IDI2_THET2
ID IDI2_THET2 Reviewed; 332 AA.
AC Q746I8;
DT 01-OCT-2014, integrated into UniProtKB/Swiss-Prot.
DT 05-JUL-2004, sequence version 1.
DT 03-AUG-2022, entry version 121.
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}; OrderedLocusNames=TT_P0067;
OS Thermus thermophilus (strain ATCC BAA-163 / DSM 7039 / HB27).
OG Plasmid pTT27.
OC Bacteria; Deinococcus-Thermus; Deinococci; Thermales; Thermaceae; Thermus.
OX NCBI_TaxID=262724;
RN [1]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=ATCC BAA-163 / DSM 7039 / HB27; PLASMID=pTT27;
RX PubMed=15064768; DOI=10.1038/nbt956;
RA Henne A., Brueggemann H., Raasch C., Wiezer A., Hartsch T., Liesegang H.,
RA Johann A., Lienard T., Gohl O., Martinez-Arias R., Jacobi C.,
RA Starkuviene V., Schlenczeck S., Dencker S., Huber R., Klenk H.-P.,
RA Kramer W., Merkl R., Gottschalk G., Fritz H.-J.;
RT "The genome sequence of the extreme thermophile Thermus thermophilus.";
RL Nat. Biotechnol. 22:547-553(2004).
RN [2]
RP FUNCTION, CATALYTIC ACTIVITY, BIOPHYSICOCHEMICAL PROPERTIES, ACTIVITY
RP REGULATION, MASS SPECTROMETRY, AND COFACTOR.
RC STRAIN=ATCC BAA-163 / DSM 7039 / HB27;
RX PubMed=17428035; DOI=10.1021/bi0616347;
RA Rothman S.C., Helm T.R., Poulter C.D.;
RT "Kinetic and spectroscopic characterization of type II isopentenyl
RT diphosphate isomerase from Thermus thermophilus: evidence for formation of
RT substrate-induced flavin species.";
RL Biochemistry 46:5437-5445(2007).
RN [3]
RP X-RAY CRYSTALLOGRAPHY (2.60 ANGSTROMS) IN COMPLEX WITH FMN, AND SUBUNIT.
RA Wada T., Park S.-Y., Tame R.H., Kuramitsu S., Yokoyama S.;
RT "Crystal Structure of IPP isomerase at I422.";
RL Submitted (MAR-2004) to the PDB data bank.
RN [4]
RP X-RAY CRYSTALLOGRAPHY (3.02 ANGSTROMS) IN COMPLEX WITH FMN, AND SUBUNIT.
RA Wada T., Park S.-Y., Tame R.H., Kuramitsu S., Yokoyama S.;
RT "Crystal Structure of IPP isomerase at P43212.";
RL Submitted (MAR-2004) to the PDB data bank.
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:17428035}.
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:17428035};
CC -!- COFACTOR:
CC Name=FMN; Xref=ChEBI:CHEBI:58210;
CC Evidence={ECO:0000255|HAMAP-Rule:MF_00354,
CC ECO:0000269|PubMed:17428035};
CC -!- COFACTOR:
CC Name=NADPH; Xref=ChEBI:CHEBI:57783;
CC Evidence={ECO:0000255|HAMAP-Rule:MF_00354,
CC ECO:0000269|PubMed:17428035};
CC -!- COFACTOR:
CC Name=Mg(2+); Xref=ChEBI:CHEBI:18420;
CC Evidence={ECO:0000255|HAMAP-Rule:MF_00354,
CC ECO:0000269|PubMed:17428035};
CC -!- ACTIVITY REGULATION: Competitively inhibited by N,N-dimethyl-2-amino-1-
CC ethyl diphosphate (NIPP) and isopentyl diphosphate.
CC {ECO:0000269|PubMed:17428035}.
CC -!- BIOPHYSICOCHEMICAL PROPERTIES:
CC Kinetic parameters:
CC KM=5.6 uM for IPP (at pH 7.6 and 37 degrees Celsius)
CC {ECO:0000269|PubMed:17428035};
CC Note=kcat is 17.9 sec(-1) for isomerase activity with IPP (at pH 7.6
CC and 37 degrees Celsius).;
CC Temperature dependence:
CC Optimum temperature is 60 degrees Celsius.
