IDI2_BACSU
ID IDI2_BACSU Reviewed; 349 AA.
AC P50740;
DT 01-OCT-1996, integrated into UniProtKB/Swiss-Prot.
DT 27-APR-2001, sequence version 2.
DT 03-AUG-2022, entry version 141.
DE RecName: Full=Isopentenyl-diphosphate delta-isomerase {ECO:0000255|HAMAP-Rule:MF_00354};
DE Short=IPP isomerase {ECO:0000255|HAMAP-Rule:MF_00354};
DE EC=5.3.3.2 {ECO:0000255|HAMAP-Rule:MF_00354};
DE AltName: Full=Isopentenyl diphosphate:dimethylallyl diphosphate isomerase {ECO:0000255|HAMAP-Rule:MF_00354};
DE AltName: Full=Isopentenyl pyrophosphate isomerase {ECO:0000255|HAMAP-Rule:MF_00354};
DE AltName: Full=Type 2 isopentenyl diphosphate isomerase {ECO:0000255|HAMAP-Rule:MF_00354};
DE Short=IDI-2 {ECO:0000255|HAMAP-Rule:MF_00354};
GN Name=fni {ECO:0000255|HAMAP-Rule:MF_00354}; Synonyms=idi, ypgA;
GN OrderedLocusNames=BSU22870;
OS Bacillus subtilis (strain 168).
OC Bacteria; Firmicutes; Bacilli; Bacillales; Bacillaceae; Bacillus.
OX NCBI_TaxID=224308;
RN [1]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA].
RA Kuzuyama T.;
RT "Isopentenyl diphosphate isomerase from Bacillus subtilis.";
RL Submitted (AUG-2000) to the EMBL/GenBank/DDBJ databases.
RN [2]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA].
RC STRAIN=168 / Marburg / ATCC 6051 / DSM 10 / JCM 1465 / NBRC 13719 / NCIMB
RC 3610 / NRRL NRS-744 / VKM B-501;
RX PubMed=8760912; DOI=10.1099/13500872-142-8-2005;
RA Sorokin A.V., Azevedo V., Zumstein E., Galleron N., Ehrlich S.D.,
RA Serror P.;
RT "Sequence analysis of the Bacillus subtilis chromosome region between the
RT serA and kdg loci cloned in a yeast artificial chromosome.";
RL Microbiology 142:2005-2016(1996).
RN [3]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=168;
RX PubMed=9384377; DOI=10.1038/36786;
RA Kunst F., Ogasawara N., Moszer I., Albertini A.M., Alloni G., Azevedo V.,
RA Bertero M.G., Bessieres P., Bolotin A., Borchert S., Borriss R.,
RA Boursier L., Brans A., Braun M., Brignell S.C., Bron S., Brouillet S.,
RA Bruschi C.V., Caldwell B., Capuano V., Carter N.M., Choi S.-K.,
RA Codani J.-J., Connerton I.F., Cummings N.J., Daniel R.A., Denizot F.,
RA Devine K.M., Duesterhoeft A., Ehrlich S.D., Emmerson P.T., Entian K.-D.,
RA Errington J., Fabret C., Ferrari E., Foulger D., Fritz C., Fujita M.,
RA Fujita Y., Fuma S., Galizzi A., Galleron N., Ghim S.-Y., Glaser P.,
RA Goffeau A., Golightly E.J., Grandi G., Guiseppi G., Guy B.J., Haga K.,
RA Haiech J., Harwood C.R., Henaut A., Hilbert H., Holsappel S., Hosono S.,
RA Hullo M.-F., Itaya M., Jones L.-M., Joris B., Karamata D., Kasahara Y.,
RA Klaerr-Blanchard M., Klein C., Kobayashi Y., Koetter P., Koningstein G.,
RA Krogh S., Kumano M., Kurita K., Lapidus A., Lardinois S., Lauber J.,
