TDH_PYRHO
ID TDH_PYRHO Reviewed; 348 AA.
AC O58389;
DT 28-MAR-2003, integrated into UniProtKB/Swiss-Prot.
DT 01-AUG-1998, sequence version 1.
DT 03-AUG-2022, entry version 144.
DE RecName: Full=L-threonine 3-dehydrogenase {ECO:0000255|HAMAP-Rule:MF_00627};
DE Short=L-ThrDH {ECO:0000303|PubMed:15902509};
DE Short=TDH {ECO:0000255|HAMAP-Rule:MF_00627, ECO:0000303|PubMed:16233775};
DE EC=1.1.1.103 {ECO:0000255|HAMAP-Rule:MF_00627, ECO:0000269|PubMed:15902509, ECO:0000269|PubMed:16233775};
DE AltName: Full=L-threonine dehydrogenase {ECO:0000303|PubMed:15902509, ECO:0000303|PubMed:16233775};
GN Name=tdh {ECO:0000255|HAMAP-Rule:MF_00627}; OrderedLocusNames=PH0655;
OS Pyrococcus horikoshii (strain ATCC 700860 / DSM 12428 / JCM 9974 / NBRC
OS 100139 / OT-3).
OC Archaea; Euryarchaeota; Thermococci; Thermococcales; Thermococcaceae;
OC Pyrococcus.
OX NCBI_TaxID=70601;
RN [1]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=ATCC 700860 / DSM 12428 / JCM 9974 / NBRC 100139 / OT-3;
RX PubMed=9679194; DOI=10.1093/dnares/5.2.55;
RA Kawarabayasi Y., Sawada M., Horikawa H., Haikawa Y., Hino Y., Yamamoto S.,
RA Sekine M., Baba S., Kosugi H., Hosoyama A., Nagai Y., Sakai M., Ogura K.,
RA Otsuka R., Nakazawa H., Takamiya M., Ohfuku Y., Funahashi T., Tanaka T.,
RA Kudoh Y., Yamazaki J., Kushida N., Oguchi A., Aoki K., Yoshizawa T.,
RA Nakamura Y., Robb F.T., Horikoshi K., Masuchi Y., Shizuya H., Kikuchi H.;
RT "Complete sequence and gene organization of the genome of a hyper-
RT thermophilic archaebacterium, Pyrococcus horikoshii OT3.";
RL DNA Res. 5:55-76(1998).
RN [2]
RP FUNCTION, CATALYTIC ACTIVITY, SUBSTRATE SPECIFICITY, BIOPHYSICOCHEMICAL
RP PROPERTIES, COFACTOR, ACTIVITY REGULATION, AND SUBUNIT.
RC STRAIN=ATCC 700860 / DSM 12428 / JCM 9974 / NBRC 100139 / OT-3;
RX PubMed=15902509; DOI=10.1007/s00792-005-0447-2;
RA Shimizu Y., Sakuraba H., Kawakami R., Goda S., Kawarabayasi Y., Ohshima T.;
RT "L-Threonine dehydrogenase from the hyperthermophilic archaeon Pyrococcus
RT horikoshii OT3: gene cloning and enzymatic characterization.";
RL Extremophiles 9:317-324(2005).
RN [3]
RP FUNCTION, CATALYTIC ACTIVITY, BIOPHYSICOCHEMICAL PROPERTIES, SUBUNIT,
RP COFACTOR, AND ACTIVITY REGULATION.
RX PubMed=16233775; DOI=10.1263/jbb.99.175;
RA Higashi N., Fukada H., Ishikawa K.;
RT "Kinetic study of thermostable L-threonine dehydrogenase from an archaeon
RT Pyrococcus horikoshii.";
RL J. Biosci. Bioeng. 99:175-180(2005).
RN [4]
RP REACTION MECHANISM, ACTIVE SITE, AND MUTAGENESIS OF THR-44; GLU-152 AND
RP ARG-294.
RX PubMed=18390572; DOI=10.1093/jb/mvn041;
RA Higashi N., Tanimoto K., Nishioka M., Ishikawa K., Taya M.;
RT "Investigating a catalytic mechanism of hyperthermophilic L-threonine
RT dehydrogenase from Pyrococcus horikoshii.";
RL J. Biochem. 144:77-85(2008).