CC {ECO:0000269|PubMed:17428035};
CC -!- SUBUNIT: Homooctamer. Dimer of tetramers. {ECO:0000255|HAMAP-
CC Rule:MF_00354, ECO:0000269|Ref.3, ECO:0000269|Ref.4}.
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; AE017222; AAS82397.1; -; Genomic_DNA.
DR RefSeq; WP_011174493.1; NC_005838.1.
DR PDB; 1VCF; X-ray; 2.60 A; A/B=1-332.
DR PDB; 1VCG; X-ray; 3.02 A; A/B/C/D=1-332.
DR PDBsum; 1VCF; -.
DR PDBsum; 1VCG; -.
DR AlphaFoldDB; Q746I8; -.
DR SMR; Q746I8; -.
DR STRING; 262724.TT_P0067; -.
DR DrugBank; DB03247; Flavin mononucleotide.
DR EnsemblBacteria; AAS82397; AAS82397; TT_P0067.
DR KEGG; tth:TT_P0067; -.
DR eggNOG; COG1304; Bacteria.
DR HOGENOM; CLU_065515_1_0_0; -.
DR OMA; WDWGIPT; -.
DR OrthoDB; 1186741at2; -.
DR EvolutionaryTrace; Q746I8; -.
DR Proteomes; UP000000592; Plasmid pTT27.
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; 2.
DR PIRSF; PIRSF003314; IPP_isomerase; 1.
DR TIGRFAMs; TIGR02151; IPP_isom_2; 1.
PE 1: Evidence at protein level;
KW 3D-structure; Cadmium; Cytoplasm; Flavoprotein; FMN; Isomerase;
KW Isoprene biosynthesis; Magnesium; Metal-binding; NADP; Nucleotide-binding;
KW Plasmid.
FT CHAIN 1..332
FT /note="Isopentenyl-diphosphate delta-isomerase"
FT /id="PRO_0000430350"
FT BINDING 6..7
FT /ligand="substrate"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00354"
FT BINDING 65..67
FT /ligand="FMN"
FT /ligand_id="ChEBI:CHEBI:58210"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00354,
FT ECO:0000269|Ref.3, ECO:0000269|Ref.4"
FT BINDING 95..97
FT /ligand="substrate"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00354"
FT BINDING 95
FT /ligand="FMN"
FT /ligand_id="ChEBI:CHEBI:58210"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00354,
FT ECO:0000269|Ref.3, ECO:0000269|Ref.4"
FT BINDING 123
FT /ligand="FMN"
FT /ligand_id="ChEBI:CHEBI:58210"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00354,
FT ECO:0000269|Ref.3, ECO:0000269|Ref.4"
FT BINDING 157
FT /ligand="substrate"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00354"
FT BINDING 158
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00354"
FT BINDING 187
FT /ligand="FMN"
FT /ligand_id="ChEBI:CHEBI:58210"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00354,
FT ECO:0000269|Ref.3, ECO:0000269|Ref.4"
FT BINDING 217
FT /ligand="FMN"
FT /ligand_id="ChEBI:CHEBI:58210"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00354,
FT ECO:0000269|Ref.3, ECO:0000269|Ref.4"
FT BINDING 264..266
FT /ligand="FMN"
FT /ligand_id="ChEBI:CHEBI:58210"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00354,
FT ECO:0000269|Ref.3, ECO:0000269|Ref.4"