RA Lazarevic V., Lee S.-M., Levine A., Liu H., Masuda S., Mauel C.,
RA Medigue C., Medina N., Mellado R.P., Mizuno M., Moestl D., Nakai S.,
RA Noback M., Noone D., O'Reilly M., Ogawa K., Ogiwara A., Oudega B.,
RA Park S.-H., Parro V., Pohl T.M., Portetelle D., Porwollik S.,
RA Prescott A.M., Presecan E., Pujic P., Purnelle B., Rapoport G., Rey M.,
RA Reynolds S., Rieger M., Rivolta C., Rocha E., Roche B., Rose M., Sadaie Y.,
RA Sato T., Scanlan E., Schleich S., Schroeter R., Scoffone F., Sekiguchi J.,
RA Sekowska A., Seror S.J., Serror P., Shin B.-S., Soldo B., Sorokin A.,
RA Tacconi E., Takagi T., Takahashi H., Takemaru K., Takeuchi M.,
RA Tamakoshi A., Tanaka T., Terpstra P., Tognoni A., Tosato V., Uchiyama S.,
RA Vandenbol M., Vannier F., Vassarotti A., Viari A., Wambutt R., Wedler E.,
RA Wedler H., Weitzenegger T., Winters P., Wipat A., Yamamoto H., Yamane K.,
RA Yasumoto K., Yata K., Yoshida K., Yoshikawa H.-F., Zumstein E.,
RA Yoshikawa H., Danchin A.;
RT "The complete genome sequence of the Gram-positive bacterium Bacillus
RT subtilis.";
RL Nature 390:249-256(1997).
RN [4]
RP X-RAY CRYSTALLOGRAPHY (1.90 ANGSTROMS) IN COMPLEX WITH FMN, COFACTOR, AND
RP SUBUNIT.
RX PubMed=12798687; DOI=10.1016/s0022-2836(03)00527-8;
RA Steinbacher S., Kaiser J., Gerhardt S., Eisenreich W., Huber R., Bacher A.,
RA Rohdich F.;
RT "Crystal structure of the type II isopentenyl diphosphate:dimethylallyl
RT diphosphate isomerase from Bacillus subtilis.";
RL J. Mol. Biol. 329:973-982(2003).
CC -!- FUNCTION: Involved in the biosynthesis of isoprenoids. Catalyzes the
CC 1,3-allylic rearrangement of the homoallylic substrate isopentenyl
CC (IPP) to its allylic isomer, dimethylallyl diphosphate (DMAPP).
CC {ECO:0000255|HAMAP-Rule:MF_00354}.
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_00354};
CC -!- COFACTOR:
CC Name=FMN; Xref=ChEBI:CHEBI:58210;
CC Evidence={ECO:0000255|HAMAP-Rule:MF_00354,
CC ECO:0000269|PubMed:12798687};
CC -!- COFACTOR:
CC Name=NADPH; Xref=ChEBI:CHEBI:57783;
CC Evidence={ECO:0000255|HAMAP-Rule:MF_00354};
CC -!- COFACTOR:
CC Name=Mg(2+); Xref=ChEBI:CHEBI:18420;
CC Evidence={ECO:0000255|HAMAP-Rule:MF_00354};
CC -!- SUBUNIT: Homooctamer. Dimer of tetramers. {ECO:0000255|HAMAP-
CC Rule:MF_00354, ECO:0000269|PubMed:12798687}.
CC -!- SUBCELLULAR LOCATION: Cytoplasm {ECO:0000255|HAMAP-Rule:MF_00354}.
CC -!- SIMILARITY: Belongs to the IPP isomerase type 2 family.
CC {ECO:0000255|HAMAP-Rule:MF_00354}.
CC -!- SEQUENCE CAUTION:
CC Sequence=AAC83963.1; Type=Erroneous initiation; Note=Truncated N-terminus.; Evidence={ECO:0000305};
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DR EMBL; AB047343; BAB32625.1; -; Genomic_DNA.
DR EMBL; L47648; AAC83963.1; ALT_INIT; Genomic_DNA.
