; 2.30 A; A=1-412.
DR PDBsum; 6N10; -.
DR AlphaFoldDB; O23722; -.
DR SMR; O23722; -.
DR STRING; 3702.AT2G38700.1; -.
DR PaxDb; O23722; -.
DR PRIDE; O23722; -.
DR ProteomicsDB; 251369; -.
DR EnsemblPlants; AT2G38700.1; AT2G38700.1; AT2G38700.
DR GeneID; 818452; -.
DR Gramene; AT2G38700.1; AT2G38700.1; AT2G38700.
DR KEGG; ath:AT2G38700; -.
DR Araport; AT2G38700; -.
DR TAIR; locus:2064092; AT2G38700.
DR eggNOG; KOG2833; Eukaryota.
DR HOGENOM; CLU_040369_4_4_1; -.
DR InParanoid; O23722; -.
DR OMA; EIAYTFD; -.
DR OrthoDB; 1065019at2759; -.
DR PhylomeDB; O23722; -.
DR BioCyc; ARA:AT2G38700-MON; -.
DR BioCyc; MetaCyc:AT2G38700-MON; -.
DR BRENDA; 4.1.1.33; 399.
DR UniPathway; UPA00057; UER00100.
DR PRO; PR:O23722; -.
DR Proteomes; UP000006548; Chromosome 2.
DR ExpressionAtlas; O23722; baseline and differential.
DR GO; GO:0005829; C:cytosol; HDA:TAIR.
DR GO; GO:0005777; C:peroxisome; IDA:UniProtKB.
DR GO; GO:0005524; F:ATP binding; IEA:UniProtKB-KW.
DR GO; GO:0004163; F:diphosphomevalonate decarboxylase activity; IDA:UniProtKB.
DR GO; GO:0042802; F:identical protein binding; IPI:UniProtKB.
DR GO; GO:0019287; P:isopentenyl diphosphate biosynthetic process, mevalonate pathway; IDA:UniProtKB.
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 3D-structure; 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..412
FT /note="Diphosphomevalonate decarboxylase MVD1, peroxisomal"
FT /id="PRO_0000435607"
FT MOTIF 40..48
FT /note="Peroxisomal targeting signal PTS2"
FT /evidence="ECO:0000305|PubMed:21655959"
FT BINDING 23..26
FT /ligand="(R)-5-diphosphomevalonate"
FT /ligand_id="ChEBI:CHEBI:57557"
FT /evidence="ECO:0000269|PubMed:31268677,
FT ECO:0007744|PDB:6N10"
FT BINDING 78
FT /ligand="(R)-5-diphosphomevalonate"
FT /ligand_id="ChEBI:CHEBI:57557"
FT /evidence="ECO:0000269|PubMed:31268677,
FT ECO:0007744|PDB:6N10"
FT BINDING 161..166
FT /ligand="(R)-5-diphosphomevalonate"
FT /ligand_id="ChEBI:CHEBI:57557"
FT /evidence="ECO:0000269|PubMed:31268677,
FT ECO:0007744|PDB:6N10"
FT BINDING 217
FT /ligand="(R)-5-diphosphomevalonate"
FT /ligand_id="ChEBI:CHEBI:57557"
FT /evidence="ECO:0000269|PubMed:31268677,
FT ECO:0007744|PDB:6N10"
FT STRAND 8..14
FT /evidence="ECO:0007829|PDB:6N10"
FT STRAND 17..21
FT /evidence="ECO:0007829|PDB:6N10"
FT STRAND 26..28
FT /evidence="ECO:0007829|PDB:6N10"
FT TURN 29..32
FT /evidence="ECO:0007829|PDB:6N10"
FT STRAND 33..36
FT /evidence="ECO:0007829|PDB:6N10"
FT STRAND 38..43
FT /evidence="ECO:0007829|PDB:6N10"
FT TURN 46..48
