TDH_THEKO
ID TDH_THEKO Reviewed; 350 AA.
AC Q5JI69;
DT 07-JUN-2005, integrated into UniProtKB/Swiss-Prot.
DT 15-FEB-2005, sequence version 1.
DT 03-AUG-2022, entry version 117.
DE RecName: Full=L-threonine 3-dehydrogenase {ECO:0000255|HAMAP-Rule:MF_00627};
DE Short=TDH {ECO:0000255|HAMAP-Rule:MF_00627, ECO:0000303|PubMed:19616102};
DE EC=1.1.1.103 {ECO:0000255|HAMAP-Rule:MF_00627, ECO:0000269|PubMed:19307254};
DE AltName: Full=L-threonine dehydrogenase {ECO:0000303|PubMed:19307254, ECO:0000303|PubMed:19616102};
GN Name=tdh {ECO:0000255|HAMAP-Rule:MF_00627}; OrderedLocusNames=TK0916;
OS Thermococcus kodakarensis (strain ATCC BAA-918 / JCM 12380 / KOD1)
OS (Pyrococcus kodakaraensis (strain KOD1)).
OC Archaea; Euryarchaeota; Thermococci; Thermococcales; Thermococcaceae;
OC Thermococcus.
OX NCBI_TaxID=69014;
RN [1]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=ATCC BAA-918 / JCM 12380 / KOD1;
RX PubMed=15710748; DOI=10.1101/gr.3003105;
RA Fukui T., Atomi H., Kanai T., Matsumi R., Fujiwara S., Imanaka T.;
RT "Complete genome sequence of the hyperthermophilic archaeon Thermococcus
RT kodakaraensis KOD1 and comparison with Pyrococcus genomes.";
RL Genome Res. 15:352-363(2005).
RN [2]
RP FUNCTION, CATALYTIC ACTIVITY, SUBSTRATE SPECIFICITY, COFACTOR,
RP BIOPHYSICOCHEMICAL PROPERTIES, AND SUBUNIT.
RC STRAIN=ATCC BAA-918 / JCM 12380 / KOD1;
RX PubMed=19307254; DOI=10.1093/jb/mvp051;
RA Bashir Q., Rashid N., Jamil F., Imanaka T., Akhtar M.;
RT "Highly thermostable L-threonine dehydrogenase from the hyperthermophilic
RT archaeon Thermococcus kodakaraensis.";
RL J. Biochem. 146:95-102(2009).
RN [3]
RP X-RAY CRYSTALLOGRAPHY (2.40 ANGSTROMS) IN COMPLEX WITH NAD, AND SUBUNIT.
RX PubMed=19616102; DOI=10.1016/j.jsb.2009.07.011;
RA Bowyer A., Mikolajek H., Stuart J.W., Wood S.P., Jamil F., Rashid N.,
RA Akhtar M., Cooper J.B.;
RT "Structure and function of the L-threonine dehydrogenase (TkTDH) from the
RT hyperthermophilic archaeon Thermococcus kodakaraensis.";
RL J. Struct. Biol. 168:294-304(2009).
CC -!- FUNCTION: Catalyzes the NAD(+)-dependent oxidation of L-threonine to 2-
CC amino-3-ketobutyrate. To a lesser extent, also catalyzes the oxidation
CC of L-serine. {ECO:0000269|PubMed:19307254}.
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:19307254};
CC -!- COFACTOR:
CC Name=Zn(2+); Xref=ChEBI:CHEBI:29105;
CC Evidence={ECO:0000255|HAMAP-Rule:MF_00627,
CC ECO:0000269|PubMed:19307254};
CC Note=Binds 2 Zn(2+) ions per subunit (By similarity). Zn(2+) can be
CC replaced by Cu(2+), Co(2+), Ca(2+) or Mn(2+) to some extent
CC (PubMed:19307254). {ECO:0000255|HAMAP-Rule:MF_00627,
CC ECO:0000269|PubMed:19307254};
CC -!- BIOPHYSICOCHEMICAL PROPERTIES:
CC Kinetic parameters:
CC KM=1.6 mM for L-threonine (at 50 degrees Celsius)
CC {ECO:0000269|PubMed:19307254};
CC KM=0.028 mM for NAD(+) (at 50 degrees Celsius)
CC {ECO:0000269|PubMed:19307254};
CC pH dependence:
CC Optimum pH is 12. Is active over a wide pH range from 6.5 to 12.5.