DR EMBL; AL009126; CAB14203.2; -; Genomic_DNA.
DR PIR; D69935; D69935.
DR RefSeq; NP_390168.3; NC_000964.3.
DR RefSeq; WP_004399098.1; NZ_JNCM01000036.1.
DR PDB; 1P0K; X-ray; 1.90 A; A/B=1-349.
DR PDB; 1P0N; X-ray; 2.80 A; A/B=1-349.
DR PDBsum; 1P0K; -.
DR PDBsum; 1P0N; -.
DR AlphaFoldDB; P50740; -.
DR SMR; P50740; -.
DR STRING; 224308.BSU22870; -.
DR DrugBank; DB03247; Flavin mononucleotide.
DR PaxDb; P50740; -.
DR PRIDE; P50740; -.
DR EnsemblBacteria; CAB14203; CAB14203; BSU_22870.
DR GeneID; 938985; -.
DR KEGG; bsu:BSU22870; -.
DR PATRIC; fig|224308.179.peg.2494; -.
DR eggNOG; COG1304; Bacteria.
DR InParanoid; P50740; -.
DR OMA; WDWGIPT; -.
DR PhylomeDB; P50740; -.
DR BioCyc; BSUB:BSU22870-MON; -.
DR BRENDA; 5.3.3.2; 658.
DR EvolutionaryTrace; P50740; -.
DR Proteomes; UP000001570; Chromosome.
DR GO; GO:0005737; C:cytoplasm; IEA:UniProtKB-SubCell.
DR GO; GO:0010181; F:FMN binding; IEA:UniProtKB-UniRule.
DR GO; GO:0004452; F:isopentenyl-diphosphate delta-isomerase activity; IEA:UniProtKB-UniRule.
DR GO; GO:0000287; F:magnesium ion binding; IEA:UniProtKB-UniRule.
DR GO; GO:0070402; F:NADPH binding; IEA:UniProtKB-UniRule.
DR GO; GO:0016491; F:oxidoreductase activity; IEA:InterPro.
DR GO; GO:0008299; P:isoprenoid biosynthetic process; IEA:UniProtKB-UniRule.
DR CDD; cd02811; IDI-2_FMN; 1.
DR Gene3D; 3.20.20.70; -; 1.
DR HAMAP; MF_00354; Idi_2; 1.
DR InterPro; IPR013785; Aldolase_TIM.
DR InterPro; IPR000262; FMN-dep_DH.
DR InterPro; IPR011179; IPdP_isomerase.
DR PANTHER; PTHR43665; PTHR43665; 1.
DR Pfam; PF01070; FMN_dh; 1.
DR PIRSF; PIRSF003314; IPP_isomerase; 1.
DR TIGRFAMs; TIGR02151; IPP_isom_2; 1.
PE 1: Evidence at protein level;
KW 3D-structure; Cytoplasm; Flavoprotein; FMN; Isomerase;
KW Isoprene biosynthesis; Magnesium; Metal-binding; NADP; Reference proteome.
