HICDH_THET2
ID HICDH_THET2 Reviewed; 334 AA.
AC Q72IW9; Q8RQU4;
DT 29-MAY-2013, integrated into UniProtKB/Swiss-Prot.
DT 05-JUL-2004, sequence version 1.
DT 03-AUG-2022, entry version 100.
DE RecName: Full=Isocitrate/homoisocitrate dehydrogenase {ECO:0000305|PubMed:27601325};
DE EC=1.1.1.286 {ECO:0000269|PubMed:12427751, ECO:0000269|PubMed:27601325};
DE AltName: Full=Homoisocitrate dehydrogenase {ECO:0000303|PubMed:27601325};
DE Short=HICDH {ECO:0000303|PubMed:27601325};
GN Name=hicd; Synonyms=hdh, hicdh; OrderedLocusNames=TT_C1012;
OS Thermus thermophilus (strain ATCC BAA-163 / DSM 7039 / HB27).
OC Bacteria; Deinococcus-Thermus; Deinococci; Thermales; Thermaceae; Thermus.
OX NCBI_TaxID=262724;
RN [1]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA], CATALYTIC ACTIVITY, FUNCTION, SUBUNIT,
RP DISRUPTION PHENOTYPE, PATHWAY, BIOPHYSICOCHEMICAL PROPERTIES, AND
RP MUTAGENESIS OF ARG-85.
RC STRAIN=ATCC BAA-163 / DSM 7039 / HB27;
RX PubMed=12427751; DOI=10.1074/jbc.m205133200;
RA Miyazaki J., Kobashi N., Nishiyama M., Yamane H.;
RT "Characterization of homoisocitrate dehydrogenase involved in lysine
RT biosynthesis of an extremely thermophilic bacterium, Thermus thermophilus
RT HB27, and evolutionary implication of beta-decarboxylating dehydrogenase.";
RL J. Biol. Chem. 278:1864-1871(2003).
RN [2]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=ATCC BAA-163 / DSM 7039 / HB27;
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 [3]
RP X-RAY CRYSTALLOGRAPHY (1.85 ANGSTROMS), CATALYTIC ACTIVITY, MUTAGENESIS OF
RP TYR-125 AND VAL-135, AND SUBUNIT.
RC STRAIN=ATCC BAA-163 / DSM 7039 / HB27;
RX PubMed=16166541; DOI=10.1128/jb.187.19.6779-6788.2005;
RA Miyazaki J., Asada K., Fushinobu S., Kuzuyama T., Nishiyama M.;
RT "Crystal structure of tetrameric homoisocitrate dehydrogenase from an
RT extreme thermophile, Thermus thermophilus: involvement of hydrophobic
RT dimer-dimer interaction in extremely high thermotolerance.";
RL J. Bacteriol. 187:6779-6788(2005).
RN [4]
RP X-RAY CRYSTALLOGRAPHY (2.40 ANGSTROMS) OF MUTANT
RP VAL-57/ILE-72/MET-85/ALA-86/THR-208/TYR-217/MET-238/MET-310, CATALYTIC
RP ACTIVITY, FUNCTION, AND MUTAGENESIS OF GLU-57; SER-72; ARG-85; TYR-86;
RP MET-208; PHE-217; VAL-238 AND ARG-310.
RC STRAIN=ATCC BAA-163 / DSM 7039 / HB27;
RX PubMed=20735360; DOI=10.1042/bj20101246;
RA Suzuki Y., Asada K., Miyazaki J., Tomita T., Kuzuyama T., Nishiyama M.;
RT "Enhancement of the latent 3-isopropylmalate dehydrogenase activity of
RT promiscuous homoisocitrate dehydrogenase by directed evolution.";
RL Biochem. J. 431:401-410(2010).
RN [5] {ECO:0007744|PDB:4YB4}
RP X-RAY CRYSTALLOGRAPHY (2.50 ANGSTROMS) IN COMPLEX WITH
RP (1R,2S)-HOMOISOCITRATE; MAGNESIUM AND NAD, FUNCTION, CATALYTIC ACTIVITY,
RP COFACTOR, AND BIOPHYSICOCHEMICAL PROPERTIES.
RX PubMed=27601325; DOI=10.1016/j.bbrc.2016.09.004;
RA Takahashi K., Tomita T., Kuzuyama T., Nishiyama M.;
RT "Determinants of dual substrate specificity revealed by the crystal
RT structure of homoisocitrate dehydrogenase from Thermus thermophilus in
RT complex with homoisocitrate, Mg(2+) and NADH.";
RL Biochem. Biophys. Res. Commun. 478:1688-1693(2016).