CC {ECO:0000269|PubMed:19307254};
CC Temperature dependence:
CC Optimum temperature is 90 degrees Celsius. Extremely thermostable.
CC The half-life of the enzyme is more than 2 hours at 85 degrees
CC Celsius and 24 minutes in boiling water.
CC {ECO:0000269|PubMed:19307254};
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:19307254,
CC ECO:0000305|PubMed:19616102}.
CC -!- SUBUNIT: Homotetramer. {ECO:0000269|PubMed:19307254,
CC ECO:0000269|PubMed:19616102}.
CC -!- SUBCELLULAR LOCATION: Cytoplasm {ECO:0000255|HAMAP-Rule:MF_00627}.
CC -!- MISCELLANEOUS: Docking studies suggest a mode of interaction of TDH
CC with 2-amino-3-ketobutyrate CoA ligase (KBL), the subsequent enzyme in
CC the pathway for conversion of threonine to glycine. TDH is known to
CC form a stable functional complex with KBL, most probably to shield the
CC unstable intermediate and permit its channelling between the active
CC sites of both enzymes. {ECO:0000305|PubMed:19616102}.
CC -!- SIMILARITY: Belongs to the zinc-containing alcohol dehydrogenase
CC family. {ECO:0000255|HAMAP-Rule:MF_00627}.
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DR EMBL; AP006878; BAD85105.1; -; Genomic_DNA.
DR RefSeq; WP_011249867.1; NC_006624.1.
DR PDB; 3GFB; X-ray; 2.40 A; A/B/C/D=1-350.
DR PDBsum; 3GFB; -.
DR AlphaFoldDB; Q5JI69; -.
DR SMR; Q5JI69; -.
DR STRING; 69014.TK0916; -.
DR EnsemblBacteria; BAD85105; BAD85105; TK0916.
DR GeneID; 3234058; -.
DR KEGG; tko:TK0916; -.
DR PATRIC; fig|69014.16.peg.896; -.
DR eggNOG; arCOG01459; Archaea.
DR HOGENOM; CLU_026673_11_0_2; -.
DR InParanoid; Q5JI69; -.
DR OMA; GVFHNTP; -.
DR OrthoDB; 67758at2157; -.
DR PhylomeDB; Q5JI69; -.
DR BRENDA; 1.1.1.103; 5246.
DR UniPathway; UPA00046; UER00505.
DR EvolutionaryTrace; Q5JI69; -.
DR Proteomes; UP000000536; 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: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; Oxidoreductase;
KW Reference proteome; Zinc.
FT CHAIN 1..350
FT /note="L-threonine 3-dehydrogenase"
FT /id="PRO_0000160878"
FT ACT_SITE 44
FT /note="Charge relay system"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00627"
FT ACT_SITE 47
FT /note="Charge relay system"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00627"
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 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 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 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 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 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 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 BINDING 179
FT /ligand="NAD(+)"
FT /ligand_id="ChEBI:CHEBI:57540"
FT /evidence="ECO:0000269|PubMed:19616102"
FT BINDING 199
FT /ligand="NAD(+)"
FT /ligand_id="ChEBI:CHEBI:57540"
FT /evidence="ECO:0000269|PubMed:19616102"
FT BINDING 204
FT /ligand="NAD(+)"
FT /ligand_id="ChEBI:CHEBI:57540"
FT /evidence="ECO:0000269|PubMed:19616102,