RN [5]
RP X-RAY CRYSTALLOGRAPHY (2.05 ANGSTROMS) IN COMPLEX WITH NAD AND ZINC.
RA Asada Y., Kunishima N.;
RT "Crystal structure of PH0655 from Pyrococcus horikoshii OT3.";
RL Submitted (DEC-2005) to the PDB data bank.
RN [6]
RP X-RAY CRYSTALLOGRAPHY (2.05 ANGSTROMS) OF 2-348 IN COMPLEX WITH NAD AND
RP ZINC, SUBUNIT, AND MUTAGENESIS OF GLU-199 AND ARG-204.
RX PubMed=17188300; DOI=10.1016/j.jmb.2006.11.060;
RA Ishikawa K., Higashi N., Nakamura T., Matsuura T., Nakagawa A.;
RT "The first crystal structure of L-threonine dehydrogenase.";
RL J. Mol. Biol. 366:857-867(2007).
CC -!- FUNCTION: Catalyzes the NAD(+)-dependent oxidation of L-threonine to 2-
CC amino-3-ketobutyrate (PubMed:16233775, PubMed:15902509). Is much less
CC efficient when using NADP(+) instead of NAD(+) (PubMed:16233775). To a
CC lesser extent, also catalyzes the oxidation of L-serine and DL-threo-3-
CC phenylserine, but not that of L-allo-threonine, D-threonine and D-allo-
CC threonine and many other L-amino acids (PubMed:15902509).
CC {ECO:0000269|PubMed:15902509, ECO:0000269|PubMed:16233775}.
CC -!- CATALYTIC ACTIVITY:
CC Reaction=L-threonine + NAD(+) = (2S)-2-amino-3-oxobutanoate + H(+) +
CC NADH; Xref=Rhea:RHEA:13161, ChEBI:CHEBI:15378, ChEBI:CHEBI:57540,
CC ChEBI:CHEBI:57926, ChEBI:CHEBI:57945, ChEBI:CHEBI:78948;
CC EC=1.1.1.103; Evidence={ECO:0000255|HAMAP-Rule:MF_00627,
CC ECO:0000269|PubMed:15902509, ECO:0000269|PubMed:16233775};
CC -!- COFACTOR:
CC Name=Zn(2+); Xref=ChEBI:CHEBI:29105;
CC Evidence={ECO:0000255|HAMAP-Rule:MF_00627,
CC ECO:0000269|PubMed:15902509, ECO:0000269|PubMed:16233775};
CC Note=Binds 2 Zn(2+) ions per subunit. Contains one structural ion and
CC one catalytic ion that seems to be less tightly bound at the site
CC (PubMed:16233775). Zn(2+) can be replaced by Mn(2+) or Co(2+) to some
CC extent (PubMed:15902509). {ECO:0000255|HAMAP-Rule:MF_00627,
CC ECO:0000269|PubMed:15902509, ECO:0000305|PubMed:16233775};
CC -!- ACTIVITY REGULATION: Is totally inhibited by EDTA in vitro.
CC {ECO:0000269|PubMed:15902509, ECO:0000269|PubMed:16233775}.
CC -!- BIOPHYSICOCHEMICAL PROPERTIES:
CC Kinetic parameters:
CC KM=0.20 mM for L-threonine (at 50 degrees Celsius)
CC {ECO:0000269|PubMed:15902509};
CC KM=0.024 mM for NAD(+) (at 50 degrees Celsius)
CC {ECO:0000269|PubMed:15902509};
CC KM=0.013 mM for L-threonine (in the presence of NAD(+) as
CC cosubstrate, at 65 degrees Celsius) {ECO:0000269|PubMed:16233775};
CC KM=0.010 mM for NAD(+) (at 65 degrees Celsius)
CC {ECO:0000269|PubMed:16233775};
CC KM=0.447 mM for L-threonine (in the presence of NAD(+) as
CC cosubstrate, at 65 degrees Celsius) {ECO:0000269|PubMed:16233775};
CC KM=0.689 mM for NADP(+) (at 65 degrees Celsius)
CC {ECO:0000269|PubMed:16233775};
CC Vmax=1.75 mmol/min/mg enzyme for the NAD(+) oxidation of L-threonine
CC (at 65 degrees Celsius) {ECO:0000269|PubMed:16233775};
CC Vmax=1.32 mmol/min/mg enzyme for the NADP(+) oxidation of L-threonine
CC (at 65 degrees Celsius) {ECO:0000269|PubMed:16233775};
CC pH dependence:
CC Optimum pH is around 10. Below and above pH 10, the marked decrease
CC of activity is observed: the relative activities are 50, 22 and 55%
CC at pH 9.5, 9.2 and 12, respectively. Is stable over a wide pH range:
CC upon heating at 50 degrees Celsius for 20 minutes, the enzyme does
CC not lose activity at pH 4.5-10.0. {ECO:0000269|PubMed:15902509};
CC Temperature dependence:
CC Optimum tempreature is 70 degrees Celsius. Extremely thermostable,
CC the activity is not lost after incubation at 100 degrees Celsius for
CC 20 minutes. {ECO:0000269|PubMed:15902509,
CC ECO:0000269|PubMed:16233775};
CC -!- PATHWAY: Amino-acid degradation; L-threonine degradation via oxydo-
CC reductase pathway; glycine from L-threonine: step 1/2.
