IDI2_ARATH
ID IDI2_ARATH Reviewed; 284 AA.
AC Q42553;
DT 30-MAY-2000, integrated into UniProtKB/Swiss-Prot.
DT 01-NOV-1996, sequence version 1.
DT 03-AUG-2022, entry version 153.
DE RecName: Full=Isopentenyl-diphosphate Delta-isomerase II, chloroplastic;
DE EC=5.3.3.2;
DE AltName: Full=Isopentenyl pyrophosphate isomerase II;
DE Short=IPP isomerase II;
DE Flags: Precursor;
GN Name=IPP2; OrderedLocusNames=At3g02780; ORFNames=F13E7.28;
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 [MRNA].
RX PubMed=9484444; DOI=10.1023/a:1005935516274;
RA Campbell M., Hahn F.M., Poulter C.D., Leustek T.;
RT "Analysis of the isopentenyl diphosphate isomerase gene family from
RT Arabidopsis thaliana.";
RL Plant Mol. Biol. 36:323-328(1998).
RN [2]
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 [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 ACETYLATION [LARGE SCALE ANALYSIS] AT ALA-46, CLEAVAGE OF TRANSIT PEPTIDE
RP [LARGE SCALE ANALYSIS] AFTER ARG-45, AND IDENTIFICATION BY MASS
RP SPECTROMETRY [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).
CC -!- FUNCTION: Catalyzes the 1,3-allylic rearrangement of the homoallylic
CC substrate isopentenyl (IPP) to its highly electrophilic allylic isomer,
CC dimethylallyl diphosphate (DMAPP). {ECO:0000250}.
CC -!- CATALYTIC ACTIVITY:
CC Reaction=isopentenyl diphosphate = dimethylallyl diphosphate;
CC Xref=Rhea:RHEA:23284, ChEBI:CHEBI:57623, ChEBI:CHEBI:128769;
CC EC=5.3.3.2;
CC -!- COFACTOR:
CC Name=Mg(2+); Xref=ChEBI:CHEBI:18420; Evidence={ECO:0000250};
CC Note=Binds 1 Mg(2+) ion per subunit. {ECO:0000250};
CC -!- PATHWAY: Isoprenoid biosynthesis; dimethylallyl diphosphate
CC biosynthesis; dimethylallyl diphosphate from isopentenyl diphosphate:
CC step 1/1.
CC -!- PATHWAY: Porphyrin-containing compound metabolism; chlorophyll
CC biosynthesis.
CC -!- SUBCELLULAR LOCATION: Plastid, chloroplast {ECO:0000305}.
CC -!- SIMILARITY: Belongs to the IPP isomerase type 1 family. {ECO:0000305}.
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DR EMBL; U49259; AAC49920.1; -; mRNA.
DR EMBL; AC018363; AAF26982.1; -; Genomic_DNA.
DR EMBL; CP002686; AEE73859.1; -; Genomic_DNA.
DR EMBL; AF428343; AAL16273.1; -; mRNA.
DR EMBL; AY127023; AAM83247.1; -; mRNA.
DR EMBL; AY143845; AAN28784.1; -; mRNA.
DR PIR; S71370; S71370.
DR RefSeq; NP_186927.1; NM_111146.4.
DR AlphaFoldDB; Q42553; -.
DR SMR; Q42553; -.
DR BioGRID; 6293; 1.
DR IntAct; Q42553; 1.
DR STRING; 3702.AT3G02780.1; -.
DR iPTMnet; Q42553; -.
DR MetOSite; Q42553; -.
DR PaxDb; Q42553; -.
DR PRIDE; Q42553; -.
DR ProteomicsDB; 232199; -.
DR DNASU; 820960; -.
DR EnsemblPlants; AT3G02780.1; AT3G02780.1; AT3G02780.
DR GeneID; 820960; -.
DR Gramene; AT3G02780.1; AT3G02780.1; AT3G02780.
DR KEGG; ath:AT3G02780; -.
DR Araport; AT3G02780; -.
DR TAIR; locus:2075412; AT3G02780.
DR eggNOG; KOG0142; Eukaryota.
DR HOGENOM; CLU_060552_0_0_1; -.
DR InParanoid; Q42553; -.
DR OrthoDB; 1281908at2759; -.
DR PhylomeDB; Q42553; -.
DR BioCyc; ARA:AT3G02780-MON; -.
