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L-threonine 3-dehydrogenase (L-ThrDH) (TDH) (EC 1.1.1.103) (L-threonine dehydrogenase)

 TDH_PYRHO               Reviewed;         348 AA.
O58389;
28-MAR-2003, integrated into UniProtKB/Swiss-Prot.
01-AUG-1998, sequence version 1.
25-OCT-2017, entry version 123.
RecName: Full=L-threonine 3-dehydrogenase {ECO:0000255|HAMAP-Rule:MF_00627};
Short=L-ThrDH {ECO:0000303|PubMed:15902509};
Short=TDH {ECO:0000255|HAMAP-Rule:MF_00627, ECO:0000303|PubMed:16233775};
EC=1.1.1.103 {ECO:0000255|HAMAP-Rule:MF_00627, ECO:0000269|PubMed:15902509, ECO:0000269|PubMed:16233775};
AltName: Full=L-threonine dehydrogenase {ECO:0000303|PubMed:15902509, ECO:0000303|PubMed:16233775};
Name=tdh {ECO:0000255|HAMAP-Rule:MF_00627}; OrderedLocusNames=PH0655;
Pyrococcus horikoshii (strain ATCC 700860 / DSM 12428 / JCM 9974 /
NBRC 100139 / OT-3).
Archaea; Euryarchaeota; Thermococci; Thermococcales; Thermococcaceae;
Pyrococcus.
NCBI_TaxID=70601;
[1]
NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
STRAIN=ATCC 700860 / DSM 12428 / JCM 9974 / NBRC 100139 / OT-3;
PubMed=9679194; DOI=10.1093/dnares/5.2.55;
Kawarabayasi Y., Sawada M., Horikawa H., Haikawa Y., Hino Y.,
Yamamoto S., Sekine M., Baba S., Kosugi H., Hosoyama A., Nagai Y.,
Sakai M., Ogura K., Otsuka R., Nakazawa H., Takamiya M., Ohfuku Y.,
Funahashi T., Tanaka T., Kudoh Y., Yamazaki J., Kushida N., Oguchi A.,
Aoki K., Yoshizawa T., Nakamura Y., Robb F.T., Horikoshi K.,
Masuchi Y., Shizuya H., Kikuchi H.;
"Complete sequence and gene organization of the genome of a hyper-
thermophilic archaebacterium, Pyrococcus horikoshii OT3.";
DNA Res. 5:55-76(1998).
[2]
FUNCTION, CATALYTIC ACTIVITY, SUBSTRATE SPECIFICITY,
BIOPHYSICOCHEMICAL PROPERTIES, COFACTOR, ENZYME REGULATION, AND
SUBUNIT.
STRAIN=ATCC 700860 / DSM 12428 / JCM 9974 / NBRC 100139 / OT-3;
PubMed=15902509; DOI=10.1007/s00792-005-0447-2;
Shimizu Y., Sakuraba H., Kawakami R., Goda S., Kawarabayasi Y.,
Ohshima T.;
"L-Threonine dehydrogenase from the hyperthermophilic archaeon
Pyrococcus horikoshii OT3: gene cloning and enzymatic
characterization.";
Extremophiles 9:317-324(2005).
[3]
FUNCTION, CATALYTIC ACTIVITY, BIOPHYSICOCHEMICAL PROPERTIES, SUBUNIT,
COFACTOR, AND ENZYME REGULATION.
PubMed=16233775; DOI=10.1263/jbb.99.175;
Higashi N., Fukada H., Ishikawa K.;
"Kinetic study of thermostable L-threonine dehydrogenase from an
archaeon Pyrococcus horikoshii.";
J. Biosci. Bioeng. 99:175-180(2005).
[4]
REACTION MECHANISM, ACTIVE SITE, AND MUTAGENESIS OF THR-44; GLU-152
AND ARG-294.
PubMed=18390572; DOI=10.1093/jb/mvn041;
Higashi N., Tanimoto K., Nishioka M., Ishikawa K., Taya M.;
"Investigating a catalytic mechanism of hyperthermophilic L-threonine
dehydrogenase from Pyrococcus horikoshii.";
J. Biochem. 144:77-85(2008).
[5]
X-RAY CRYSTALLOGRAPHY (2.05 ANGSTROMS) IN COMPLEX WITH NAD AND ZINC.