FT BINDING 285..286
FT /ligand="FMN"
FT /ligand_id="ChEBI:CHEBI:58210"
FT /evidence="ECO:0000305|Ref.3, ECO:0000305|Ref.4"
FT BINDING 285
FT /ligand="FMN"
FT /ligand_id="ChEBI:CHEBI:58210"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00354,
FT ECO:0000269|Ref.3, ECO:0000269|Ref.4"
FT HELIX 10..16
FT /evidence="ECO:0007829|PDB:1VCG"
FT HELIX 28..30
FT /evidence="ECO:0007829|PDB:1VCF"
FT STRAND 31..33
FT /evidence="ECO:0007829|PDB:1VCF"
FT HELIX 43..45
FT /evidence="ECO:0007829|PDB:1VCF"
FT STRAND 50..52
FT /evidence="ECO:0007829|PDB:1VCF"
FT STRAND 55..63
FT /evidence="ECO:0007829|PDB:1VCF"
FT HELIX 73..87
FT /evidence="ECO:0007829|PDB:1VCF"
FT STRAND 90..95
FT /evidence="ECO:0007829|PDB:1VCF"
FT HELIX 97..101
FT /evidence="ECO:0007829|PDB:1VCF"
FT TURN 103..105
FT /evidence="ECO:0007829|PDB:1VCF"
FT HELIX 106..109
FT /evidence="ECO:0007829|PDB:1VCF"
FT TURN 112..114
FT /evidence="ECO:0007829|PDB:1VCF"
FT STRAND 116..118
FT /evidence="ECO:0007829|PDB:1VCF"
FT STRAND 120..125
FT /evidence="ECO:0007829|PDB:1VCF"
FT HELIX 126..130
FT /evidence="ECO:0007829|PDB:1VCF"
FT HELIX 134..144
FT /evidence="ECO:0007829|PDB:1VCF"
FT STRAND 147..152
FT /evidence="ECO:0007829|PDB:1VCF"
FT HELIX 155..160
FT /evidence="ECO:0007829|PDB:1VCF"
FT HELIX 170..177
FT /evidence="ECO:0007829|PDB:1VCF"
FT STRAND 184..187
FT /evidence="ECO:0007829|PDB:1VCF"
FT STRAND 189..191
FT /evidence="ECO:0007829|PDB:1VCF"
FT HELIX 195..201
FT /evidence="ECO:0007829|PDB:1VCF"
FT STRAND 207..210
FT /evidence="ECO:0007829|PDB:1VCF"
FT HELIX 219..224
FT /evidence="ECO:0007829|PDB:1VCF"
FT HELIX 234..237
FT /evidence="ECO:0007829|PDB:1VCG"
FT HELIX 243..253
FT /evidence="ECO:0007829|PDB:1VCF"
FT STRAND 255..257
FT /evidence="ECO:0007829|PDB:1VCF"
FT STRAND 259..264
FT /evidence="ECO:0007829|PDB:1VCF"
FT HELIX 268..277
FT /evidence="ECO:0007829|PDB:1VCF"
FT STRAND 280..284
FT /evidence="ECO:0007829|PDB:1VCF"
FT HELIX 286..288
FT /evidence="ECO:0007829|PDB:1VCF"
FT HELIX 289..292
FT /evidence="ECO:0007829|PDB:1VCF"
FT HELIX 296..317
FT /evidence="ECO:0007829|PDB:1VCF"
FT HELIX 322..325
FT /evidence="ECO:0007829|PDB:1VCF"
FT STRAND 329..331
FT /evidence="ECO:0007829|PDB:1VCF"
SQ SEQUENCE 332 AA; 35901 MW; 842EC8FDD2BA9551 CRC64;
MNIRERKRKH LEACLEGEVA YQKTTTGLEG FRLRYQALAG LALGEVDLTT PFLGKTLKAP
FLIGAMTGGE ENGERINLAL AEAAEALGVG MMLGSGRILL ERPEALRSFR VRKVAPKALL
IANLGLAQLR RYGRDDLLRL VEALEADALA FHVNPLQEAV QRGDTDFRGL VERLAELLPL
PFPVMVKEVG HGLSREAALA LRDLPLAAVD VAGAGGTSWA RVEEWVRFGE VRHPELCEIG
IPTARAILEV REVLPHLPLV ASGGVYTGTD GAKALALGAD LLAVARPLLR PALEGAERVA
AWIGDYLEEL RTALFAIGAK NPKEARGRVE RV