FT CHAIN 1..349
FT /note="Isopentenyl-diphosphate delta-isomerase"
FT /id="PRO_0000134404"
FT BINDING 6..7
FT /ligand="substrate"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00354"
FT BINDING 62..64
FT /ligand="FMN"
FT /ligand_id="ChEBI:CHEBI:58210"
FT /evidence="ECO:0000305|PubMed:12798687"
FT BINDING 93
FT /ligand="FMN"
FT /ligand_id="ChEBI:CHEBI:58210"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00354,
FT ECO:0000269|PubMed:12798687"
FT BINDING 122
FT /ligand="FMN"
FT /ligand_id="ChEBI:CHEBI:58210"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00354,
FT ECO:0000269|PubMed:12798687"
FT BINDING 152
FT /ligand="substrate"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00354"
FT BINDING 153
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00354"
FT BINDING 184
FT /ligand="FMN"
FT /ligand_id="ChEBI:CHEBI:58210"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00354,
FT ECO:0000269|PubMed:12798687"
FT BINDING 214
FT /ligand="FMN"
FT /ligand_id="ChEBI:CHEBI:58210"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00354"
FT BINDING 258..259
FT /ligand="FMN"
FT /ligand_id="ChEBI:CHEBI:58210"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00354,
FT ECO:0000269|PubMed:12798687"
FT BINDING 280..281
FT /ligand="FMN"
FT /ligand_id="ChEBI:CHEBI:58210"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00354,
FT ECO:0000269|PubMed:12798687"
FT HELIX 25..27
FT /evidence="ECO:0007829|PDB:1P0K"
FT STRAND 28..30
FT /evidence="ECO:0007829|PDB:1P0K"
FT HELIX 40..42
FT /evidence="ECO:0007829|PDB:1P0K"
FT STRAND 47..49
FT /evidence="ECO:0007829|PDB:1P0K"
FT STRAND 52..55
FT /evidence="ECO:0007829|PDB:1P0K"
FT STRAND 57..61
FT /evidence="ECO:0007829|PDB:1P0K"
FT HELIX 68..85
FT /evidence="ECO:0007829|PDB:1P0K"
FT TURN 95..99
FT /evidence="ECO:0007829|PDB:1P0K"
FT HELIX 101..113
FT /evidence="ECO:0007829|PDB:1P0K"
FT STRAND 115..117
FT /evidence="ECO:0007829|PDB:1P0K"
FT STRAND 119..124
FT /evidence="ECO:0007829|PDB:1P0K"
FT HELIX 129..138
FT /evidence="ECO:0007829|PDB:1P0K"
FT STRAND 142..148
FT /evidence="ECO:0007829|PDB:1P0K"
FT TURN 150..153
FT /evidence="ECO:0007829|PDB:1P0K"
FT HELIX 166..176
FT /evidence="ECO:0007829|PDB:1P0K"
FT STRAND 181..188
FT /evidence="ECO:0007829|PDB:1P0K"
FT HELIX 192..201
FT /evidence="ECO:0007829|PDB:1P0K"
FT STRAND 204..209
FT /evidence="ECO:0007829|PDB:1P0K"
FT HELIX 228..231
FT /evidence="ECO:0007829|PDB:1P0K"
FT HELIX 238..248
FT /evidence="ECO:0007829|PDB:1P0K"
FT STRAND 252..259
FT /evidence="ECO:0007829|PDB:1P0K"
FT HELIX 263..271
FT /evidence="ECO:0007829|PDB:1P0K"
FT STRAND 275..279
FT /evidence="ECO:0007829|PDB:1P0K"
FT HELIX 281..313
FT /evidence="ECO:0007829|PDB:1P0K"
FT HELIX 318..321
FT /evidence="ECO:0007829|PDB:1P0K"
FT STRAND 326..328
FT /evidence="ECO:0007829|PDB:1P0K"
FT HELIX 330..338
FT /evidence="ECO:0007829|PDB:1P0K"
FT HELIX 344..348
FT /evidence="ECO:0007829|PDB:1P0K"
SQ SEQUENCE 349 AA; 37221 MW; 3EA275B6EDEAB587 CRC64;
MTRAERKRQH INHALSIGQK RETGLDDITF VHVSLPDLAL EQVDISTKIG ELSSSSPIFI
NAMTGGGGKL TYEINKSLAR AASQAGIPLA VGSQMSALKD PSERLSYEIV RKENPNGLIF
ANLGSEATAA QAKEAVEMIG ANALQIHLNV IQEIVMPEGD RSFSGALKRI EQICSRVSVP
VIVKEVGFGM SKASAGKLYE AGAAAVDIGG YGGTNFSKIE NLRRQRQISF FNSWGISTAA
SLAEIRSEFP ASTMIASGGL QDALDVAKAI ALGASCTGMA GHFLKALTDS GEEGLLEEIQ
LILEELKLIM TVLGARTIAD LQKAPLVIKG ETHHWLTERG VNTSSYSVR
