IDI2_SACSH
ID IDI2_SACSH Reviewed; 368 AA.
AC P61615;
DT 24-MAY-2004, integrated into UniProtKB/Swiss-Prot.
DT 24-MAY-2004, sequence version 1.
DT 03-AUG-2022, entry version 78.
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;
OS Saccharolobus shibatae (Sulfolobus shibatae).
OC Archaea; Crenarchaeota; Thermoprotei; Sulfolobales; Sulfolobaceae;
OC Saccharolobus.
OX NCBI_TaxID=2286;
RN [1]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA].
RX PubMed=15009187; DOI=10.1111/j.1432-1033.2004.04010.x;
RA Yamashita S., Hemmi H., Ikeda Y., Nakayama T., Nishino T.;
RT "Type 2 isopentenyl diphosphate isomerase from a thermoacidophilic archaeon
RT Sulfolobus shibatae.";
RL Eur. J. Biochem. 271:1087-1093(2004).
RN [2]
RP X-RAY CRYSTALLOGRAPHY (2.00 ANGSTROMS) IN COMPLEX WITH FMN; SUBSTRATE
RP ANALOGS AND MAGNESIUM, FUNCTION, MUTAGENESIS OF ARG-7; LYS-8; HIS-11;
RP THR-68; SER-96; ASN-125; HIS-155; ASN-157; GLN-160; GLU-161; LYS-193;
RP GLU-194; ASP-216; GLU-229 AND ARG-232, COFACTOR, AND SUBUNIT.
RX PubMed=19158086; DOI=10.1074/jbc.m808438200;
RA Unno H., Yamashita S., Ikeda Y., Sekiguchi S.Y., Yoshida N., Yoshimura T.,
RA Kusunoki M., Nakayama T., Nishino T., Hemmi H.;
RT "New role of flavin as a general acid-base catalyst with no redox function
RT in type 2 isopentenyl-diphosphate isomerase.";
RL J. Biol. Chem. 284:9160-9167(2009).
RN [3]
RP X-RAY CRYSTALLOGRAPHY (2.20 ANGSTROMS) IN COMPLEX WITH FMN; SUBSTRATE
RP ANALOGS AND MAGNESIUM, FUNCTION, CATALYTIC ACTIVITY, MUTAGENESIS OF
RP GLN-160, BIOPHYSICOCHEMICAL PROPERTIES, COFACTOR, AND SUBUNIT.
RX PubMed=22158896; DOI=10.1073/pnas.1115749108;
RA Nagai T., Unno H., Janczak M.W., Yoshimura T., Poulter C.D., Hemmi H.;
RT "Covalent modification of reduced flavin mononucleotide in type-2
RT isopentenyl diphosphate isomerase by active-site-directed inhibitors.";
RL Proc. Natl. Acad. Sci. U.S.A. 108:20461-20466(2011).
RN [4]
RP X-RAY CRYSTALLOGRAPHY (1.70 ANGSTROMS) IN COMPLEX WITH FMN ANALOG,
RP FUNCTION, MUTAGENESIS OF GLU-13 AND ARG-235, COFACTOR, AND SUBUNIT.
RX PubMed=22505674; DOI=10.1128/jb.00068-12;
RA Nakatani H., Goda S., Unno H., Nagai T., Yoshimura T., Hemmi H.;
RT "Substrate-induced change in the quaternary structure of type 2 isopentenyl
RT diphosphate isomerase from Sulfolobus shibatae.";
RL J. Bacteriol. 194:3216-3224(2012).
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, ECO:0000269|PubMed:19158086,
CC ECO:0000269|PubMed:22158896, ECO:0000269|PubMed:22505674}.
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 ECO:0000269|PubMed:22158896};
CC -!- COFACTOR:
CC Name=FMN; Xref=ChEBI:CHEBI:58210;
CC Evidence={ECO:0000269|PubMed:19158086, ECO:0000269|PubMed:22158896,
CC ECO:0000269|PubMed:22505674};
CC -!- COFACTOR:
CC Name=NADPH; Xref=ChEBI:CHEBI:57783;
CC Evidence={ECO:0000269|PubMed:19158086};
CC -!- COFACTOR:
CC Name=Mg(2+); Xref=ChEBI:CHEBI:18420;
CC Evidence={ECO:0000269|PubMed:19158086, ECO:0000269|PubMed:22158896};
CC -!- BIOPHYSICOCHEMICAL PROPERTIES:
CC Kinetic parameters:
CC KM=7.39 uM for IPP (at pH 6 and 60 degrees Celsius)
CC {ECO:0000269|PubMed:22158896};
CC Note=kcat is 29.9 sec(-1) for isomerase activity with IPP (at pH 6
CC and 60 degrees Celsius).;
CC -!- SUBUNIT: Homooctamer. Dimer of tetramers. {ECO:0000255|HAMAP-
CC Rule:MF_00354, ECO:0000269|PubMed:19158086,
CC ECO:0000269|PubMed:22158896, ECO:0000269|PubMed:22505674}.
