IDI_RHOCB
ID IDI_RHOCB Reviewed; 176 AA.
AC P26173; D5ANT5;
DT 01-MAY-1992, integrated into UniProtKB/Swiss-Prot.
DT 01-MAY-1992, sequence version 1.
DT 03-AUG-2022, entry version 119.
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=Bacteriochlorophyll synthase 20 kDa chain;
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};
GN OrderedLocusNames=RCAP_rcc00674;
OS Rhodobacter capsulatus (strain ATCC BAA-309 / NBRC 16581 / SB1003).
OC Bacteria; Proteobacteria; Alphaproteobacteria; Rhodobacterales;
OC Rhodobacteraceae; Rhodobacter.
OX NCBI_TaxID=272942;
RN [1]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA].
RC STRAIN=ATCC BAA-309 / NBRC 16581 / SB1003;
RA Burke D.H., Alberti M., Armstrong G.A., Hearst J.E.;
RL Submitted (NOV-1991) to the EMBL/GenBank/DDBJ databases.
RN [2]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=ATCC BAA-309 / NBRC 16581 / SB1003;
RX PubMed=20418398; DOI=10.1128/jb.00366-10;
RA Strnad H., Lapidus A., Paces J., Ulbrich P., Vlcek C., Paces V.,
RA Haselkorn R.;
RT "Complete genome sequence of the photosynthetic purple nonsulfur bacterium
RT Rhodobacter capsulatus SB 1003.";
RL J. Bacteriol. 192:3545-3546(2010).
RN [3]
RP CHARACTERIZATION.
RX PubMed=8550491; DOI=10.1128/jb.178.3.619-624.1996;
RA Hahn F.M., Baker J.A., Poulter C.D.;
RT "Open reading frame 176 in the photosynthesis gene cluster of Rhodobacter
RT capsulatus encodes idi, a gene for isopentenyl diphosphate isomerase.";
RL J. Bacteriol. 178:619-624(1996).
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 -!- PATHWAY: Porphyrin-containing compound metabolism; chlorophyll
CC biosynthesis. {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}.
CC -!- SEQUENCE CAUTION:
CC Sequence=ADE84439.1; Type=Erroneous initiation; Note=Extended N-terminus.; Evidence={ECO:0000305};
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DR EMBL; Z11165; CAA77535.1; -; Genomic_DNA.
DR EMBL; CP001312; ADE84439.1; ALT_INIT; Genomic_DNA.
DR PIR; S17819; S17819.
DR AlphaFoldDB; P26173; -.
DR SMR; P26173; -.
DR STRING; 272942.RCAP_rcc00674; -.
DR EnsemblBacteria; ADE84439; ADE84439; RCAP_rcc00674.
DR KEGG; rcp:RCAP_rcc00674; -.
DR eggNOG; COG1443; Bacteria.
DR HOGENOM; CLU_060552_2_1_5; -.
DR UniPathway; UPA00059; UER00104.
DR UniPathway; UPA00668; -.
DR Proteomes; UP000002361; 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:0015995; P:chlorophyll biosynthetic process; IEA:UniProtKB-UniRule.
DR GO; GO:0050992; P:dimethylallyl diphosphate biosynthetic process; IEA:UniProtKB-UniPathway.
DR GO; GO:0008299; P:isoprenoid biosynthetic process; IEA:UniProtKB-UniRule.
DR GO; GO:0015979; P:photosynthesis; 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 Chlorophyll biosynthesis; Cytoplasm; Isomerase; Isoprene biosynthesis;
KW Magnesium; Manganese; Metal-binding; Photosynthesis; Reference proteome.
FT CHAIN 1..176
FT /note="Isopentenyl-diphosphate Delta-isomerase"
FT /id="PRO_0000205260"
FT DOMAIN 27..161
FT /note="Nudix hydrolase"
FT ACT_SITE 63
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00202"
FT ACT_SITE 111
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00202"
FT BINDING 23
FT /ligand="Mn(2+)"
FT /ligand_id="ChEBI:CHEBI:29035"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00202"
FT BINDING 29
FT /ligand="Mn(2+)"
FT /ligand_id="ChEBI:CHEBI:29035"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00202"
FT BINDING 63
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00202"
FT BINDING 65
FT /ligand="Mn(2+)"
FT /ligand_id="ChEBI:CHEBI:29035"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00202"
FT BINDING 83
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00202"
FT BINDING 109
FT /ligand="Mn(2+)"
FT /ligand_id="ChEBI:CHEBI:29035"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00202"
FT BINDING 111
FT /ligand="Mn(2+)"
FT /ligand_id="ChEBI:CHEBI:29035"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00202"
SQ SEQUENCE 176 AA; 20052 MW; CE7A65030E062737 CRC64;
MAEEMIPAWV EGVLQPVEKL EAHRKGLRHL AISVFVTRGN KVLLQQRALS KYHTPGLWAN
TCCTHPYWGE DAPTCAARRL GQELGIVGLK LRHMGQLEYR ADVNNGMIEH EVVEVFTAEA
PEGIEPQPDP EEVADTEWVR IDALRSEIHA NPERFTPWLK IYIEQHRDMI FPPVTA