FT ECO:0007744|PDB:3GFB"
FT BINDING 266..268
FT /ligand="NAD(+)"
FT /ligand_id="ChEBI:CHEBI:57540"
FT /evidence="ECO:0000269|PubMed:19616102,
FT ECO:0007744|PDB:3GFB"
FT BINDING 291..292
FT /ligand="NAD(+)"
FT /ligand_id="ChEBI:CHEBI:57540"
FT /evidence="ECO:0000269|PubMed:19616102,
FT ECO:0007744|PDB:3GFB"
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:0000255|HAMAP-Rule:MF_00627"
FT STRAND 4..10
FT /evidence="ECO:0007829|PDB:3GFB"
FT STRAND 12..16
FT /evidence="ECO:0007829|PDB:3GFB"
FT STRAND 18..23
FT /evidence="ECO:0007829|PDB:3GFB"
FT STRAND 31..41
FT /evidence="ECO:0007829|PDB:3GFB"
FT HELIX 43..50
FT /evidence="ECO:0007829|PDB:3GFB"
FT HELIX 53..58
FT /evidence="ECO:0007829|PDB:3GFB"
FT STRAND 61..64
FT /evidence="ECO:0007829|PDB:3GFB"
FT STRAND 68..76
FT /evidence="ECO:0007829|PDB:3GFB"
FT STRAND 88..91
FT /evidence="ECO:0007829|PDB:3GFB"
FT STRAND 98..100
FT /evidence="ECO:0007829|PDB:3GFB"
FT HELIX 101..104
FT /evidence="ECO:0007829|PDB:3GFB"
FT STRAND 114..116
FT /evidence="ECO:0007829|PDB:3GFB"
FT TURN 117..119
FT /evidence="ECO:0007829|PDB:3GFB"
FT STRAND 126..132
FT /evidence="ECO:0007829|PDB:3GFB"
FT HELIX 133..135
FT /evidence="ECO:0007829|PDB:3GFB"
FT STRAND 136..138
FT /evidence="ECO:0007829|PDB:3GFB"
FT HELIX 145..149
FT /evidence="ECO:0007829|PDB:3GFB"
FT HELIX 151..161
FT /evidence="ECO:0007829|PDB:3GFB"
FT STRAND 171..174
FT /evidence="ECO:0007829|PDB:3GFB"
FT HELIX 178..189
FT /evidence="ECO:0007829|PDB:3GFB"
FT STRAND 193..198
FT /evidence="ECO:0007829|PDB:3GFB"
FT HELIX 202..211
FT /evidence="ECO:0007829|PDB:3GFB"
FT STRAND 214..217
FT /evidence="ECO:0007829|PDB:3GFB"
FT HELIX 219..221
FT /evidence="ECO:0007829|PDB:3GFB"
FT HELIX 224..231
FT /evidence="ECO:0007829|PDB:3GFB"
FT TURN 232..234
FT /evidence="ECO:0007829|PDB:3GFB"
FT STRAND 237..242
FT /evidence="ECO:0007829|PDB:3GFB"
FT HELIX 247..256
FT /evidence="ECO:0007829|PDB:3GFB"
FT STRAND 257..265
FT /evidence="ECO:0007829|PDB:3GFB"
FT STRAND 273..275
FT /evidence="ECO:0007829|PDB:3GFB"
FT HELIX 277..280
FT /evidence="ECO:0007829|PDB:3GFB"
FT TURN 281..285
FT /evidence="ECO:0007829|PDB:3GFB"
FT STRAND 287..290
FT /evidence="ECO:0007829|PDB:3GFB"
FT HELIX 298..308
FT /evidence="ECO:0007829|PDB:3GFB"
FT TURN 315..317
FT /evidence="ECO:0007829|PDB:3GFB"
FT STRAND 318..323
FT /evidence="ECO:0007829|PDB:3GFB"
FT TURN 324..327
FT /evidence="ECO:0007829|PDB:3GFB"
FT HELIX 328..336
FT /evidence="ECO:0007829|PDB:3GFB"
FT STRAND 341..347
FT /evidence="ECO:0007829|PDB:3GFB"
SQ SEQUENCE 350 AA; 38101 MW; 047A8ACF9FF479AA CRC64;
MAEKMQAIMK TKPAYGAELV EVDVPKPGPG EVLIKVLATS ICGTDLHIYE WNEWAQSRIK
PPQIMGHEVA GEVVEVGPGV EDLQVGDYIS VETHIVCGKC YACKHNRYHV CQNTKIFGVD
MDGVFAHYAI VPAKNAWKNP KDMPPEYAAL QEPLGNAVDT VLAGPIAGRS TLITGAGPLG
LLGIAVAKAS GAYPVIVSEP SEFRRKLAKK VGADYVVNPF EEDPVKFVMD ITDGAGVEVF
LEFSGAPKAL EQGLKAVTPG GRVSLLGLFP REVTIDFNNL IIFKALEVHG ITGRHLWETW
YTVSSLIQSG KLNLDPIITH KYKGFDKFEE AFELMRAGKT GKVVFFPHKG