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}.
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DR EMBL; AB118244; BAC82424.1; -; Genomic_DNA.
DR PDB; 2ZRU; X-ray; 2.00 A; A/B/C/D=1-368.
DR PDB; 2ZRV; X-ray; 2.30 A; A/B/C/D=1-368.
DR PDB; 2ZRW; X-ray; 2.40 A; A/B/C/D=1-368.
DR PDB; 2ZRX; X-ray; 3.00 A; A/B/C/D=1-368.
DR PDB; 2ZRY; X-ray; 2.64 A; A/B/C/D=1-368.
DR PDB; 2ZRZ; X-ray; 2.90 A; A/B/C/D=1-368.
DR PDB; 3B03; X-ray; 2.20 A; A/B/C/D=1-368.
DR PDB; 3B04; X-ray; 2.30 A; A/B/C/D=1-368.
DR PDB; 3B05; X-ray; 2.20 A; A/B/C/D=1-368.
DR PDB; 3B06; X-ray; 2.29 A; A/B/C/D=1-368.
DR PDB; 3VKJ; X-ray; 1.70 A; A/B/C/D=1-368.
DR PDBsum; 2ZRU; -.
DR PDBsum; 2ZRV; -.
DR PDBsum; 2ZRW; -.
DR PDBsum; 2ZRX; -.
DR PDBsum; 2ZRY; -.
DR PDBsum; 2ZRZ; -.
DR PDBsum; 3B03; -.
DR PDBsum; 3B04; -.
DR PDBsum; 3B05; -.
DR PDBsum; 3B06; -.
DR PDBsum; 3VKJ; -.
DR AlphaFoldDB; P61615; -.
DR SMR; P61615; -.
DR BioCyc; MetaCyc:MON-14625; -.
DR BRENDA; 5.3.3.2; 6162.
DR SABIO-RK; P61615; -.
DR EvolutionaryTrace; P61615; -.
DR GO; GO:0005737; C:cytoplasm; IEA:UniProtKB-SubCell.
DR GO; GO:0010181; F:FMN binding; IDA:UniProtKB.
DR GO; GO:0004452; F:isopentenyl-diphosphate delta-isomerase activity; IDA:UniProtKB.
DR GO; GO:0000287; F:magnesium ion binding; IDA:UniProtKB.
DR GO; GO:0070402; F:NADPH binding; IDA:UniProtKB.
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.
FT CHAIN 1..368
FT /note="Isopentenyl-diphosphate delta-isomerase"
FT /id="PRO_0000134454"
FT BINDING 7..8
FT /ligand="substrate"
FT BINDING 65
FT /ligand="FMN"
FT /ligand_id="ChEBI:CHEBI:58210"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00354,
FT ECO:0000269|PubMed:19158086, ECO:0000269|PubMed:22158896"
FT BINDING 66..68
FT /ligand="FMN"
FT /ligand_id="ChEBI:CHEBI:58210"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00354,
FT ECO:0000269|PubMed:19158086, ECO:0000269|PubMed:22158896"
FT BINDING 96..98
FT /ligand="substrate"
FT BINDING 96
FT /ligand="FMN"
FT /ligand_id="ChEBI:CHEBI:58210"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00354,
FT ECO:0000269|PubMed:19158086, ECO:0000269|PubMed:22158896"
FT BINDING 125
FT /ligand="FMN"
FT /ligand_id="ChEBI:CHEBI:58210"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00354,
FT ECO:0000269|PubMed:19158086, ECO:0000269|PubMed:22158896"
FT BINDING 160
FT /ligand="substrate"
FT BINDING 161
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00354,
FT ECO:0000269|PubMed:19158086, ECO:0000269|PubMed:22158896"
FT BINDING 193
FT /ligand="FMN"
FT /ligand_id="ChEBI:CHEBI:58210"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00354,
FT ECO:0000269|PubMed:19158086, ECO:0000269|PubMed:22158896"
FT BINDING 218
FT /ligand="FMN"
FT /ligand_id="ChEBI:CHEBI:58210"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00354,
FT ECO:0000269|PubMed:19158086, ECO:0000269|PubMed:22158896"
FT BINDING 223
FT /ligand="FMN"
FT /ligand_id="ChEBI:CHEBI:58210"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00354,
FT ECO:0000269|PubMed:19158086, ECO:0000269|PubMed:22158896"
FT BINDING 275..277
FT /ligand="FMN"
FT /ligand_id="ChEBI:CHEBI:58210"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00354,
FT ECO:0000269|PubMed:19158086, ECO:0000269|PubMed:22158896"
FT BINDING 296..297
FT /ligand="FMN"
FT /ligand_id="ChEBI:CHEBI:58210"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00354,
FT ECO:0000269|PubMed:19158086, ECO:0000269|PubMed:22158896"
FT MUTAGEN 7
FT /note="R->A: Does not affect the proper folding of the
FT enzyme, but it shows significant loss of isomerase
FT activity."
