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IDI_CLAMS
ID   IDI_CLAMS               Reviewed;         190 AA.
AC   B0RIB7;
DT   20-MAY-2008, integrated into UniProtKB/Swiss-Prot.
DT   08-APR-2008, sequence version 1.
DT   03-AUG-2022, entry version 95.
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=CMS2609;
OS   Clavibacter michiganensis subsp. sepedonicus (strain ATCC 33113 / DSM 20744
OS   / JCM 9667 / LMG 2889 / C-1) (Corynebacterium sepedonicum).
OC   Bacteria; Actinobacteria; Micrococcales; Microbacteriaceae; Clavibacter.
OX   NCBI_TaxID=31964;
RN   [1]
RP   NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC   STRAIN=ATCC 33113 / DSM 20744 / JCM 9667 / LMG 2889 / C-1;
RX   PubMed=18192393; DOI=10.1128/jb.01598-07;
RA   Bentley S.D., Corton C., Brown S.E., Barron A., Clark L., Doggett J.,
RA   Harris B., Ormond D., Quail M.A., May G., Francis D., Knudson D.,
RA   Parkhill J., Ishimaru C.A.;
RT   "Genome of the actinomycete plant pathogen Clavibacter michiganensis subsp.
RT   sepedonicus suggests recent niche adaptation.";
RL   J. Bacteriol. 190:2150-2160(2008).
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; AM849034; CAQ02688.1; -; Genomic_DNA.
DR   RefSeq; WP_012299869.1; NZ_MZMN01000003.1.
DR   AlphaFoldDB; B0RIB7; -.
DR   SMR; B0RIB7; -.
DR   STRING; 31964.CMS2609; -.
DR   EnsemblBacteria; CAQ02688; CAQ02688; CMS2609.
DR   KEGG; cms:CMS2609; -.
DR   eggNOG; COG1443; Bacteria.
DR   HOGENOM; CLU_060552_2_0_11; -.
DR   OMA; FPLRWAN; -.
DR   UniPathway; UPA00059; UER00104.
DR   Proteomes; UP000001318; 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   3: Inferred from homology;
KW   Cytoplasm; Isomerase; Isoprene biosynthesis; Magnesium; Manganese;
KW   Metal-binding; Reference proteome.
FT   CHAIN           1..190
FT                   /note="Isopentenyl-diphosphate Delta-isomerase"
FT                   /id="PRO_1000077740"
FT   DOMAIN          32..166
FT                   /note="Nudix hydrolase"
FT   ACT_SITE        69
FT                   /evidence="ECO:0000255|HAMAP-Rule:MF_00202"
FT   ACT_SITE        118
FT                   /evidence="ECO:0000255|HAMAP-Rule:MF_00202"
FT   BINDING         27
FT                   /ligand="Mn(2+)"
FT                   /ligand_id="ChEBI:CHEBI:29035"
FT                   /evidence="ECO:0000255|HAMAP-Rule:MF_00202"
FT   BINDING         34
FT                   /ligand="Mn(2+)"
FT                   /ligand_id="ChEBI:CHEBI:29035"
FT                   /evidence="ECO:0000255|HAMAP-Rule:MF_00202"
FT   BINDING         71
FT                   /ligand="Mn(2+)"
FT                   /ligand_id="ChEBI:CHEBI:29035"
FT                   /evidence="ECO:0000255|HAMAP-Rule:MF_00202"
FT   BINDING         89
FT                   /ligand="Mg(2+)"
FT                   /ligand_id="ChEBI:CHEBI:18420"
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   BINDING         118
FT                   /ligand="Mn(2+)"
FT                   /ligand_id="ChEBI:CHEBI:29035"
FT                   /evidence="ECO:0000255|HAMAP-Rule:MF_00202"
SQ   SEQUENCE   190 AA;  20780 MW;  26B854EE9CA188EF CRC64;
     MPQHTELVVL LDDDGETIGT APKATVHTRD TALHLAFSCH VFDAEGRILV TRRAIGKLTW
     PGVWTNSFCG HPAPDEDMLE AVHRRAEQEL GLTLESVELV LPDFRYRATD AAGVVENEIC
     PVFRAVAATP VDPRPEEVGE YQWVDPEQLI PAVAHTPWAF SPWLTLQLPL LYPEHAAHAG
     LADAAAVPAA
 
 
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