CC -!- FUNCTION: Catalyzes the NAD(+)-dependent oxidative decarboxylation of
CC homoisocitrate to 2-oxoadipate (alpha-ketoadipate), a reaction involved
CC in lysine biosynthesis through the alpha-aminoadipate pathway. In
CC addition, has high activity with isocitrate, but is inactive with 3-
CC isopropylmalate. {ECO:0000269|PubMed:12427751,
CC ECO:0000269|PubMed:20735360, ECO:0000269|PubMed:27601325}.
CC -!- CATALYTIC ACTIVITY:
CC Reaction=(2R,3S)-homoisocitrate + NAD(+) = 2-oxoadipate + CO2 + NADH;
CC Xref=Rhea:RHEA:11900, ChEBI:CHEBI:15404, ChEBI:CHEBI:16526,
CC ChEBI:CHEBI:57499, ChEBI:CHEBI:57540, ChEBI:CHEBI:57945;
CC EC=1.1.1.286; Evidence={ECO:0000269|PubMed:12427751,
CC ECO:0000269|PubMed:16166541, ECO:0000269|PubMed:20735360,
CC ECO:0000269|PubMed:27601325};
CC PhysiologicalDirection=left-to-right; Xref=Rhea:RHEA:11901;
CC Evidence={ECO:0000305|PubMed:27601325};
CC -!- CATALYTIC ACTIVITY:
CC Reaction=D-threo-isocitrate + NAD(+) = 2-oxoglutarate + CO2 + NADH;
CC Xref=Rhea:RHEA:23632, ChEBI:CHEBI:15562, ChEBI:CHEBI:16526,
CC ChEBI:CHEBI:16810, ChEBI:CHEBI:57540, ChEBI:CHEBI:57945;
CC EC=1.1.1.286; Evidence={ECO:0000269|PubMed:12427751,
CC ECO:0000269|PubMed:27601325};
CC PhysiologicalDirection=left-to-right; Xref=Rhea:RHEA:23633;
CC Evidence={ECO:0000305|PubMed:27601325};
CC -!- COFACTOR:
CC Name=Mg(2+); Xref=ChEBI:CHEBI:18420;
CC Evidence={ECO:0000269|PubMed:27601325};
CC Note=Binds 1 Mg(2+) ion per subunit. {ECO:0000269|PubMed:27601325};
CC -!- BIOPHYSICOCHEMICAL PROPERTIES:
CC Kinetic parameters:
CC KM=7486 uM for (1R,2S)-homoisocitrate {ECO:0000269|PubMed:12427751};
CC KM=405 uM for D-threo-isocitrate {ECO:0000269|PubMed:12427751};
CC KM=210 uM for (1R,2S)-homoisocitrate {ECO:0000269|PubMed:27601325};
CC KM=290 uM for D-threo-isocitrate {ECO:0000269|PubMed:27601325};
CC Note=kcat is 33 sec(-1) with (1R,2S)-homoisocitrate as substrate.
CC kcat is 76 sec(-1) with D-threo-isocitrate as substrate.;
CC -!- PATHWAY: Amino-acid biosynthesis; L-lysine biosynthesis via AAA
CC pathway; L-alpha-aminoadipate from 2-oxoglutarate: step 4/5.
CC {ECO:0000269|PubMed:12427751}.
CC -!- SUBUNIT: Homotetramer. Dimer of dimers. The homotetramer can
CC transiently dissociate into homodimers. {ECO:0000269|PubMed:12427751,
CC ECO:0000269|PubMed:16166541}.
CC -!- DISRUPTION PHENOTYPE: Does not grow on minimal medium. Requires alpha-
CC aminoadipate or lysine for growth. {ECO:0000269|PubMed:12427751}.
CC -!- MISCELLANEOUS: In vitro directed evolution leads to mutagenesis of key
CC residues and increased activity with 3-isopropylmalate.
CC -!- SIMILARITY: Belongs to the isocitrate and isopropylmalate
CC dehydrogenases family. {ECO:0000305}.
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DR EMBL; AB075751; BAB88861.1; -; Genomic_DNA.
DR EMBL; AE017221; AAS81354.1; -; Genomic_DNA.
DR RefSeq; WP_011173431.1; NC_005835.1.
DR PDB; 1X0L; X-ray; 1.85 A; A/B=2-334.
DR PDB; 3AH3; X-ray; 2.40 A; A/B/C/D=1-334.