Asada Y., Kunishima N.;
"Crystal structure of PH0655 from Pyrococcus horikoshii OT3.";
Submitted (DEC-2005) to the PDB data bank.
[6]
X-RAY CRYSTALLOGRAPHY (2.05 ANGSTROMS) OF 2-348 IN COMPLEX WITH NAD
AND ZINC, SUBUNIT, AND MUTAGENESIS OF GLU-199 AND ARG-204.
PubMed=17188300; DOI=10.1016/j.jmb.2006.11.060;
Ishikawa K., Higashi N., Nakamura T., Matsuura T., Nakagawa A.;
"The first crystal structure of L-threonine dehydrogenase.";
J. Mol. Biol. 366:857-867(2007).
-!- FUNCTION: Catalyzes the NAD(+)-dependent oxidation of L-threonine
to 2-amino-3-ketobutyrate (PubMed:16233775, PubMed:15902509). Is
much less efficient when using NADP(+) instead of NAD(+)
(PubMed:16233775). To a lesser extent, also catalyzes the
oxidation of L-serine and DL-threo-3-phenylserine, but not that of
L-allo-threonine, D-threonine and D-allo-threonine and many other
L-amino acids (PubMed:15902509). {ECO:0000269|PubMed:15902509,
ECO:0000269|PubMed:16233775}.
-!- CATALYTIC ACTIVITY: L-threonine + NAD(+) = L-2-amino-3-
oxobutanoate + NADH. {ECO:0000255|HAMAP-Rule:MF_00627,
ECO:0000269|PubMed:15902509, ECO:0000269|PubMed:16233775}.
-!- COFACTOR:
Name=Zn(2+); Xref=ChEBI:CHEBI:29105;
Evidence={ECO:0000255|HAMAP-Rule:MF_00627,
ECO:0000269|PubMed:15902509, ECO:0000269|PubMed:16233775};
Note=Binds 2 Zn(2+) ions per subunit. Contains one structural ion
and one catalytic ion that seems to be less tightly bound at the
site (PubMed:16233775). Zn(2+) can be replaced by Mn(2+) or Co(2+)
to some extent (PubMed:15902509). {ECO:0000255|HAMAP-
Rule:MF_00627, ECO:0000269|PubMed:15902509,
ECO:0000305|PubMed:16233775};
-!- ENZYME REGULATION: Is totally inhibited by EDTA in vitro.
{ECO:0000269|PubMed:15902509, ECO:0000269|PubMed:16233775}.
-!- BIOPHYSICOCHEMICAL PROPERTIES:
Kinetic parameters:
KM=0.20 mM for L-threonine (at 50 degrees Celsius)
{ECO:0000269|PubMed:15902509};
KM=0.024 mM for NAD(+) (at 50 degrees Celsius)
{ECO:0000269|PubMed:15902509};
KM=0.013 mM for L-threonine (in the presence of NAD(+) as
cosubstrate, at 65 degrees Celsius)
{ECO:0000269|PubMed:16233775};
KM=0.010 mM for NAD(+) (at 65 degrees Celsius)
{ECO:0000269|PubMed:16233775};
KM=0.447 mM for L-threonine (in the presence of NAD(+) as
cosubstrate, at 65 degrees Celsius)
{ECO:0000269|PubMed:16233775};
KM=0.689 mM for NADP(+) (at 65 degrees Celsius)
{ECO:0000269|PubMed:16233775};
Vmax=1.75 mmol/min/mg enzyme for the NAD(+) oxidation of L-
threonine (at 65 degrees Celsius) {ECO:0000269|PubMed:16233775};
Vmax=1.32 mmol/min/mg enzyme for the NADP(+) oxidation of L-
threonine (at 65 degrees Celsius) {ECO:0000269|PubMed:16233775};
pH dependence:
Optimum pH is around 10. Below and above pH 10, the marked
decrease of activity is observed: the relative activities are
50, 22 and 55% at pH 9.5, 9.2 and 12, respectively. Is stable
over a wide pH range: upon heating at 50 degrees Celsius for 20
minutes, the enzyme does not lose activity at pH 4.5-10.0.
