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Homoisocitrate dehydrogenase (HICDH) (EC 1.1.1.87)

 HICDH_THET2             Reviewed;         334 AA.
Q72IW9; Q8RQU4;
29-MAY-2013, integrated into UniProtKB/Swiss-Prot.
05-JUL-2004, sequence version 1.
07-JUN-2017, entry version 83.
RecName: Full=Homoisocitrate dehydrogenase;
Short=HICDH;
EC=1.1.1.87;
Name=hicd; Synonyms=hdh, hicdh; OrderedLocusNames=TT_C1012;
Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039).
Bacteria; Deinococcus-Thermus; Deinococci; Thermales; Thermaceae;
Thermus.
NCBI_TaxID=262724;
[1]
NUCLEOTIDE SEQUENCE [GENOMIC DNA], CATALYTIC ACTIVITY, FUNCTION,
SUBUNIT, DISRUPTION PHENOTYPE, PATHWAY, BIOPHYSICOCHEMICAL PROPERTIES,
AND MUTAGENESIS OF ARG-85.
STRAIN=HB27 / ATCC BAA-163 / DSM 7039;
PubMed=12427751; DOI=10.1074/jbc.M205133200;
Miyazaki J., Kobashi N., Nishiyama M., Yamane H.;
"Characterization of homoisocitrate dehydrogenase involved in lysine
biosynthesis of an extremely thermophilic bacterium, Thermus
thermophilus HB27, and evolutionary implication of beta-
decarboxylating dehydrogenase.";
J. Biol. Chem. 278:1864-1871(2003).
[2]
NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
STRAIN=HB27 / ATCC BAA-163 / DSM 7039;
PubMed=15064768; DOI=10.1038/nbt956;
Henne A., Brueggemann H., Raasch C., Wiezer A., Hartsch T.,
Liesegang H., Johann A., Lienard T., Gohl O., Martinez-Arias R.,
Jacobi C., Starkuviene V., Schlenczeck S., Dencker S., Huber R.,
Klenk H.-P., Kramer W., Merkl R., Gottschalk G., Fritz H.-J.;
"The genome sequence of the extreme thermophile Thermus
thermophilus.";
Nat. Biotechnol. 22:547-553(2004).
[3]
X-RAY CRYSTALLOGRAPHY (1.85 ANGSTROMS), CATALYTIC ACTIVITY,
MUTAGENESIS OF TYR-125 AND VAL-135, AND SUBUNIT.
STRAIN=HB27 / ATCC BAA-163 / DSM 7039;
PubMed=16166541; DOI=10.1128/JB.187.19.6779-6788.2005;
Miyazaki J., Asada K., Fushinobu S., Kuzuyama T., Nishiyama M.;
"Crystal structure of tetrameric homoisocitrate dehydrogenase from an
extreme thermophile, Thermus thermophilus: involvement of hydrophobic
dimer-dimer interaction in extremely high thermotolerance.";
J. Bacteriol. 187:6779-6788(2005).
[4]
X-RAY CRYSTALLOGRAPHY (2.40 ANGSTROMS) OF MUTANT
VAL-57/ILE-72/MET-85/ALA-86/THR-208/TYR-217/MET-238/MET-310, CATALYTIC
ACTIVITY, FUNCTION, AND MUTAGENESIS OF GLU-57; SER-72; ARG-85; TYR-86;
MET-208; PHE-217; VAL-238 AND ARG-310.
STRAIN=HB27 / ATCC BAA-163 / DSM 7039;
PubMed=20735360; DOI=10.1042/BJ20101246;
Suzuki Y., Asada K., Miyazaki J., Tomita T., Kuzuyama T.,
Nishiyama M.;
"Enhancement of the latent 3-isopropylmalate dehydrogenase activity of
promiscuous homoisocitrate dehydrogenase by directed evolution.";
Biochem. J. 431:401-410(2010).
-!- FUNCTION: Catalyzes the NAD(+)-dependent conversion of
homoisocitrate to alpha-ketoadipate. In addition, has high
activity with citrate, but is inactive with 3-isopropylmalate.
{ECO:0000269|PubMed:12427751, ECO:0000269|PubMed:20735360}.
-!- CATALYTIC ACTIVITY: (1R,2S)-1-hydroxybutane-1,2,4-tricarboxylate +
NAD(+) = 2-oxoadipate + CO(2) + NADH.
{ECO:0000269|PubMed:12427751, ECO:0000269|PubMed:16166541,
ECO:0000269|PubMed:20735360}.