DR PDB; 4YB4; X-ray; 2.50 A; A/B/C/D=1-334.
DR PDBsum; 1X0L; -.
DR PDBsum; 3AH3; -.
DR PDBsum; 4YB4; -.
DR AlphaFoldDB; Q72IW9; -.
DR SMR; Q72IW9; -.
DR STRING; 262724.TT_C1012; -.
DR EnsemblBacteria; AAS81354; AAS81354; TT_C1012.
DR GeneID; 3169501; -.
DR KEGG; tth:TT_C1012; -.
DR eggNOG; COG0473; Bacteria.
DR HOGENOM; CLU_031953_0_1_0; -.
DR OMA; TCAHKAN; -.
DR OrthoDB; 1551125at2; -.
DR BRENDA; 1.1.1.286; 2305.
DR BRENDA; 1.1.1.85; 2305.
DR SABIO-RK; Q72IW9; -.
DR UniPathway; UPA00033; UER00030.
DR Proteomes; UP000000592; Chromosome.
DR GO; GO:0047046; F:homoisocitrate dehydrogenase activity; IDA:UniProtKB.
DR GO; GO:0004449; F:isocitrate dehydrogenase (NAD+) activity; IEA:RHEA.
DR GO; GO:0046872; F:metal ion binding; IEA:UniProtKB-KW.
DR GO; GO:0019878; P:lysine biosynthetic process via aminoadipic acid; IMP:UniProtKB.
DR InterPro; IPR024084; IsoPropMal-DH-like_dom.
DR Pfam; PF00180; Iso_dh; 1.
DR SMART; SM01329; Iso_dh; 1.
PE 1: Evidence at protein level;
KW 3D-structure; Amino-acid biosynthesis; Lysine biosynthesis; Magnesium;
KW Metal-binding; NAD; Oxidoreductase.
FT CHAIN 1..334
FT /note="Isocitrate/homoisocitrate dehydrogenase"
FT /id="PRO_0000422304"
FT BINDING 70..72
FT /ligand="NADH"
FT /ligand_id="ChEBI:CHEBI:57945"
FT /evidence="ECO:0000269|PubMed:27601325,
FT ECO:0007744|PDB:4YB4"
FT BINDING 72
FT /ligand="(2R,3S)-homoisocitrate"
FT /ligand_id="ChEBI:CHEBI:15404"
FT /ligand_note="ligand shared between homodimeric partners"
FT /note="in other chain"
FT /evidence="ECO:0000269|PubMed:27601325,
FT ECO:0007744|PDB:4YB4"
FT BINDING 85
FT /ligand="(2R,3S)-homoisocitrate"
FT /ligand_id="ChEBI:CHEBI:15404"
FT /ligand_note="ligand shared between homodimeric partners"
FT /note="in other chain"
FT /evidence="ECO:0000269|PubMed:27601325,
FT ECO:0007744|PDB:4YB4"
FT BINDING 88
FT /ligand="(2R,3S)-homoisocitrate"
FT /ligand_id="ChEBI:CHEBI:15404"
FT /ligand_note="ligand shared between homodimeric partners"
FT /note="in other chain"
FT /evidence="ECO:0000269|PubMed:27601325,
FT ECO:0007744|PDB:4YB4"
FT BINDING 98
FT /ligand="(2R,3S)-homoisocitrate"
FT /ligand_id="ChEBI:CHEBI:15404"
FT /ligand_note="ligand shared between homodimeric partners"
FT /note="in other chain"
FT /evidence="ECO:0000269|PubMed:27601325,
FT ECO:0007744|PDB:4YB4"
FT BINDING 118
FT /ligand="(2R,3S)-homoisocitrate"
FT /ligand_id="ChEBI:CHEBI:15404"
FT /ligand_note="ligand shared between homodimeric partners"
FT /note="in other chain"
FT /evidence="ECO:0000269|PubMed:27601325,
FT ECO:0007744|PDB:4YB4"
FT BINDING 125
FT /ligand="(2R,3S)-homoisocitrate"
FT /ligand_id="ChEBI:CHEBI:15404"
FT /ligand_note="ligand shared between homodimeric partners"
FT /note="in other chain"
FT /evidence="ECO:0000269|PubMed:27601325,
FT ECO:0007744|PDB:4YB4"
FT BINDING 171
FT /ligand="(2R,3S)-homoisocitrate"
FT /ligand_id="ChEBI:CHEBI:15404"
FT /ligand_note="ligand shared between homodimeric partners"
FT /evidence="ECO:0000269|PubMed:27601325,
FT ECO:0007744|PDB:4YB4"
FT BINDING 173
FT /ligand="(2R,3S)-homoisocitrate"
FT /ligand_id="ChEBI:CHEBI:15404"
FT /ligand_note="ligand shared between homodimeric partners"
FT /evidence="ECO:0000269|PubMed:27601325,
FT ECO:0007744|PDB:4YB4"