CC {ECO:0000255|HAMAP-Rule:MF_00627, ECO:0000305|PubMed:16233775}.
CC -!- SUBUNIT: Homodimer (PubMed:16233775). Homotetramer; dimer of dimers
CC (PubMed:17188300) (PubMed:15902509). {ECO:0000269|PubMed:15902509,
CC ECO:0000269|PubMed:16233775, ECO:0000269|PubMed:17188300}.
CC -!- SUBCELLULAR LOCATION: Cytoplasm {ECO:0000255|HAMAP-Rule:MF_00627}.
CC -!- MISCELLANEOUS: The enzyme shows pro-R stereospecificity for hydrogen
CC transfer at the C4 position of the nicotinamide moiety of NADH.
CC {ECO:0000269|PubMed:15902509}.
CC -!- SIMILARITY: Belongs to the zinc-containing alcohol dehydrogenase
CC family. {ECO:0000255|HAMAP-Rule:MF_00627}.
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DR EMBL; BA000001; BAA29746.1; -; Genomic_DNA.
DR PIR; H71110; H71110.
DR RefSeq; WP_010884751.1; NC_000961.1.
DR PDB; 2D8A; X-ray; 2.05 A; A=1-348.
DR PDB; 2DFV; X-ray; 2.05 A; A/B/C=2-348.
DR PDBsum; 2D8A; -.
DR PDBsum; 2DFV; -.
DR AlphaFoldDB; O58389; -.
DR SMR; O58389; -.
DR MINT; O58389; -.
DR STRING; 70601.3257063; -.
DR EnsemblBacteria; BAA29746; BAA29746; BAA29746.
DR GeneID; 1442986; -.
DR KEGG; pho:PH0655; -.
DR eggNOG; arCOG01459; Archaea.
DR OMA; GVFHNTP; -.
DR OrthoDB; 67758at2157; -.
DR BRENDA; 1.1.1.103; 5244.
DR SABIO-RK; O58389; -.
DR UniPathway; UPA00046; UER00505.
DR EvolutionaryTrace; O58389; -.
DR Proteomes; UP000000752; Chromosome.
DR GO; GO:0005737; C:cytoplasm; IEA:UniProtKB-SubCell.
DR GO; GO:0016597; F:amino acid binding; IDA:UniProtKB.
DR GO; GO:0008743; F:L-threonine 3-dehydrogenase activity; IDA:UniProtKB.
DR GO; GO:0070403; F:NAD+ binding; IDA:UniProtKB.
DR GO; GO:0070401; F:NADP+ binding; IDA:UniProtKB.
DR GO; GO:0008270; F:zinc ion binding; IDA:UniProtKB.
DR GO; GO:0019518; P:L-threonine catabolic process to glycine; IEA:UniProtKB-UniPathway.
DR GO; GO:0051289; P:protein homotetramerization; IDA:UniProtKB.
DR GO; GO:0006566; P:threonine metabolic process; IDA:UniProtKB.
DR HAMAP; MF_00627; Thr_dehydrog; 1.
DR InterPro; IPR013149; ADH-like_C.
DR InterPro; IPR013154; ADH_N.
DR InterPro; IPR002328; ADH_Zn_CS.
DR InterPro; IPR011032; GroES-like_sf.
DR InterPro; IPR004627; L-Threonine_3-DHase.