FT /evidence="ECO:0007829|PDB:6N10"
FT STRAND 50..56
FT /evidence="ECO:0007829|PDB:6N10"
FT STRAND 64..67
FT /evidence="ECO:0007829|PDB:6N10"
FT STRAND 70..72
FT /evidence="ECO:0007829|PDB:6N10"
FT HELIX 77..87
FT /evidence="ECO:0007829|PDB:6N10"
FT STRAND 93..95
FT /evidence="ECO:0007829|PDB:6N10"
FT TURN 96..99
FT /evidence="ECO:0007829|PDB:6N10"
FT STRAND 100..102
FT /evidence="ECO:0007829|PDB:6N10"
FT HELIX 104..108
FT /evidence="ECO:0007829|PDB:6N10"
FT STRAND 112..120
FT /evidence="ECO:0007829|PDB:6N10"
FT TURN 122..124
FT /evidence="ECO:0007829|PDB:6N10"
FT HELIX 128..143
FT /evidence="ECO:0007829|PDB:6N10"
FT HELIX 150..158
FT /evidence="ECO:0007829|PDB:6N10"
FT HELIX 162..168
FT /evidence="ECO:0007829|PDB:6N10"
FT STRAND 169..175
FT /evidence="ECO:0007829|PDB:6N10"
FT STRAND 188..192
FT /evidence="ECO:0007829|PDB:6N10"
FT TURN 196..199
FT /evidence="ECO:0007829|PDB:6N10"
FT STRAND 201..207
FT /evidence="ECO:0007829|PDB:6N10"
FT HELIX 216..226
FT /evidence="ECO:0007829|PDB:6N10"
FT HELIX 230..236
FT /evidence="ECO:0007829|PDB:6N10"
FT HELIX 238..250
FT /evidence="ECO:0007829|PDB:6N10"
FT HELIX 254..273
FT /evidence="ECO:0007829|PDB:6N10"
FT STRAND 275..277
FT /evidence="ECO:0007829|PDB:6N10"
FT HELIX 284..298
FT /evidence="ECO:0007829|PDB:6N10"
FT STRAND 305..309
FT /evidence="ECO:0007829|PDB:6N10"
FT STRAND 311..313
FT /evidence="ECO:0007829|PDB:6N10"
FT STRAND 315..321
FT /evidence="ECO:0007829|PDB:6N10"
FT HELIX 322..335
FT /evidence="ECO:0007829|PDB:6N10"
FT STRAND 339..341
FT /evidence="ECO:0007829|PDB:6N10"
FT HELIX 344..347
FT /evidence="ECO:0007829|PDB:6N10"
FT STRAND 348..350
FT /evidence="ECO:0007829|PDB:6N10"
FT TURN 353..355
FT /evidence="ECO:0007829|PDB:6N10"
FT TURN 366..368
FT /evidence="ECO:0007829|PDB:6N10"
FT HELIX 369..372
FT /evidence="ECO:0007829|PDB:6N10"
FT STRAND 380..387
FT /evidence="ECO:0007829|PDB:6N10"
FT HELIX 399..401
FT /evidence="ECO:0007829|PDB:6N10"
FT TURN 406..408
FT /evidence="ECO:0007829|PDB:6N10"
SQ SEQUENCE 412 AA; 45586 MW; 2387AD2F2B84EEA5 CRC64;
MAEEKWVVMV TAQTPTNIAV IKYWGKRDEV RILPINDSIS VTLDPDHLCT LTTVAVSPSF
DRDRMWLNGK EISLSGSRYQ NCLREIRSRA DDVEDKEKGI KIAKKDWEKL HLHIASHNNF
PTAAGLASSA AGFACLVFAL AKLMNVNEDP SQLSAIARQG SGSACRSLFG GFVKWNMGNK
EDGSDSVAVQ LVDDKHWDDL VIIIAVVSSR QKETSSTSGM RESVETSLLL QHRAKEVVPV
RILQMEEAIK NRDFTSFTKL TCSDSNQFHA VCMDTSPPIF YMNDTSHRII SLVEKWNRSA
GTPEIAYTFD AGPNAVMIAR NRKVAVELLQ GLLYCFPPKP DTDMKSYVLG DTSIVKEAGL
EGELPQGIKD KIGSQDQKGE VSYFICSRPG RGPVVLQDQT QALLHPQTGL PK