{ECO:0000269|PubMed:15902509};
Temperature dependence:
Optimum tempreature is 70 degrees Celsius. Extremely
thermostable, the activity is not lost after incubation at 100
degrees Celsius for 20 minutes. {ECO:0000269|PubMed:15902509,
ECO:0000269|PubMed:16233775};
-!- PATHWAY: Amino-acid degradation; L-threonine degradation via
oxydo-reductase pathway; glycine from L-threonine: step 1/2.
{ECO:0000255|HAMAP-Rule:MF_00627, ECO:0000305|PubMed:16233775}.
-!- SUBUNIT: Homodimer (PubMed:16233775). Homotetramer; dimer of
dimers (PubMed:17188300) (PubMed:15902509).
{ECO:0000269|PubMed:15902509, ECO:0000269|PubMed:16233775,
ECO:0000269|PubMed:17188300}.
-!- SUBCELLULAR LOCATION: Cytoplasm {ECO:0000255|HAMAP-Rule:MF_00627}.
-!- MISCELLANEOUS: The enzyme shows pro-R stereospecificity for
hydrogen transfer at the C4 position of the nicotinamide moiety of
NADH. {ECO:0000269|PubMed:15902509}.
-!- SIMILARITY: Belongs to the zinc-containing alcohol dehydrogenase
family. {ECO:0000255|HAMAP-Rule:MF_00627}.
-----------------------------------------------------------------------
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EMBL; BA000001; BAA29746.1; -; Genomic_DNA.
PIR; H71110; H71110.
RefSeq; WP_010884751.1; NC_000961.1.
PDB; 2D8A; X-ray; 2.05 A; A=1-348.
PDB; 2DFV; X-ray; 2.05 A; A/B/C=2-348.
PDBsum; 2D8A; -.
PDBsum; 2DFV; -.
ProteinModelPortal; O58389; -.
SMR; O58389; -.
MINT; MINT-1502021; -.
STRING; 70601.PH0655; -.
EnsemblBacteria; BAA29746; BAA29746; BAA29746.
GeneID; 1442986; -.
KEGG; pho:PH0655; -.
eggNOG; arCOG01459; Archaea.
eggNOG; COG1063; LUCA.
HOGENOM; HOG000294686; -.
KO; K00060; -.
OMA; QIMGHEV; -.
OrthoDB; POG093Z05R9; -.
BRENDA; 1.1.1.103; 5244.
SABIO-RK; O58389; -.
UniPathway; UPA00046; UER00505.
EvolutionaryTrace; O58389; -.
Proteomes; UP000000752; Chromosome.
GO; GO:0005737; C:cytoplasm; IEA:UniProtKB-SubCell.
GO; GO:0016597; F:amino acid binding; IDA:UniProtKB.
GO; GO:0008743; F:L-threonine 3-dehydrogenase activity; IDA:UniProtKB.
GO; GO:0070403; F:NAD+ binding; IDA:UniProtKB.
GO; GO:0070401; F:NADP+ binding; IDA:UniProtKB.
GO; GO:0008270; F:zinc ion binding; IDA:UniProtKB.
GO; GO:0019518; P:L-threonine catabolic process to glycine; IEA:UniProtKB-UniPathway.
GO; GO:0051289; P:protein homotetramerization; IDA:UniProtKB.
GO; GO:0006566; P:threonine metabolic process; IDA:UniProtKB.
HAMAP; MF_00627; Thr_dehydrog; 1.
InterPro; IPR013149; ADH_C.
InterPro; IPR013154; ADH_N.
InterPro; IPR002328; ADH_Zn_CS.
InterPro; IPR011032; GroES-like.
InterPro; IPR004627; L-Threonine_3-DHase.
InterPro; IPR036291; NAD(P)-bd_dom_sf.
InterPro; IPR020843; PKS_ER.
Pfam; PF08240; ADH_N; 1.