FT /evidence="ECO:0000269|PubMed:19158086"
FT MUTAGEN 8
FT /note="K->A: Does not affect the proper folding of the
FT enzyme, but it shows significant loss of isomerase
FT activity."
FT /evidence="ECO:0000269|PubMed:19158086"
FT MUTAGEN 11
FT /note="H->A: Does not affect the proper folding of the
FT enzyme, but it shows significant reduction of isomerase
FT activity."
FT /evidence="ECO:0000269|PubMed:19158086"
FT MUTAGEN 13
FT /note="E->R: This mutant is heat stable and its affinity
FT binding for IPP is smaller than that of the wild-type. It
FT is in the tetrameric state even at a concentration where
FT the wild-type enzyme dominantly formed an octamer; when
FT associated with E-235."
FT /evidence="ECO:0000269|PubMed:22505674"
FT MUTAGEN 68
FT /note="T->A: Does not affect the proper folding of the
FT enzyme, but it shows significant reduction of isomerase
FT activity."
FT /evidence="ECO:0000269|PubMed:19158086"
FT MUTAGEN 96
FT /note="S->A: Does not affect the proper folding of the
FT enzyme, but it shows significant reduction of isomerase
FT activity."
FT /evidence="ECO:0000269|PubMed:19158086"
FT MUTAGEN 125
FT /note="N->A: Does not affect the proper folding of the
FT enzyme, but it shows significant reduction of isomerase
FT activity."
FT /evidence="ECO:0000269|PubMed:19158086"
FT MUTAGEN 155
FT /note="H->A: Does not affect the proper folding of the
FT enzyme, but it shows significant reduction of isomerase
FT activity."
FT /evidence="ECO:0000269|PubMed:19158086"
FT MUTAGEN 157
FT /note="N->A: Does not affect the proper folding of the
FT enzyme, but it shows significant loss of isomerase
FT activity."
FT /evidence="ECO:0000269|PubMed:19158086"
FT MUTAGEN 160
FT /note="Q->A: Does not affect the proper folding of the
FT enzyme, but it shows significant loss of isomerase
FT activity."
FT /evidence="ECO:0000269|PubMed:19158086,
FT ECO:0000269|PubMed:22158896"
FT MUTAGEN 160
FT /note="Q->E: 10-fold decrease in the catalytic efficiency."
FT /evidence="ECO:0000269|PubMed:19158086,
FT ECO:0000269|PubMed:22158896"
FT MUTAGEN 160
FT /note="Q->H: 23-fold decrease in the catalytic efficiency."
FT /evidence="ECO:0000269|PubMed:19158086,
FT ECO:0000269|PubMed:22158896"
FT MUTAGEN 160
FT /note="Q->L: 28-fold decrease in the catalytic efficiency
FT and 5-fold decrease in the affinity binding for IPP."
FT /evidence="ECO:0000269|PubMed:19158086,
FT ECO:0000269|PubMed:22158896"
FT MUTAGEN 160
FT /note="Q->N: 150-fold decrease in the catalytic efficiency
FT and 2-fold decrease in the affinity binding for IPP."
FT /evidence="ECO:0000269|PubMed:19158086,
FT ECO:0000269|PubMed:22158896"
FT MUTAGEN 161
FT /note="E->A: Does not affect the proper folding of the
FT enzyme, but it shows significant loss of isomerase
FT activity."
FT /evidence="ECO:0000269|PubMed:19158086"
FT MUTAGEN 193
FT /note="K->A: Shows significant loss of isomerase activity.
FT Binds FMN with very low affinity, but the global structure
FT of the mutant has not been altered by the mutation."
FT /evidence="ECO:0000269|PubMed:19158086"
FT MUTAGEN 194
FT /note="E->A: Does not affect the proper folding of the
FT enzyme, but it shows significant reduction of isomerase
FT activity."
FT /evidence="ECO:0000269|PubMed:19158086"
FT MUTAGEN 216
FT /note="D->A: Does not affect the proper folding of the
FT enzyme, but it shows significant reduction of isomerase
FT activity."
FT /evidence="ECO:0000269|PubMed:19158086"
FT MUTAGEN 229
FT /note="E->A: Does not affect the proper folding of the
FT enzyme, but it shows significant reduction of isomerase
FT activity."
FT /evidence="ECO:0000269|PubMed:19158086"
FT MUTAGEN 232
FT /note="R->A: Does not affect the proper folding of the
FT enzyme, but it shows significant reduction of isomerase
FT activity."