-!- COFACTOR:
Name=Mg(2+); Xref=ChEBI:CHEBI:18420; Evidence={ECO:0000250};
Name=Mn(2+); Xref=ChEBI:CHEBI:29035; Evidence={ECO:0000250};
Note=Binds 1 Mg(2+) or Mn(2+) ion per subunit. {ECO:0000250};
-!- BIOPHYSICOCHEMICAL PROPERTIES:
Kinetic parameters:
KM=7486 uM for homoisocitrate {ECO:0000269|PubMed:12427751};
KM=405 uM for isocitrate {ECO:0000269|PubMed:12427751};
-!- PATHWAY: Amino-acid biosynthesis; L-lysine biosynthesis via AAA
pathway; L-alpha-aminoadipate from 2-oxoglutarate: step 4/5.
{ECO:0000269|PubMed:12427751}.
-!- SUBUNIT: Homotetramer. Dimer of dimers. The homotetramer can
transiently dissociate into homodimers.
{ECO:0000269|PubMed:12427751, ECO:0000269|PubMed:16166541}.
-!- DISRUPTION PHENOTYPE: Does not grow on minimal medium. Requires
alpha-aminoadipate or lysine for growth.
{ECO:0000269|PubMed:12427751}.
-!- MISCELLANEOUS: In vitro directed evolution leads to mutagenesis of
key residues and increased activity with 3-isopropylmalate.
-!- SIMILARITY: Belongs to the isocitrate and isopropylmalate
dehydrogenases family. {ECO:0000305}.
-----------------------------------------------------------------------
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-----------------------------------------------------------------------
EMBL; AB075751; BAB88861.1; -; Genomic_DNA.
EMBL; AE017221; AAS81354.1; -; Genomic_DNA.
RefSeq; WP_011173431.1; NC_005835.1.
PDB; 1X0L; X-ray; 1.85 A; A/B=2-334.
PDB; 3AH3; X-ray; 2.40 A; A/B/C/D=1-334.
PDB; 4YB4; X-ray; 2.50 A; A/B/C/D=1-334.
PDBsum; 1X0L; -.
PDBsum; 3AH3; -.
PDBsum; 4YB4; -.
ProteinModelPortal; Q72IW9; -.
SMR; Q72IW9; -.
STRING; 262724.TTC1012; -.
EnsemblBacteria; AAS81354; AAS81354; TT_C1012.
KEGG; tth:TT_C1012; -.
eggNOG; ENOG4105C0C; Bacteria.
eggNOG; COG0473; LUCA.
KO; K05824; -.
OMA; GTSMFEP; -.
BRENDA; 1.1.1.85; 2305.
UniPathway; UPA00033; UER00030.
Proteomes; UP000000592; Chromosome.
GO; GO:0047046; F:homoisocitrate dehydrogenase activity; IDA:UniProtKB.
GO; GO:0046872; F:metal ion binding; IEA:UniProtKB-KW.
GO; GO:0019878; P:lysine biosynthetic process via aminoadipic acid; IMP:UniProtKB.
InterPro; IPR024084; IsoPropMal-DH-like_dom.
Pfam; PF00180; Iso_dh; 1.
SMART; SM01329; Iso_dh; 1.
1: Evidence at protein level;
3D-structure; Amino-acid biosynthesis; Complete proteome;
Lysine biosynthesis; Magnesium; Manganese; Metal-binding; NAD;
Oxidoreductase.
CHAIN 1 334 Homoisocitrate dehydrogenase.
/FTId=PRO_0000422304.
METAL 204 204 Magnesium or manganese. {ECO:0000250}.
METAL 228 228 Magnesium or manganese. {ECO:0000250}.
METAL 232 232 Magnesium or manganese. {ECO:0000250}.
BINDING 88 88 Substrate. {ECO:0000250}.
BINDING 98 98 Substrate. {ECO:0000250}.
BINDING 118 118 Substrate. {ECO:0000250}.
BINDING 204 204 Substrate. {ECO:0000250}.
SITE 85 85 Important for substrate specificity and
discrimination against 3-isopropylmalate.
SITE 125 125 Critical for catalysis. {ECO:0000250}.
SITE 171 171 Critical for catalysis. {ECO:0000250}.
MUTAGEN 57 57 E->V: Confers enzyme activity with 3-
isopropylmalate; when associated with I-
72; M-85; A-86; T-208; Y-217; M-238 and
M-310. {ECO:0000269|PubMed:20735360}.
MUTAGEN 72 72 S->I: Confers enzyme activity with 3-
isopropylmalate; when associated with V-
57; M-85; A-86; T-208; Y-217; M-238 and
M-310. {ECO:0000269|PubMed:20735360}.
MUTAGEN 78 86 PGFFGAIRY->EGYSSPIVA: Reduces activity
with homoisocitrate. Abolishes activity
with isocitrate. No activity with 3-
isopropylmalate.
MUTAGEN 78 83 PGFFGA->EGYSSP: Reduces activity with
homoisocitrate. Reduces activity with
isocitrate. No activity with 3-
isopropylmalate.