Pfam; PF00107; ADH_zinc_N; 1.
SMART; SM00829; PKS_ER; 1.
SUPFAM; SSF50129; SSF50129; 1.
SUPFAM; SSF51735; SSF51735; 1.
TIGRFAMs; TIGR00692; tdh; 1.
PROSITE; PS00059; ADH_ZINC; 1.
1: Evidence at protein level;
3D-structure; Complete proteome; Cytoplasm; Metal-binding; NAD; NADP;
Oxidoreductase; Zinc.
CHAIN 1 348 L-threonine 3-dehydrogenase.
/FTId=PRO_0000160877.
NP_BIND 266 268 NAD. {ECO:0000244|PDB:2D8A,
ECO:0000269|Ref.5}.
NP_BIND 291 292 NAD. {ECO:0000244|PDB:2D8A,
ECO:0000269|Ref.5}.
ACT_SITE 44 44 Charge relay system.
{ECO:0000305|PubMed:18390572}.
ACT_SITE 47 47 Charge relay system.
{ECO:0000305|PubMed:18390572}.
METAL 42 42 Zinc 1; catalytic. {ECO:0000244|PDB:2D8A,
ECO:0000255|HAMAP-Rule:MF_00627,
ECO:0000269|Ref.5,
ECO:0000305|PubMed:17188300,
ECO:0000305|PubMed:18390572}.
METAL 67 67 Zinc 1; via tele nitrogen; catalytic.
{ECO:0000244|PDB:2D8A, ECO:0000255|HAMAP-
Rule:MF_00627, ECO:0000269|Ref.5,
ECO:0000305|PubMed:17188300,
ECO:0000305|PubMed:18390572}.
METAL 68 68 Zinc 1; catalytic. {ECO:0000244|PDB:2D8A,
ECO:0000255|HAMAP-Rule:MF_00627,
ECO:0000269|Ref.5,
ECO:0000305|PubMed:17188300,
ECO:0000305|PubMed:18390572}.
METAL 97 97 Zinc 2. {ECO:0000244|PDB:2DFV,
ECO:0000255|HAMAP-Rule:MF_00627,
ECO:0000269|PubMed:17188300}.
METAL 100 100 Zinc 2. {ECO:0000244|PDB:2DFV,
ECO:0000255|HAMAP-Rule:MF_00627,
ECO:0000269|PubMed:17188300}.
METAL 103 103 Zinc 2. {ECO:0000244|PDB:2DFV,
ECO:0000255|HAMAP-Rule:MF_00627,
ECO:0000269|PubMed:17188300}.
METAL 111 111 Zinc 2. {ECO:0000244|PDB:2DFV,
ECO:0000255|HAMAP-Rule:MF_00627,
ECO:0000269|PubMed:17188300}.
BINDING 179 179 NAD; via amide nitrogen.
{ECO:0000269|PubMed:17188300,
ECO:0000269|Ref.5}.
BINDING 199 199 NAD. {ECO:0000244|PDB:2D8A,
ECO:0000244|PDB:2DFV,
ECO:0000269|PubMed:17188300,
ECO:0000269|Ref.5}.
BINDING 204 204 NAD. {ECO:0000244|PDB:2D8A,
ECO:0000244|PDB:2DFV,
ECO:0000269|PubMed:17188300,
ECO:0000269|Ref.5}.
SITE 152 152 Important for catalytic activity for the
proton relay mechanism but does not
participate directly in the coordination
of zinc atom.
{ECO:0000305|PubMed:18390572}.
MUTAGEN 44 44 T->A: Total loss of enzymatic activity.
{ECO:0000269|PubMed:18390572}.
MUTAGEN 152 152 E->A,Q: Almost complete loss of enzymatic
activity. {ECO:0000269|PubMed:18390572}.
MUTAGEN 152 152 E->C: 120-fold decrease in catalytic
efficiency.
{ECO:0000269|PubMed:18390572}.
MUTAGEN 152 152 E->D: Shows 3-fold higher turnover rate
and reduced affinities toward L-threonine
and NAD(+), compared to wild-type.
{ECO:0000269|PubMed:18390572}.
