L-threonine dehydratase catabolic TdcB - Escherichia coli (strain K12)

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P0AGF6 (TDCB_ECOLI) Reviewed, UniProtKB/Swiss-Prot

Last modified May 1, 2013. Version 65. History...

Clusters with 100%, 90%, 50% identity |

Documents (3) |

Third-party data

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Names·Attributes·General annotation·Ontologies·Sequence annotation·Sequences·References·Cross-refs·Entry info·Documents Customize order

Names and origin

Protein names

Recommended name:
L-threonine dehydratase catabolic TdcB
EC=4.3.1.19

Alternative name(s):
L-serine dehydratase
EC=4.3.1.17
Threonine deaminase

Gene names

Name:	tdcB
Ordered Locus Names:	b3117, JW3088

Organism

Escherichia coli (strain K12) [Reference proteome] [HAMAP]

Taxonomic identifier

83333 [NCBI]

Taxonomic lineage

Bacteria › Proteobacteria › Gammaproteobacteria › Enterobacteriales › Enterobacteriaceae › Escherichia ›

Protein attributes

Sequence length	329 AA.
Sequence status	Complete.
Protein existence	Evidence at protein level

General annotation (Comments)

Function	Catalyzes the anaerobic formation of alpha-ketobutyrate and ammonia from threonine in a two-step reaction. The first step involved a dehydration of threonine and a production of enamine intermediates (aminocrotonate), which tautomerizes to its imine form (iminobutyrate). Both intermediates are unstable and short-lived. The second step is the nonenzymatic hydrolysis of the enamine/imine intermediates to form 2-ketobutyrate and free ammonia. In the low water environment of the cell, the second step is accelerated by RidA. TdcB also dehydrates serine to yield pyruvate via analogous enamine/imine intermediates. Ref.7 Ref.8 Ref.10
Catalytic activity	L-threonine = 2-oxobutanoate + NH₃. L-serine = pyruvate + NH₃.
Cofactor	Pyridoxal phosphate. Ref.9
Enzyme regulation	Each protein molecule can bind up to four molecules of AMP, which act as an allosteric activator to the enzyme. The enzyme is also inhibited by alpha-keto acids and other catabolites. Ref.7 Ref.8
Pathway	Amino-acid degradation; L-threonine degradation via propanoate pathway; propanoate from L-threonine: step 1/4.
Subunit structure	In the native structure, TdcB is in a dimeric form, whereas in the TdcB-AMP complex, it exists in a tetrameric form (dimer of dimers) By similarity.
Induction	In the absence of glucose and oxygen,. Ref.7 Ref.8
Sequence similarities	Belongs to the serine/threonine dehydratase family.
Biophysicochemical properties	Kinetic parameters: K_M=0.30 µM for L-threonine (at 37 dregrees Celsius and at pH 7.8) Ref.7 K_M=0.35 µM for L-serine (at 37 dregrees Celsius and at pH 7.8)

Ontologies

Keywords
Ligand	Nucleotide-binding Pyridoxal phosphate
Molecular function	Lyase
Technical term	Allosteric enzyme Complete proteome Direct protein sequencing Reference proteome
Gene Ontology (GO)
Biological_process	L-serine catabolic process Inferred from direct assay PubMed 4889010. Source: EcoCyc L-threonine catabolic process to propionate Inferred from electronic annotation. Source: UniProtKB-UniPathway threonine catabolic process Inferred from direct assay PubMed 4889010. Source: EcoCyc
Molecular_function	L-serine ammonia-lyase activity Inferred from direct assay PubMed 4889010. Source: EcoCyc L-threonine ammonia-lyase activity Inferred from direct assay PubMed 4889010. Source: EcoCyc amino acid binding Inferred from direct assay Ref.1. Source: EcoliWiki nucleotide binding Inferred from electronic annotation. Source: UniProtKB-KW pyridoxal phosphate binding Inferred from direct assay Ref.5. Source: EcoliWiki threonine aldolase activity Inferred from direct assay Ref.1. Source: EcoliWiki
Complete GO annotation...

Sequence annotation (Features)

Feature key

Position(s)

Length

Description

Graphical view

Feature identifier

Molecule processing

Chain

1 – 329

329

L-threonine dehydratase catabolic TdcB

PRO_0000185582

Regions

Nucleotide binding

53 – 54

AMP By similarity

Nucleotide binding

119 – 120

AMP By similarity

Sites

Binding site

AMP By similarity

Binding site

314

AMP By similarity

Amino acid modifications

Modified residue

N6-(pyridoxal phosphate)lysine By similarity

Sequences

Sequence

Length

Mass (Da)

Tools

P0AGF6 [UniParc].