MUTAGEN 80 83 FFGA->YSSP: Strongly reduces activity
with homoisocitrate. Reduces activity
with isocitrate. No activity with 3-
isopropylmalate.
MUTAGEN 85 85 R->M: Confers enzyme activity with 3-
isopropylmalate; when associated with V-
57; I-72; A-86; T-208; Y-217; M-238 and
M-310. {ECO:0000269|PubMed:12427751,
ECO:0000269|PubMed:20735360}.
MUTAGEN 85 85 R->V: Confers low enzyme activity with 3-
isopropylmalate. Reduces activity with
homoisocitrate. Abolishes activity with
isocitrate. {ECO:0000269|PubMed:12427751,
ECO:0000269|PubMed:20735360}.
MUTAGEN 86 86 Y->A: Confers enzyme activity with 3-
isopropylmalate; when associated with V-
57; I-72; M-85; T-208; Y-217; M-238 and
M-310. {ECO:0000269|PubMed:20735360}.
MUTAGEN 125 125 Y->A: Reduces catalytic efficiency with
isocitrate.
{ECO:0000269|PubMed:16166541}.
MUTAGEN 135 135 V->M: Formation of homodimers instead of
homotetramers. Increased affinity for
isocitrate. Reduces enzyme activity with
isocitrate.
{ECO:0000269|PubMed:16166541}.
MUTAGEN 208 208 M->T: Confers enzyme activity with 3-
isopropylmalate; when associated with V-
57; I-72; M-85; A-86; T-208; Y-217; M-238
and M-310. {ECO:0000269|PubMed:20735360}.
MUTAGEN 217 217 F->Y: Confers enzyme activity with 3-
isopropylmalate; when associated with V-
57; I-72; M-85; A-86; T-208; M-238 and M-
310. {ECO:0000269|PubMed:20735360}.
MUTAGEN 238 238 V->M: Confers enzyme activity with 3-
isopropylmalate; when associated with V-
57; I-72; M-85; A-86; T-208; Y-217; and
M-310. {ECO:0000269|PubMed:20735360}.
MUTAGEN 310 310 R->M: Confers enzyme activity with 3-
isopropylmalate; when associated with V-
57; I-72; M-85; A-86; T-208; Y-217; and
M-238. {ECO:0000269|PubMed:20735360}.
STRAND 3 11 {ECO:0000244|PDB:1X0L}.
HELIX 14 26 {ECO:0000244|PDB:1X0L}.
TURN 27 29 {ECO:0000244|PDB:1X0L}.
STRAND 32 37 {ECO:0000244|PDB:1X0L}.
HELIX 41 47 {ECO:0000244|PDB:1X0L}.
STRAND 48 51 {ECO:0000244|PDB:1X0L}.
HELIX 53 60 {ECO:0000244|PDB:1X0L}.
STRAND 62 69 {ECO:0000244|PDB:1X0L}.
STRAND 74 76 {ECO:0000244|PDB:3AH3}.
HELIX 83 90 {ECO:0000244|PDB:1X0L}.
STRAND 95 101 {ECO:0000244|PDB:1X0L}.
STRAND 113 119 {ECO:0000244|PDB:1X0L}.
HELIX 121 123 {ECO:0000244|PDB:1X0L}.
HELIX 124 126 {ECO:0000244|PDB:4YB4}.
STRAND 129 132 {ECO:0000244|PDB:1X0L}.
STRAND 135 143 {ECO:0000244|PDB:1X0L}.
HELIX 144 159 {ECO:0000244|PDB:1X0L}.
STRAND 165 170 {ECO:0000244|PDB:1X0L}.
TURN 172 174 {ECO:0000244|PDB:1X0L}.
HELIX 178 190 {ECO:0000244|PDB:1X0L}.
STRAND 196 202 {ECO:0000244|PDB:1X0L}.
HELIX 203 212 {ECO:0000244|PDB:1X0L}.
HELIX 214 216 {ECO:0000244|PDB:1X0L}.
STRAND 218 222 {ECO:0000244|PDB:1X0L}.
HELIX 224 237 {ECO:0000244|PDB:1X0L}.
TURN 241 243 {ECO:0000244|PDB:4YB4}.
STRAND 245 249 {ECO:0000244|PDB:1X0L}.
STRAND 254 260 {ECO:0000244|PDB:1X0L}.
HELIX 264 266 {ECO:0000244|PDB:1X0L}.
HELIX 275 288 {ECO:0000244|PDB:1X0L}.
HELIX 291 307 {ECO:0000244|PDB:1X0L}.
HELIX 312 314 {ECO:0000244|PDB:1X0L}.
HELIX 320 332 {ECO:0000244|PDB:1X0L}.
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


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