MUTAGEN 152 152 E->K: Total loss of enzymatic activity.
{ECO:0000269|PubMed:18390572}.
MUTAGEN 199 199 E->A: Large decrease in affinity for
NAD(+). {ECO:0000269|PubMed:17188300}.
MUTAGEN 204 204 R->A: Large decrease in affinity for
NAD(+). {ECO:0000269|PubMed:17188300}.
MUTAGEN 294 294 R->A: 4000-fold decrease in catalytic
efficiency.
{ECO:0000269|PubMed:18390572}.
STRAND 4 10 {ECO:0000244|PDB:2D8A}.
STRAND 12 16 {ECO:0000244|PDB:2D8A}.
STRAND 18 23 {ECO:0000244|PDB:2D8A}.
STRAND 31 40 {ECO:0000244|PDB:2D8A}.
HELIX 43 50 {ECO:0000244|PDB:2D8A}.
HELIX 55 58 {ECO:0000244|PDB:2D8A}.
STRAND 61 64 {ECO:0000244|PDB:2D8A}.
STRAND 68 76 {ECO:0000244|PDB:2D8A}.
STRAND 88 91 {ECO:0000244|PDB:2D8A}.
HELIX 101 104 {ECO:0000244|PDB:2DFV}.
HELIX 108 110 {ECO:0000244|PDB:2DFV}.
TURN 117 119 {ECO:0000244|PDB:2D8A}.
STRAND 124 132 {ECO:0000244|PDB:2D8A}.
HELIX 133 135 {ECO:0000244|PDB:2D8A}.
STRAND 136 138 {ECO:0000244|PDB:2D8A}.
HELIX 145 148 {ECO:0000244|PDB:2D8A}.
HELIX 151 161 {ECO:0000244|PDB:2D8A}.
STRAND 171 174 {ECO:0000244|PDB:2D8A}.
HELIX 178 189 {ECO:0000244|PDB:2D8A}.
STRAND 194 198 {ECO:0000244|PDB:2D8A}.
HELIX 202 211 {ECO:0000244|PDB:2D8A}.
STRAND 214 217 {ECO:0000244|PDB:2D8A}.
TURN 219 221 {ECO:0000244|PDB:2D8A}.
HELIX 224 231 {ECO:0000244|PDB:2D8A}.
TURN 232 234 {ECO:0000244|PDB:2D8A}.
STRAND 237 242 {ECO:0000244|PDB:2D8A}.
HELIX 247 256 {ECO:0000244|PDB:2D8A}.
STRAND 257 265 {ECO:0000244|PDB:2D8A}.
HELIX 277 280 {ECO:0000244|PDB:2D8A}.
TURN 281 285 {ECO:0000244|PDB:2D8A}.
STRAND 287 290 {ECO:0000244|PDB:2D8A}.
HELIX 297 309 {ECO:0000244|PDB:2D8A}.
TURN 315 317 {ECO:0000244|PDB:2D8A}.
STRAND 318 325 {ECO:0000244|PDB:2D8A}.
HELIX 328 336 {ECO:0000244|PDB:2D8A}.
STRAND 341 346 {ECO:0000244|PDB:2D8A}.
SEQUENCE 348 AA; 37786 MW; 313F368AE83F793E CRC64;
MSEKMVAIMK TKPGYGAELV EVDVPKPGPG EVLIKVLATS ICGTDLHIYE WNEWAQSRIK
PPQIMGHEVA GEVVEIGPGV EGIEVGDYVS VETHIVCGKC YACRRGQYHV CQNTKIFGVD
TDGVFAEYAV VPAQNIWKNP KSIPPEYATL QEPLGNAVDT VLAGPISGKS VLITGAGPLG
LLGIAVAKAS GAYPVIVSEP SDFRRELAKK VGADYVINPF EEDVVKEVMD ITDGNGVDVF
LEFSGAPKAL EQGLQAVTPA GRVSLLGLYP GKVTIDFNNL IIFKALTIYG ITGRHLWETW
YTVSRLLQSG KLNLDPIITH KYKGFDKYEE AFELMRAGKT GKVVFMLK


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