IDI_AGRRH
ID IDI_AGRRH Reviewed; 209 AA.
AC Q9KWD1;
DT 27-APR-2001, integrated into UniProtKB/Swiss-Prot.
DT 01-OCT-2000, sequence version 1.
DT 03-AUG-2022, entry version 103.
DE RecName: Full=Isopentenyl-diphosphate Delta-isomerase {ECO:0000255|HAMAP-Rule:MF_00202};
DE Short=IPP isomerase {ECO:0000255|HAMAP-Rule:MF_00202};
DE EC=5.3.3.2 {ECO:0000255|HAMAP-Rule:MF_00202};
DE AltName: Full=IPP:DMAPP isomerase {ECO:0000255|HAMAP-Rule:MF_00202};
DE AltName: Full=Isopentenyl pyrophosphate isomerase {ECO:0000255|HAMAP-Rule:MF_00202};
GN Name=idi {ECO:0000255|HAMAP-Rule:MF_00202}; ORFNames=riorf53;
OS Agrobacterium rhizogenes.
OG Plasmid pRi1724.
OC Bacteria; Proteobacteria; Alphaproteobacteria; Hyphomicrobiales;
OC Rhizobiaceae; Rhizobium/Agrobacterium group; Agrobacterium.
OX NCBI_TaxID=359;
RN [1]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA].
RC STRAIN=MAFF03-01724;
RX PubMed=10907845; DOI=10.1093/dnares/7.3.157;
RA Moriguchi K., Maeda Y., Satou M., Kataoka M., Tanaka N., Yoshida K.;
RT "Analysis of unique variable region of a plant root inducing plasmid,
RT pRi1724, by the construction of its physical map and library.";
RL DNA Res. 7:157-163(2000).
RN [2]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA].
RC STRAIN=MAFF03-01724;
RX PubMed=11273700; DOI=10.1006/jmbi.2001.4488;
RA Moriguchi K., Maeda Y., Satou M., Hardayani N.S.N., Kataoka M., Tanaka N.,
RA Yoshida K.;
RT "The complete nucleotide sequence of a plant root-inducing (Ri) plasmid
RT indicates its chimeric structure and evolutionary relationship between
RT tumor-inducing (Ti) and symbiotic (Sym) plasmids in Rhizobiaceae.";
RL J. Mol. Biol. 307:771-784(2001).
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:0000255|HAMAP-Rule:MF_00202}.
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; Evidence={ECO:0000255|HAMAP-Rule:MF_00202};
CC -!- COFACTOR:
CC Name=Mg(2+); Xref=ChEBI:CHEBI:18420;
CC Evidence={ECO:0000255|HAMAP-Rule:MF_00202};
CC Note=Binds 1 Mg(2+) ion per subunit. The magnesium ion binds only when
CC substrate is bound. {ECO:0000255|HAMAP-Rule:MF_00202};
CC -!- COFACTOR:
CC Name=Mn(2+); Xref=ChEBI:CHEBI:29035;
CC Evidence={ECO:0000255|HAMAP-Rule:MF_00202};
CC Note=Binds 1 Mn(2+) ion per subunit. {ECO:0000255|HAMAP-Rule:MF_00202};
CC -!- PATHWAY: Isoprenoid biosynthesis; dimethylallyl diphosphate
CC biosynthesis; dimethylallyl diphosphate from isopentenyl diphosphate:
CC step 1/1. {ECO:0000255|HAMAP-Rule:MF_00202}.
CC -!- SUBCELLULAR LOCATION: Cytoplasm {ECO:0000255|HAMAP-Rule:MF_00202}.
CC -!- SIMILARITY: Belongs to the IPP isomerase type 1 family.
CC {ECO:0000255|HAMAP-Rule:MF_00202}.
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DR EMBL; AB039932; BAA97764.1; -; Genomic_DNA.
DR EMBL; AP002086; BAB16172.1; -; Genomic_DNA.
DR RefSeq; NP_066634.1; NC_002575.1.
DR RefSeq; WP_010900243.1; NZ_KY000038.1.
DR AlphaFoldDB; Q9KWD1; -.
DR SMR; Q9KWD1; -.
DR UniPathway; UPA00059; UER00104.
DR GO; GO:0005737; C:cytoplasm; IEA:UniProtKB-SubCell.
DR GO; GO:0004452; F:isopentenyl-diphosphate delta-isomerase activity; IEA:UniProtKB-UniRule.
DR GO; GO:0046872; F:metal ion binding; IEA:UniProtKB-KW.
DR GO; GO:0050992; P:dimethylallyl diphosphate biosynthetic process; IEA:UniProtKB-UniPathway.
DR GO; GO:0008299; P:isoprenoid biosynthetic process; IEA:UniProtKB-UniRule.
DR CDD; cd02885; IPP_Isomerase; 1.
DR HAMAP; MF_00202; Idi; 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 PIRSF; PIRSF018427; Isopntndiph_ism; 1.
DR SUPFAM; SSF55811; SSF55811; 1.
DR TIGRFAMs; TIGR02150; IPP_isom_1; 1.
DR PROSITE; PS51462; NUDIX; 1.
PE 3: Inferred from homology;
KW Cytoplasm; Isomerase; Isoprene biosynthesis; Magnesium; Manganese;
KW Metal-binding; Plasmid.
FT CHAIN 1..209
FT /note="Isopentenyl-diphosphate Delta-isomerase"
FT /id="PRO_0000205239"
FT DOMAIN 36..171
FT /note="Nudix hydrolase"
FT ACT_SITE 73
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00202"
FT ACT_SITE 122
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00202"
FT BINDING 31
FT /ligand="Mn(2+)"
FT /ligand_id="ChEBI:CHEBI:29035"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00202"
FT BINDING 38
FT /ligand="Mn(2+)"
FT /ligand_id="ChEBI:CHEBI:29035"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00202"
FT BINDING 73
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00202"
FT BINDING 75
FT /ligand="Mn(2+)"
FT /ligand_id="ChEBI:CHEBI:29035"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00202"
FT BINDING 93
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00202"
FT BINDING 120
FT /ligand="Mn(2+)"
FT /ligand_id="ChEBI:CHEBI:29035"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00202"
FT BINDING 122
FT /ligand="Mn(2+)"
FT /ligand_id="ChEBI:CHEBI:29035"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00202"
SQ SEQUENCE 209 AA; 23460 MW; 4700E820DA6C64A8 CRC64;
MTLPANQSPE MVILCNELGE ATGTAPKSEI HHSDTPLHLA FSVYIFNGDN KLLVTRRASD
KITWPGVLSN SCCGHPQPGE PLTEAIERRV HEELRIRADD IRLVLPEFSY RASMTNGITE
NELCPVFAAH CKTSGVNPDL NEVSAWEWVH WQWFFESVQA ERLLVSPWCR AQVDLLAPLG
ANPSQWPVAE ERRLPKAART KIDVQLKVS