FT BINDING 173
FT /ligand="NADH"
FT /ligand_id="ChEBI:CHEBI:57945"
FT /evidence="ECO:0000269|PubMed:27601325,
FT ECO:0007744|PDB:4YB4"
FT BINDING 204
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /evidence="ECO:0000269|PubMed:27601325,
FT ECO:0000312|PDB:4YB4"
FT BINDING 228
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /evidence="ECO:0000269|PubMed:27601325,
FT ECO:0000312|PDB:4YB4"
FT BINDING 232
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /evidence="ECO:0000269|PubMed:27601325,
FT ECO:0000312|PDB:4YB4"
FT BINDING 261..265
FT /ligand="NADH"
FT /ligand_id="ChEBI:CHEBI:57945"
FT /evidence="ECO:0000269|PubMed:27601325,
FT ECO:0007744|PDB:4YB4"
FT BINDING 273
FT /ligand="NADH"
FT /ligand_id="ChEBI:CHEBI:57945"
FT /evidence="ECO:0000269|PubMed:27601325,
FT ECO:0007744|PDB:4YB4"
FT SITE 85
FT /note="Important for substrate specificity and
FT discrimination against 3-isopropylmalate"
FT MUTAGEN 57
FT /note="E->V: Confers enzyme activity with 3-
FT isopropylmalate; when associated with I-72; M-85; A-86; T-
FT 208; Y-217; M-238 and M-310."
FT /evidence="ECO:0000269|PubMed:20735360"
FT MUTAGEN 72
FT /note="S->I: Confers enzyme activity with 3-
FT isopropylmalate; when associated with V-57; M-85; A-86; T-
FT 208; Y-217; M-238 and M-310."
FT /evidence="ECO:0000269|PubMed:20735360"
FT MUTAGEN 78..86
FT /note="PGFFGAIRY->EGYSSPIVA: Reduces activity with
FT homoisocitrate. Abolishes activity with isocitrate. No
FT activity with 3-isopropylmalate."
FT MUTAGEN 78..83
FT /note="PGFFGA->EGYSSP: Reduces activity with
FT homoisocitrate. Reduces activity with isocitrate. No
FT activity with 3-isopropylmalate."
FT MUTAGEN 80..83
FT /note="FFGA->YSSP: Strongly reduces activity with
FT homoisocitrate. Reduces activity with isocitrate. No
FT activity with 3-isopropylmalate."
FT MUTAGEN 85
FT /note="R->M: Confers enzyme activity with 3-
FT isopropylmalate; when associated with V-57; I-72; A-86; T-
FT 208; Y-217; M-238 and M-310."
FT /evidence="ECO:0000269|PubMed:12427751,
FT ECO:0000269|PubMed:20735360"
FT MUTAGEN 85
FT /note="R->V: Confers low enzyme activity with 3-
FT isopropylmalate. Reduces activity with homoisocitrate.
FT Abolishes activity with isocitrate."
FT /evidence="ECO:0000269|PubMed:12427751,
FT ECO:0000269|PubMed:20735360"
FT MUTAGEN 86
FT /note="Y->A: Confers enzyme activity with 3-
FT isopropylmalate; when associated with V-57; I-72; M-85; T-
FT 208; Y-217; M-238 and M-310."
FT /evidence="ECO:0000269|PubMed:20735360"
FT MUTAGEN 125
FT /note="Y->A: Reduces catalytic efficiency with isocitrate."
FT /evidence="ECO:0000269|PubMed:16166541"
FT MUTAGEN 135
FT /note="V->M: Formation of homodimers instead of
FT homotetramers. Increased affinity for isocitrate. Reduces
FT enzyme activity with isocitrate."
FT /evidence="ECO:0000269|PubMed:16166541"
FT MUTAGEN 208
FT /note="M->T: Confers enzyme activity with 3-
FT isopropylmalate; when associated with V-57; I-72; M-85; A-
FT 86; T-208; Y-217; M-238 and M-310."
FT /evidence="ECO:0000269|PubMed:20735360"
FT MUTAGEN 217
FT /note="F->Y: Confers enzyme activity with 3-
FT isopropylmalate; when associated with V-57; I-72; M-85; A-
FT 86; T-208; M-238 and M-310."