DR InterPro; IPR036291; NAD(P)-bd_dom_sf.
DR InterPro; IPR020843; PKS_ER.
DR Pfam; PF08240; ADH_N; 1.
DR Pfam; PF00107; ADH_zinc_N; 1.
DR SMART; SM00829; PKS_ER; 1.
DR SUPFAM; SSF50129; SSF50129; 1.
DR SUPFAM; SSF51735; SSF51735; 1.
DR TIGRFAMs; TIGR00692; tdh; 1.
DR PROSITE; PS00059; ADH_ZINC; 1.
PE 1: Evidence at protein level;
KW 3D-structure; Cytoplasm; Metal-binding; NAD; NADP; Oxidoreductase; Zinc.
FT CHAIN 1..348
FT /note="L-threonine 3-dehydrogenase"
FT /id="PRO_0000160877"
FT ACT_SITE 44
FT /note="Charge relay system"
FT /evidence="ECO:0000305|PubMed:18390572"
FT ACT_SITE 47
FT /note="Charge relay system"
FT /evidence="ECO:0000305|PubMed:18390572"
FT BINDING 42
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_label="1"
FT /ligand_note="catalytic"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00627,
FT ECO:0000269|Ref.5, ECO:0000305|PubMed:17188300,
FT ECO:0000305|PubMed:18390572, ECO:0007744|PDB:2D8A"
FT BINDING 67
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_label="1"
FT /ligand_note="catalytic"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00627,
FT ECO:0000269|Ref.5, ECO:0000305|PubMed:17188300,
FT ECO:0000305|PubMed:18390572, ECO:0007744|PDB:2D8A"
FT BINDING 68
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_label="1"
FT /ligand_note="catalytic"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00627,
FT ECO:0000269|Ref.5, ECO:0000305|PubMed:17188300,
FT ECO:0000305|PubMed:18390572, ECO:0007744|PDB:2D8A"
FT BINDING 97
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_label="2"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00627,
FT ECO:0000269|PubMed:17188300, ECO:0007744|PDB:2DFV"
FT BINDING 100
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_label="2"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00627,
FT ECO:0000269|PubMed:17188300, ECO:0007744|PDB:2DFV"
FT BINDING 103
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_label="2"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00627,
FT ECO:0000269|PubMed:17188300, ECO:0007744|PDB:2DFV"
FT BINDING 111
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_label="2"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00627,
FT ECO:0000269|PubMed:17188300, ECO:0007744|PDB:2DFV"
FT BINDING 179
FT /ligand="NAD(+)"
FT /ligand_id="ChEBI:CHEBI:57540"
FT /evidence="ECO:0000269|PubMed:17188300, ECO:0000269|Ref.5"
FT BINDING 199
FT /ligand="NAD(+)"
FT /ligand_id="ChEBI:CHEBI:57540"
FT /evidence="ECO:0000269|PubMed:17188300, ECO:0000269|Ref.5,
FT ECO:0007744|PDB:2D8A, ECO:0007744|PDB:2DFV"
FT BINDING 204
FT /ligand="NAD(+)"
FT /ligand_id="ChEBI:CHEBI:57540"
FT /evidence="ECO:0000269|PubMed:17188300, ECO:0000269|Ref.5,
FT ECO:0007744|PDB:2D8A, ECO:0007744|PDB:2DFV"
FT BINDING 266..268
FT /ligand="NAD(+)"
FT /ligand_id="ChEBI:CHEBI:57540"
FT /evidence="ECO:0000269|Ref.5, ECO:0007744|PDB:2D8A"
FT BINDING 291..292
FT /ligand="NAD(+)"
FT /ligand_id="ChEBI:CHEBI:57540"
FT /evidence="ECO:0000269|Ref.5, ECO:0007744|PDB:2D8A"
FT SITE 152
FT /note="Important for catalytic activity for the proton
FT relay mechanism but does not participate directly in the
FT coordination of zinc atom"
FT /evidence="ECO:0000305|PubMed:18390572"
FT MUTAGEN 44
FT /note="T->A: Total loss of enzymatic activity."
FT /evidence="ECO:0000269|PubMed:18390572"
FT MUTAGEN 152
FT /note="E->A,Q: Almost complete loss of enzymatic activity."