Last modified December 20, 2005. Version 1.
Checksum: E7DF018FCCF743B1
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FASTA

329

35,232

        10         20         30         40         50         60 
MHITYDLPVA IDDIIEAKQR LAGRIYKTGM PRSNYFSERC KGEIFLKFEN MQRTGSFKIR 

        70         80         90        100        110        120 
GAFNKLSSLT DAEKRKGVVA CSAGNHAQGV SLSCAMLGID GKVVMPKGAP KSKVAATCDY 

       130        140        150        160        170        180 
SAEVVLHGDN FNDTIAKVSE IVEMEGRIFI PPYDDPKVIA GQGTIGLEIM EDLYDVDNVI 

       190        200        210        220        230        240 
VPIGGGGLIA GIAVAIKSIN PTIRVIGVQS ENVHGMAASF HSGEITTHRT TGTLADGCDV 

       250        260        270        280        290        300 
SRPGNLTYEI VRELVDDIVL VSEDEIRNSM IALIQRNKVV TEGAGALACA ALLSGKLDQY 

       310        320 
IQNRKTVSII SGGNIDLSRV SQITGFVDA

« Hide

References

	« Hide 'large scale' referencesShow 'large scale' references »
[1]	"Covalent structure of biodegradative threonine dehydratase of Escherichia coli: homology with other dehydratases." Datta P., Goss T.J., Omnaas J.R., Patil R.V. Proc. Natl. Acad. Sci. U.S.A. 84:393-397(1987) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA]. Strain: K12 / W3110 / ATCC 27325 / DSM 5911.
[2]	"The complete nucleotide sequence of the tdc region of Escherichia coli." Schweizer H., Datta P. Nucleic Acids Res. 17:3994-3994(1989) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA]. Strain: K12 / W3110 / ATCC 27325 / DSM 5911.
[3]	"The complete genome sequence of Escherichia coli K-12." Blattner F.R., Plunkett G. III, Bloch C.A., Perna N.T., Burland V., Riley M., Collado-Vides J., Glasner J.D., Rode C.K., Mayhew G.F., Gregor J., Davis N.W., Kirkpatrick H.A., Goeden M.A., Rose D.J., Mau B., Shao Y. Science 277:1453-1474(1997) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA]. Strain: K12 / MG1655 / ATCC 47076.
[4]	"Highly accurate genome sequences of Escherichia coli K-12 strains MG1655 and W3110." Hayashi K., Morooka N., Yamamoto Y., Fujita K., Isono K., Choi S., Ohtsubo E., Baba T., Wanner B.L., Mori H., Horiuchi T. Mol. Syst. Biol. 2:E1-E5(2006) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA]. Strain: K12 / W3110 / ATCC 27325 / DSM 5911.
[5]	"Chemical characterization of biodegradative threonine dehydratases from two enteric bacteria." Kim S.S., Datta P. Biochim. Biophys. Acta 706:27-35(1982) [PubMed] [Europe PMC] [Abstract] Cited for: PROTEIN SEQUENCE OF 1-25.
[6]	"Molecular characterization of the tdc operon of Escherichia coli K-12." Goss T.J., Schweizer H.P., Datta P. J. Bacteriol. 170:5352-5359(1988) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA] OF 323-329.
[7]	"Serine and threonine desaminaes of Escherichia coli; activators for a cell-free enzyme." Wood W.A., Gunsalus I.C. J. Biol. Chem. 181:171-182(1949) [PubMed] [Europe PMC] [Abstract] Cited for: FUNCTION AS A THREONINE AND SERINE DEHYDRATASE, BIOPHYSICOCHEMICAL PROPERTIES, ENZYME REGULATION.
[8]	"Threonine deamination in Escherichia coli. II. Evidence for two L-threonine deaminases." Umbarger H.E., Brown B. J. Bacteriol. 73:105-112(1957) [PubMed] [Europe PMC] [Abstract] Cited for: FUNCTION AS A THREONINE AND SERINE DEHYDRATASE, INDUCTION, ENZYME REGULATION.
[9]	"The mechanism of action of 5'-adenylic acid-activated threonine dehydrase." Phillips A.T., Wood W.A. J. Biol. Chem. 240:4703-4709(1965) [PubMed] [Europe PMC] [Abstract] Cited for: REACTION MECHANISM, COFACTOR.
[10]	"Expression of the Escherichia coli catabolic threonine dehydratase in Corynebacterium glutamicum and its effect on isoleucine production." Guillouet S., Rodal A.A., An G., Lessard P.A., Sinskey A.J. Appl. Environ. Microbiol. 65:3100-3107(1999) [PubMed] [Europe PMC] [Abstract] Cited for: FUNCTION IN CATABOLISM OF THREONINE.
[11]	"Structure and function of enzymes involved in the anaerobic degradation of L-threonine to propionate." Simanshu D.K., Chittori S., Savithri H.S., Murthy M.R. J. Biosci. 32:1195-1206(2007) [PubMed] [Europe PMC] [Abstract] Cited for: REVIEW.