DR BioCyc; MetaCyc:AT3G02780-MON; -.
DR BRENDA; 5.3.3.2; 399.
DR UniPathway; UPA00059; UER00104.
DR UniPathway; UPA00668; -.
DR PRO; PR:Q42553; -.
DR Proteomes; UP000006548; Chromosome 3.
DR ExpressionAtlas; Q42553; baseline and differential.
DR Genevisible; Q42553; AT.
DR GO; GO:0009507; C:chloroplast; HDA:TAIR.
DR GO; GO:0005737; C:cytoplasm; IBA:GO_Central.
DR GO; GO:0005829; C:cytosol; IDA:TAIR.
DR GO; GO:0005739; C:mitochondrion; IDA:TAIR.
DR GO; GO:0004452; F:isopentenyl-diphosphate delta-isomerase activity; IBA:GO_Central.
DR GO; GO:0046872; F:metal ion binding; IEA:UniProtKB-KW.
DR GO; GO:0015995; P:chlorophyll biosynthetic process; IEA:UniProtKB-UniPathway.
DR GO; GO:0050992; P:dimethylallyl diphosphate biosynthetic process; IEA:UniProtKB-UniPathway.
DR GO; GO:0009908; P:flower development; IMP:TAIR.
DR GO; GO:0009240; P:isopentenyl diphosphate biosynthetic process; IBA:GO_Central.
DR GO; GO:0015979; P:photosynthesis; IEA:UniProtKB-KW.
DR CDD; cd02885; IPP_Isomerase; 1.
DR InterPro; IPR011876; IsopentenylPP_isomerase_typ1.
DR InterPro; IPR015797; NUDIX_hydrolase-like_dom_sf.
DR InterPro; IPR000086; NUDIX_hydrolase_dom.
DR Pfam; PF00293; NUDIX; 1.
DR SUPFAM; SSF55811; SSF55811; 1.
DR TIGRFAMs; TIGR02150; IPP_isom_1; 1.
DR PROSITE; PS51462; NUDIX; 1.
PE 1: Evidence at protein level;
KW Acetylation; Chlorophyll biosynthesis; Chloroplast; Isomerase;
KW Isoprene biosynthesis; Magnesium; Metal-binding; Photosynthesis; Plastid;
KW Reference proteome; Transit peptide.
FT TRANSIT 1..45
FT /note="Chloroplast"
FT /evidence="ECO:0000255, ECO:0007744|PubMed:22223895"
FT CHAIN 46..284
FT /note="Isopentenyl-diphosphate Delta-isomerase II,
FT chloroplastic"
FT /id="PRO_0000205233"
FT DOMAIN 102..254
FT /note="Nudix hydrolase"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00794"
FT MOTIF 140..170
FT /note="Nudix box"
FT ACT_SITE 139
FT /evidence="ECO:0000250"
FT ACT_SITE 201
FT /evidence="ECO:0000250"
FT BINDING 88
FT /ligand="substrate"
FT /evidence="ECO:0000250"
FT BINDING 92
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /evidence="ECO:0000250"
FT BINDING 104
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /evidence="ECO:0000250"
FT BINDING 123
FT /ligand="substrate"
FT /evidence="ECO:0000250"
FT BINDING 127
FT /ligand="substrate"
FT /evidence="ECO:0000250"
FT BINDING 140
FT /ligand="substrate"
FT /evidence="ECO:0000250"
FT BINDING 199
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /evidence="ECO:0000250"
FT BINDING 201
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /evidence="ECO:0000250"
FT MOD_RES 46
FT /note="N-acetylalanine"
FT /evidence="ECO:0007744|PubMed:22223895"
SQ SEQUENCE 284 AA; 32607 MW; 614D02F354E242FF CRC64;
MSASSLFNLP LIRLRSLALS SSFSSFRFAH RPLSSISPRK LPNFRAFSGT AMTDTKDAGM
DAVQRRLMFE DECILVDETD RVVGHDSKYN CHLMENIEAK NLLHRAFSVF LFNSKYELLL
QQRSNTKVTF PLVWTNTCCS HPLYRESELI QDNALGVRNA AQRKLLDELG IVAEDVPVDE
FTPLGRMLYK APSDGKWGEH ELDYLLFIVR DVKVQPNPDE VAEIKYVSRE ELKELVKKAD
AGEEGLKLSP WFRLVVDNFL MKWWDHVEKG TLVEAIDMKT IHKL