FT /evidence="ECO:0000269|PubMed:18390572"
FT MUTAGEN 152
FT /note="E->C: 120-fold decrease in catalytic efficiency."
FT /evidence="ECO:0000269|PubMed:18390572"
FT MUTAGEN 152
FT /note="E->D: Shows 3-fold higher turnover rate and reduced
FT affinities toward L-threonine and NAD(+), compared to wild-
FT type."
FT /evidence="ECO:0000269|PubMed:18390572"
FT MUTAGEN 152
FT /note="E->K: Total loss of enzymatic activity."
FT /evidence="ECO:0000269|PubMed:18390572"
FT MUTAGEN 199
FT /note="E->A: Large decrease in affinity for NAD(+)."
FT /evidence="ECO:0000269|PubMed:17188300"
FT MUTAGEN 204
FT /note="R->A: Large decrease in affinity for NAD(+)."
FT /evidence="ECO:0000269|PubMed:17188300"
FT MUTAGEN 294
FT /note="R->A: 4000-fold decrease in catalytic efficiency."
FT /evidence="ECO:0000269|PubMed:18390572"
FT STRAND 4..10
FT /evidence="ECO:0007829|PDB:2D8A"
FT STRAND 12..16
FT /evidence="ECO:0007829|PDB:2D8A"
FT STRAND 18..23
FT /evidence="ECO:0007829|PDB:2D8A"
FT STRAND 31..40
FT /evidence="ECO:0007829|PDB:2D8A"
FT HELIX 43..50
FT /evidence="ECO:0007829|PDB:2D8A"
FT HELIX 55..58
FT /evidence="ECO:0007829|PDB:2D8A"
FT STRAND 61..64
FT /evidence="ECO:0007829|PDB:2D8A"
FT STRAND 68..76
FT /evidence="ECO:0007829|PDB:2D8A"
FT STRAND 88..91
FT /evidence="ECO:0007829|PDB:2D8A"
FT HELIX 101..104
FT /evidence="ECO:0007829|PDB:2DFV"
FT HELIX 108..110
FT /evidence="ECO:0007829|PDB:2DFV"
FT TURN 117..119
FT /evidence="ECO:0007829|PDB:2D8A"
FT STRAND 124..132
FT /evidence="ECO:0007829|PDB:2D8A"
FT HELIX 133..135
FT /evidence="ECO:0007829|PDB:2D8A"
FT STRAND 136..138
FT /evidence="ECO:0007829|PDB:2D8A"
FT HELIX 145..148
FT /evidence="ECO:0007829|PDB:2D8A"
FT HELIX 151..161
FT /evidence="ECO:0007829|PDB:2D8A"
FT STRAND 171..174
FT /evidence="ECO:0007829|PDB:2D8A"
FT HELIX 178..189
FT /evidence="ECO:0007829|PDB:2D8A"
FT STRAND 194..198
FT /evidence="ECO:0007829|PDB:2D8A"
FT HELIX 202..211
FT /evidence="ECO:0007829|PDB:2D8A"
FT STRAND 214..217
FT /evidence="ECO:0007829|PDB:2D8A"
FT TURN 219..221
FT /evidence="ECO:0007829|PDB:2D8A"
FT HELIX 224..231
FT /evidence="ECO:0007829|PDB:2D8A"
FT TURN 232..234
FT /evidence="ECO:0007829|PDB:2D8A"
FT STRAND 237..242
FT /evidence="ECO:0007829|PDB:2D8A"
FT HELIX 247..256
FT /evidence="ECO:0007829|PDB:2D8A"
FT STRAND 257..265
FT /evidence="ECO:0007829|PDB:2D8A"
FT HELIX 277..280
FT /evidence="ECO:0007829|PDB:2D8A"
FT TURN 281..285
FT /evidence="ECO:0007829|PDB:2D8A"
FT STRAND 287..290
FT /evidence="ECO:0007829|PDB:2D8A"
FT HELIX 297..309
FT /evidence="ECO:0007829|PDB:2D8A"
FT TURN 315..317
FT /evidence="ECO:0007829|PDB:2D8A"
FT STRAND 318..325
FT /evidence="ECO:0007829|PDB:2D8A"
FT HELIX 328..336
FT /evidence="ECO:0007829|PDB:2D8A"
FT STRAND 341..346
FT /evidence="ECO:0007829|PDB:2D8A"
SQ 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
