IDI_SALTY
ID IDI_SALTY Reviewed; 181 AA.
AC Q8ZM82;
DT 15-MAY-2002, integrated into UniProtKB/Swiss-Prot.
DT 01-MAR-2002, sequence version 1.
DT 03-AUG-2022, entry version 122.
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}; OrderedLocusNames=STM3039;
OS Salmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720).
OC Bacteria; Proteobacteria; Gammaproteobacteria; Enterobacterales;
OC Enterobacteriaceae; Salmonella.
OX NCBI_TaxID=99287;
RN [1]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=LT2 / SGSC1412 / ATCC 700720;
RX PubMed=11677609; DOI=10.1038/35101614;
RA McClelland M., Sanderson K.E., Spieth J., Clifton S.W., Latreille P.,
RA Courtney L., Porwollik S., Ali J., Dante M., Du F., Hou S., Layman D.,
RA Leonard S., Nguyen C., Scott K., Holmes A., Grewal N., Mulvaney E.,
RA Ryan E., Sun H., Florea L., Miller W., Stoneking T., Nhan M., Waterston R.,
RA Wilson R.K.;
RT "Complete genome sequence of Salmonella enterica serovar Typhimurium LT2.";
RL Nature 413:852-856(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 -!- SUBUNIT: Homodimer. {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; AE006468; AAL21914.1; -; Genomic_DNA.
DR RefSeq; NP_461955.1; NC_003197.2.
DR RefSeq; WP_000133994.1; NC_003197.2.
DR PDB; 3HYQ; X-ray; 1.52 A; A=1-181.
DR PDBsum; 3HYQ; -.
DR AlphaFoldDB; Q8ZM82; -.
DR SMR; Q8ZM82; -.
DR STRING; 99287.STM3039; -.
DR PaxDb; Q8ZM82; -.
DR EnsemblBacteria; AAL21914; AAL21914; STM3039.
DR GeneID; 1254562; -.
DR KEGG; stm:STM3039; -.
DR PATRIC; fig|99287.12.peg.3219; -.
DR HOGENOM; CLU_060552_2_0_6; -.
DR OMA; FPLRWAN; -.
DR PhylomeDB; Q8ZM82; -.
DR BioCyc; SENT99287:STM3039-MON; -.
DR UniPathway; UPA00059; UER00104.
DR EvolutionaryTrace; Q8ZM82; -.
DR Proteomes; UP000001014; Chromosome.
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 1: Evidence at protein level;
KW 3D-structure; Cytoplasm; Isomerase; Isoprene biosynthesis; Magnesium;
KW Manganese; Metal-binding; Reference proteome.
FT CHAIN 1..181
FT /note="Isopentenyl-diphosphate Delta-isomerase"
FT /id="PRO_0000205265"
FT DOMAIN 30..164
FT /note="Nudix hydrolase"
FT ACT_SITE 67
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00202"
FT ACT_SITE 116
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00202"
FT BINDING 25
FT /ligand="Mn(2+)"
FT /ligand_id="ChEBI:CHEBI:29035"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00202"
FT BINDING 32
FT /ligand="Mn(2+)"
FT /ligand_id="ChEBI:CHEBI:29035"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00202"
FT BINDING 67
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00202"
FT BINDING 69
FT /ligand="Mn(2+)"
FT /ligand_id="ChEBI:CHEBI:29035"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00202"
FT BINDING 87
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00202"
FT BINDING 114
FT /ligand="Mn(2+)"
FT /ligand_id="ChEBI:CHEBI:29035"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00202"
FT BINDING 116
FT /ligand="Mn(2+)"
FT /ligand_id="ChEBI:CHEBI:29035"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00202"
FT STRAND 35..40
FT /evidence="ECO:0007829|PDB:3HYQ"
FT STRAND 46..51
FT /evidence="ECO:0007829|PDB:3HYQ"
FT STRAND 56..58
FT /evidence="ECO:0007829|PDB:3HYQ"
FT STRAND 62..68
FT /evidence="ECO:0007829|PDB:3HYQ"
FT HELIX 76..88
FT /evidence="ECO:0007829|PDB:3HYQ"
FT STRAND 92..99
FT /evidence="ECO:0007829|PDB:3HYQ"
FT STRAND 103..107
FT /evidence="ECO:0007829|PDB:3HYQ"
FT STRAND 113..117
FT /evidence="ECO:0007829|PDB:3HYQ"
FT STRAND 120..125
FT /evidence="ECO:0007829|PDB:3HYQ"
FT TURN 133..135
FT /evidence="ECO:0007829|PDB:3HYQ"
FT STRAND 136..142
FT /evidence="ECO:0007829|PDB:3HYQ"
FT HELIX 144..153
FT /evidence="ECO:0007829|PDB:3HYQ"
FT HELIX 155..157
FT /evidence="ECO:0007829|PDB:3HYQ"
FT HELIX 160..166
FT /evidence="ECO:0007829|PDB:3HYQ"
FT HELIX 169..176
FT /evidence="ECO:0007829|PDB:3HYQ"
FT TURN 177..180
FT /evidence="ECO:0007829|PDB:3HYQ"
SQ SEQUENCE 181 AA; 20781 MW; 1B0EBEA813936526 CRC64;
MTEEHVVLLD EQDKPSGTLE KYAAHTLNTP LHLAFSCWLF NEDGQLLVTR RSLSKKAWPG
VWTNSVCGHP QQGETTEEAI IRRCRFELGV EITDLTPVYP HFSYRATDPN GIVENEVCPV
FAARATSVLQ VNSEEVMDYQ WSEFKSVWKS LLATPWAFSP WMVMQASDEQ ARERLLNYCQ
R
