IDI1_ARATH
ID IDI1_ARATH Reviewed; 291 AA.
AC Q38929; Q42552; Q9FFE1;
DT 30-MAY-2000, integrated into UniProtKB/Swiss-Prot.
DT 31-MAY-2011, sequence version 3.
DT 03-AUG-2022, entry version 161.
DE RecName: Full=Isopentenyl-diphosphate Delta-isomerase I, chloroplastic;
DE EC=5.3.3.2;
DE AltName: Full=Isopentenyl pyrophosphate isomerase I;
DE Short=IPP isomerase I;
DE Flags: Precursor;
GN Name=IPP1; Synonyms=IPI1; OrderedLocusNames=At5g16440; ORFNames=MQK4.17;
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=9330910; DOI=10.1093/dnares/4.3.215;
RA Sato S., Kotani H., Nakamura Y., Kaneko T., Asamizu E., Fukami M.,
RA Miyajima N., Tabata S.;
RT "Structural analysis of Arabidopsis thaliana chromosome 5. I. Sequence
RT features of the 1.6 Mb regions covered by twenty physically assigned P1
RT clones.";
RL DNA Res. 4:215-230(1997).
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] OF 3-291 AND 58-291.
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 NUCLEOTIDE SEQUENCE [GENOMIC DNA] OF 28-291.
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 [5]
RP NUCLEOTIDE SEQUENCE [MRNA] OF 31-291.
RA Blanc V.M., Mullin K., Pichersky E.;
RT "Nucleotide sequences of Ipi genes from Arabidopsis and Clarkia.";
RL (er) Plant Gene Register PGR96-036(1996).
RN [6]
RP ACETYLATION [LARGE SCALE ANALYSIS] AT THR-2 (ISOFORM 2), CLEAVAGE OF
RP INITIATOR METHIONINE [LARGE SCALE ANALYSIS] (ISOFORM 2), AND IDENTIFICATION
RP BY MASS 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: [Isoform 1]: Plastid, chloroplast {ECO:0000305}.
CC -!- SUBCELLULAR LOCATION: [Isoform 2]: Cytoplasm {ECO:0000305}.
CC -!- ALTERNATIVE PRODUCTS:
CC Event=Alternative initiation; Named isoforms=2;
CC Name=1;
CC IsoId=Q38929-1; Sequence=Displayed;
CC Name=2;
CC IsoId=Q38929-2; Sequence=VSP_059338;
CC -!- MISCELLANEOUS: [Isoform 2]: Produced by alternative initiation at Met-
CC 59 of isoform 1. {ECO:0000305}.
CC -!- SIMILARITY: Belongs to the IPP isomerase type 1 family. {ECO:0000305}.
CC -!- SEQUENCE CAUTION:
CC Sequence=AAB67741.1; Type=Erroneous initiation; Note=Truncated N-terminus.; Evidence={ECO:0000305};
CC Sequence=AAC49932.1; Type=Erroneous initiation; Note=Truncated N-terminus.; Evidence={ECO:0000305};
CC Sequence=AAL57687.1; Type=Erroneous initiation; Note=Truncated N-terminus.; Evidence={ECO:0000305};
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DR EMBL; AB005242; BAB09611.1; -; Genomic_DNA.
DR EMBL; CP002688; AED92292.1; -; Genomic_DNA.
DR EMBL; AY065053; AAL57687.1; ALT_INIT; mRNA.
DR EMBL; AY093749; AAM10373.1; -; mRNA.
DR EMBL; U47324; AAC49932.1; ALT_INIT; Genomic_DNA.
DR EMBL; U48961; AAB67741.1; ALT_INIT; mRNA.
DR PIR; S71369; S71369.
DR RefSeq; NP_197148.3; NM_121649.6. [Q38929-1]
DR AlphaFoldDB; Q38929; -.
DR SMR; Q38929; -.
DR BioGRID; 16781; 1.
DR STRING; 3702.AT5G16440.1; -.
DR iPTMnet; Q38929; -.
DR MetOSite; Q38929; -.
DR PaxDb; Q38929; -.
DR PRIDE; Q38929; -.
DR ProteomicsDB; 232095; -. [Q38929-1]
DR EnsemblPlants; AT5G16440.1; AT5G16440.1; AT5G16440. [Q38929-1]
DR GeneID; 831505; -.