FT /evidence="ECO:0000269|PubMed:19158086"
FT MUTAGEN 235
FT /note="R->E: This mutant is heat stable and its affinity
FT binding for IPP is smaller than that of the wild-type. It
FT is in the tetrameric state even at a concentration where
FT the wild-type enzyme dominantly formed an octamer; when
FT associated with R-13."
FT /evidence="ECO:0000269|PubMed:22505674"
FT HELIX 10..17
FT /evidence="ECO:0007829|PDB:3VKJ"
FT HELIX 29..31
FT /evidence="ECO:0007829|PDB:3VKJ"
FT STRAND 32..34
FT /evidence="ECO:0007829|PDB:3VKJ"
FT STRAND 41..43
FT /evidence="ECO:0007829|PDB:3VKJ"
FT HELIX 44..46
FT /evidence="ECO:0007829|PDB:3VKJ"
FT STRAND 51..53
FT /evidence="ECO:0007829|PDB:3VKJ"
FT STRAND 56..64
FT /evidence="ECO:0007829|PDB:3VKJ"
FT HELIX 72..88
FT /evidence="ECO:0007829|PDB:3VKJ"
FT HELIX 98..102
FT /evidence="ECO:0007829|PDB:3VKJ"
FT HELIX 104..106
FT /evidence="ECO:0007829|PDB:3VKJ"
FT HELIX 108..116
FT /evidence="ECO:0007829|PDB:3VKJ"
FT STRAND 118..120
FT /evidence="ECO:0007829|PDB:3VKJ"
FT STRAND 122..127
FT /evidence="ECO:0007829|PDB:3VKJ"
FT HELIX 128..132
FT /evidence="ECO:0007829|PDB:3VKJ"
FT HELIX 137..146
FT /evidence="ECO:0007829|PDB:3VKJ"
FT STRAND 150..155
FT /evidence="ECO:0007829|PDB:3VKJ"
FT HELIX 158..163
FT /evidence="ECO:0007829|PDB:3VKJ"
FT STRAND 164..166
FT /evidence="ECO:0007829|PDB:3VKJ"
FT HELIX 174..183
FT /evidence="ECO:0007829|PDB:3VKJ"
FT STRAND 190..193
FT /evidence="ECO:0007829|PDB:3VKJ"
FT STRAND 195..197
FT /evidence="ECO:0007829|PDB:3VKJ"
FT HELIX 201..209
FT /evidence="ECO:0007829|PDB:3VKJ"
FT STRAND 214..216
FT /evidence="ECO:0007829|PDB:3VKJ"
FT HELIX 225..235
FT /evidence="ECO:0007829|PDB:3VKJ"
FT HELIX 240..246
FT /evidence="ECO:0007829|PDB:3VKJ"
FT TURN 247..249
FT /evidence="ECO:0007829|PDB:3VKJ"
FT HELIX 254..264
FT /evidence="ECO:0007829|PDB:3VKJ"
FT STRAND 269..275
FT /evidence="ECO:0007829|PDB:3VKJ"
FT HELIX 279..288
FT /evidence="ECO:0007829|PDB:3VKJ"
FT STRAND 291..295
FT /evidence="ECO:0007829|PDB:3VKJ"
FT HELIX 297..305
FT /evidence="ECO:0007829|PDB:3VKJ"
FT HELIX 307..327
FT /evidence="ECO:0007829|PDB:3VKJ"
FT HELIX 333..337
FT /evidence="ECO:0007829|PDB:3VKJ"
FT STRAND 341..343
FT /evidence="ECO:0007829|PDB:3VKJ"
FT HELIX 345..354
FT /evidence="ECO:0007829|PDB:3VKJ"
FT HELIX 358..365
FT /evidence="ECO:0007829|PDB:3VKJ"
SQ SEQUENCE 368 AA; 40427 MW; 062245BEB52924BC CRC64;
MPDIVNRKVE HVEIAAFENV DGLSSSTFLN DVILVHQGFP GISFSEINTK TKFFRKEISV
PVMVTGMTGG RNELGRINKI IAEVAEKFGI PMGVGSQRVA IEKAEARESF AIVRKVAPTI
PIIANLGMPQ LVKGYGLKEF QDAIQMIEAD AIAVHLNPAQ EVFQPEGEPE YQIYALEKLR
DISKELSVPI IVKESGNGIS METAKLLYSY GIKNFDTSGQ GGTNWIAIEM IRDIRRGNWK
AESAKNFLDW GVPTAASIME VRYSVPDSFL VGSGGIRSGL DAAKAIALGA DIAGMALPVL
KSAIEGKESL EQFFRKIIFE LKAAMMLTGS KDVDALKKTS IVILGKLKEW AEYRGINLSI
YEKVRKRE