Cross-references

Sequence databases
EMBL GenBank DDBJ	M21312 Genomic DNA. Translation: AAA24660.1. X14430 Genomic DNA. Translation: CAA32593.1. U18997 Genomic DNA. Translation: AAA57921.1. U00096 Genomic DNA. Translation: AAC76152.1. AP009048 Genomic DNA. Translation: BAE77166.1. M23638 Genomic DNA. Translation: AAA24661.1.
PIR	DWECTD. A26367.
RefSeq	NP_417587.1. NC_000913.2. YP_491307.1. NC_007779.1.
3D structure databases
ProteinModelPortal	P0AGF6.
SMR	P0AGF6. Positions 2-325.
ModBase	Search...
Protein-protein interaction databases
DIP	DIP-48063N.
IntAct	P0AGF6. 3 interactions.
STRING	511145.b3117.
Proteomic databases
PaxDb	P0AGF6.
PRIDE	P0AGF6.
Protocols and materials databases
StructuralBiologyKnowledgebase	Search...
Genome annotation databases
EnsemblBacteria	AAC76152; AAC76152; b3117. BAE77166; BAE77166; BAE77166.
GeneID	12933425. 947633.
KEGG	ecj:Y75_p3041. eco:b3117.
PATRIC	32121650. VBIEscCol129921_3211.
Organism-specific databases
EchoBASE	EB0983.
EcoGene	EG10990. tdcB.
Phylogenomic databases
eggNOG	COG1171.
HOGENOM	HOG000046972.
KO	K01754.
OMA	DTPCVES.
ProtClustDB	PRK08638.
Enzyme and pathway databases
BioCyc	EcoCyc:THREDEHYDCAT-MONOMER. ECOL316407:JW3088-MONOMER. MetaCyc:THREDEHYDCAT-MONOMER.
UniPathway	UPA00052; UER00507.
Gene expression databases
Genevestigator	P0AGF6.
Family and domain databases
InterPro	IPR000634. Ser/Thr_deHydtase_PyrdxlP-BS. IPR005789. Thr_deHydtase_catblc. IPR001926. Trp_syn_b_sub_like_PLP_eny_SF. [Graphical view]
Pfam	PF00291. PALP. 1 hit. [Graphical view]
SUPFAM	SSF53686. PyrdxlP-dep_enz_bsu. 1 hit.
TIGRFAMs	TIGR01127. ilvA_1Cterm. 1 hit.
PROSITE	PS00165. DEHYDRATASE_SER_THR. 1 hit. [Graphical view]
ProtoNet	Search...

Entry information

Entry name

TDCB_ECOLI

Accession

Primary (citable) accession number: P0AGF6
Secondary accession number(s): P05792, Q2M990

Entry history

Integrated into UniProtKB/Swiss-Prot:	December 20, 2005
Last sequence update:	December 20, 2005
Last modified:	May 1, 2013
This is version 65 of the entry and version 1 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation program

Prokaryotic Protein Annotation Program

Relevant documents

Escherichia coli

Escherichia coli (strain K12): entries and cross-references to EcoGene

PATHWAY comments

Index of metabolic and biosynthesis pathways

SIMILARITY comments

Index of protein domains and families

Names·Attributes·General annotation·Ontologies·Sequence annotation·Sequences·References·Cross-refs·Entry info·Documents

Preferred order of sections

Names and origin

Protein attributes

General annotation (Comments)

Ontologies

Sequence annotation (Features)

Molecule processing

Regions

Sites

Amino acid modifications

Sequences

References

Cross-references

Sequence databases

3D structure databases

Protein-protein interaction databases

Proteomic databases

Protocols and materials databases

Genome annotation databases

Organism-specific databases

Phylogenomic databases

Enzyme and pathway databases

Gene expression databases

Family and domain databases

Entry information

Relevant documents