DR Gramene; AT5G16440.1; AT5G16440.1; AT5G16440. [Q38929-1]
DR KEGG; ath:AT5G16440; -.
DR Araport; AT5G16440; -.
DR TAIR; locus:2171382; AT5G16440.
DR eggNOG; KOG0142; Eukaryota.
DR HOGENOM; CLU_060552_0_0_1; -.
DR InParanoid; Q38929; -.
DR OMA; VEQEYNH; -.
DR OrthoDB; 1281908at2759; -.
DR BioCyc; ARA:AT5G16440-MON; -.
DR BioCyc; MetaCyc:AT5G16440-MON; -.
DR BRENDA; 5.3.3.2; 399.
DR UniPathway; UPA00059; UER00104.
DR UniPathway; UPA00668; -.
DR PRO; PR:Q38929; -.
DR Proteomes; UP000006548; Chromosome 5.
DR ExpressionAtlas; Q38929; baseline and differential.
DR Genevisible; Q38929; 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:0009536; C:plastid; IDA:TAIR.
DR GO; GO:0004452; F:isopentenyl-diphosphate delta-isomerase activity; IMP:TAIR.
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:0009240; P:isopentenyl diphosphate biosynthetic process; IMP:TAIR.
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; Alternative initiation; Chlorophyll biosynthesis; Chloroplast;
KW Cytoplasm; Isomerase; Isoprene biosynthesis; Magnesium; Metal-binding;
KW Photosynthesis; Plastid; Reference proteome; Transit peptide.
FT TRANSIT 1..52
FT /note="Chloroplast"
FT /evidence="ECO:0000255"
FT CHAIN 53..291
FT /note="Isopentenyl-diphosphate Delta-isomerase I,
FT chloroplastic"
FT /id="PRO_0000205232"
FT DOMAIN 109..261
FT /note="Nudix hydrolase"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00794"
FT REGION 20..43
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT MOTIF 147..177
FT /note="Nudix box"
FT COMPBIAS 20..35
FT /note="Polar residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT ACT_SITE 146
FT /evidence="ECO:0000250"
FT ACT_SITE 208
FT /evidence="ECO:0000250"
FT BINDING 95
FT /ligand="substrate"
FT /evidence="ECO:0000250"
FT BINDING 99
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /evidence="ECO:0000250"
FT BINDING 111
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /evidence="ECO:0000250"
FT BINDING 130
FT /ligand="substrate"
FT /evidence="ECO:0000250"
FT BINDING 134
FT /ligand="substrate"
FT /evidence="ECO:0000250"
FT BINDING 147
FT /ligand="substrate"
FT /evidence="ECO:0000250"
FT BINDING 206
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /evidence="ECO:0000250"
FT BINDING 208
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /evidence="ECO:0000250"
FT VAR_SEQ 1..58
FT /note="Missing (in isoform 2)"
FT /id="VSP_059338"
FT CONFLICT 254..256
FT /note="KLS -> NYL (in Ref. 4; AAC49932)"
FT /evidence="ECO:0000305"
FT INIT_MET Q38929-2:1
FT /note="Removed"
FT /evidence="ECO:0007744|PubMed:22223895"
FT MOD_RES Q38929-2:2
FT /note="N-acetylthreonine"
FT /evidence="ECO:0007744|PubMed:22223895"
SQ SEQUENCE 291 AA; 33214 MW; D626069E8B5DDC5D CRC64;
MSTASLFSFP SFHLRSLLPS LSSSSSSSSS RFAPPRLSPI RSPAPRTQLS VRAFSAVTMT
DSNDAGMDAV QRRLMFEDEC ILVDENDRVV GHDTKYNCHL MEKIEAENLL HRAFSVFLFN
SKYELLLQQR SKTKVTFPLV WTNTCCSHPL YRESELIEEN VLGVRNAAQR KLFDELGIVA
EDVPVDEFTP LGRMLYKAPS DGKWGEHEVD YLLFIVRDVK LQPNPDEVAE IKYVSREELK
ELVKKADAGD EAVKLSPWFR LVVDNFLMKW WDHVEKGTIT EAADMKTIHK L