FT /evidence="ECO:0000269|PubMed:20735360"
FT MUTAGEN 238
FT /note="V->M: Confers enzyme activity with 3-
FT isopropylmalate; when associated with V-57; I-72; M-85; A-
FT 86; T-208; Y-217; and M-310."
FT /evidence="ECO:0000269|PubMed:20735360"
FT MUTAGEN 310
FT /note="R->M: Confers enzyme activity with 3-
FT isopropylmalate; when associated with V-57; I-72; M-85; A-
FT 86; T-208; Y-217; and M-238."
FT /evidence="ECO:0000269|PubMed:20735360"
FT STRAND 3..11
FT /evidence="ECO:0007829|PDB:1X0L"
FT HELIX 14..26
FT /evidence="ECO:0007829|PDB:1X0L"
FT TURN 27..29
FT /evidence="ECO:0007829|PDB:1X0L"
FT STRAND 32..37
FT /evidence="ECO:0007829|PDB:1X0L"
FT HELIX 41..47
FT /evidence="ECO:0007829|PDB:1X0L"
FT STRAND 48..51
FT /evidence="ECO:0007829|PDB:1X0L"
FT HELIX 53..60
FT /evidence="ECO:0007829|PDB:1X0L"
FT STRAND 62..69
FT /evidence="ECO:0007829|PDB:1X0L"
FT STRAND 74..76
FT /evidence="ECO:0007829|PDB:3AH3"
FT HELIX 83..90
FT /evidence="ECO:0007829|PDB:1X0L"
FT STRAND 95..101
FT /evidence="ECO:0007829|PDB:1X0L"
FT STRAND 113..119
FT /evidence="ECO:0007829|PDB:1X0L"
FT HELIX 121..123
FT /evidence="ECO:0007829|PDB:1X0L"
FT HELIX 124..126
FT /evidence="ECO:0007829|PDB:4YB4"
FT STRAND 129..132
FT /evidence="ECO:0007829|PDB:1X0L"
FT STRAND 135..143
FT /evidence="ECO:0007829|PDB:1X0L"
FT HELIX 144..159
FT /evidence="ECO:0007829|PDB:1X0L"
FT STRAND 165..170
FT /evidence="ECO:0007829|PDB:1X0L"
FT TURN 172..174
FT /evidence="ECO:0007829|PDB:1X0L"
FT HELIX 178..190
FT /evidence="ECO:0007829|PDB:1X0L"
FT STRAND 196..202
FT /evidence="ECO:0007829|PDB:1X0L"
FT HELIX 203..212
FT /evidence="ECO:0007829|PDB:1X0L"
FT HELIX 214..216
FT /evidence="ECO:0007829|PDB:1X0L"
FT STRAND 218..222
FT /evidence="ECO:0007829|PDB:1X0L"
FT HELIX 224..237
FT /evidence="ECO:0007829|PDB:1X0L"
FT TURN 241..243
FT /evidence="ECO:0007829|PDB:4YB4"
FT STRAND 245..249
FT /evidence="ECO:0007829|PDB:1X0L"
FT STRAND 254..260
FT /evidence="ECO:0007829|PDB:1X0L"
FT HELIX 264..266
FT /evidence="ECO:0007829|PDB:1X0L"
FT HELIX 275..288
FT /evidence="ECO:0007829|PDB:1X0L"
FT HELIX 291..307
FT /evidence="ECO:0007829|PDB:1X0L"
FT HELIX 312..314
FT /evidence="ECO:0007829|PDB:1X0L"
FT HELIX 320..332
FT /evidence="ECO:0007829|PDB:1X0L"
SQ SEQUENCE 334 AA; 35922 MW; 82B018FED744FB49 CRC64;
MAYRICLIEG DGIGHEVIPA ARRVLEATGL PLEFVEAEAG WETFERRGTS VPEETVEKIL
SCHATLFGAA TSPTRKVPGF FGAIRYLRRR LDLYANVRPA KSRPVPGSRP GVDLVIVREN
TEGLYVEQER RYLDVAIADA VISKKASERI GRAALRIAEG RPRKTLHIAH KANVLPLTQG
LFLDTVKEVA KDFPLVNVQD IIVDNCAMQL VMRPERFDVI VTTNLLGDIL SDLAAGLVGG
LGLAPSGNIG DTTAVFEPVH GSAPDIAGKG IANPTAAILS AAMMLDYLGE KEAAKRVEKA
VDLVLERGPR TPDLGGDATT EAFTEAVVEA LKSL
