DB code: T00088

CATH domain 3.40.50.1100 : Rossmann fold Catalytic domain
3.40.50.1100 : Rossmann fold Catalytic domain
3.40.1020.10 : Biosynthetic Threonine Deaminase; domain 3
E.C. 4.3.1.19
CSA 1tdj
M-CSA 1tdj
MACiE

CATH domain Related DB codes (homologues)
3.40.50.1100 : Rossmann fold D00264 T00089

Uniprot Enzyme Name
UniprotKB Protein name Synonyms RefSeq Pfam
P04968 L-threonine dehydratase biosynthetic IlvA
EC 4.3.1.19
Threonine deaminase
NP_418220.1 (Protein)
NC_000913.2 (DNA/RNA sequence)
YP_491666.1 (Protein)
NC_007779.1 (DNA/RNA sequence)
PF00291 (PALP)
PF00585 (Thr_dehydrat_C)
[Graphical View]

KEGG enzyme name
threonine ammonia-lyase
threonine deaminase
L-serine dehydratase
serine deaminase
L-threonine dehydratase
threonine dehydrase
L-threonine deaminase
threonine dehydratase
L-threonine hydro-lyase (deaminating)
L-threonine ammonia-lyase

UniprotKB: Accession Number Entry name Activity Subunit Subcellular location Cofactor
P04968 THD1_ECOLI L-threonine = 2-oxobutanoate + NH(3). Homotetramer. Pyridoxal phosphate.

KEGG Pathways
Map code Pathways E.C.
MAP00290 Valine, leucine and isoleucine biosynthesis
MAP00260 Glycine, serine and threonine metabolism

Compound table
Cofactors Substrates Products Intermediates
KEGG-id C00018 C00188 C00109 C00014
E.C.
Compound Pyridoxal phosphate L-Threonine 2-Oxobutanoate NH3
Type aromatic ring (with nitrogen atoms),phosphate group/phosphate ion amino acids,carbohydrate carbohydrate,carboxyl group amine group,organic ion
ChEBI 18405
57926
16857
30831
16134
PubChem 1051
6971019
6288
58
222
1tdjA01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Bound:PLP Unbound Unbound Unbound
1tdjA02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound
1tdjA03 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound

Reference for Active-site residues
resource references E.C.
literature [24]

Active-site residues
PDB Catalytic residues Cofactor-binding residues Modified residues Main-chain involved in catalysis Comment
1tdjA01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain LYS 62 LYS 62(PLP binding)
1tdjA02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain ASN 89
1tdjA03 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain

References for Catalytic Mechanism
References Sections No. of steps in catalysis
[24]
p.468

References
[1]
Resource
Comments
Medline ID
PubMed ID 235965
Journal Biochemistry
Year 1975
Volume 14
Pages 1760-7
Authors Feldman DA, Datta P
Title Catabolite inactivation of biodegradative threonine dehydratase of Escherichia coli.
Related PDB
Related UniProtKB
[2]
Resource
Comments
Medline ID
PubMed ID 1096954
Journal Biochim Biophys Acta
Year 1975
Volume 397
Pages 220-30
Authors Koerner K, Rahimi-Laridjani I, Grimminger H
Title Purification of biosynthetic threonine deaminase from Escherichia coli.
Related PDB
Related UniProtKB
[3]
Resource
Comments
Medline ID
PubMed ID 986166
Journal Biochemistry
Year 1976
Volume 15
Pages 3745-9
Authors Kapke G, Davis L
Title Stereochemistry of the reaction of sheep liver threonine dehydratase. A nuclear magnetic resonance and optical rotatory dispersion study of its reaction pathway and products.
Related PDB
Related UniProtKB
[4]
Resource
Comments
Medline ID
PubMed ID 1262564
Journal J Dairy Res
Year 1976
Volume 43
Pages 75-83
Authors Lees GJ, Jago GR
Title Formation of acetaldehyde from threonine by lactic acid bacteria.
Related PDB
Related UniProtKB
[5]
Resource
Comments
Medline ID
PubMed ID 885705
Journal Ital J Biochem
Year 1977
Volume 26
Pages 144-61
Authors Pagani R, Lusini P, Di Stefano A, Aleo F, Marinello E
Title Purification and properties of rat liver L-threonine deaminase.
Related PDB
Related UniProtKB
[6]
Resource
Comments
Medline ID
PubMed ID 909449
Journal Methods Enzymol
Year 1977
Volume 46
Pages 59-69
Authors Phillips AT
Title Differential labeling: a general technique for selective modification of binding sites.
Related PDB
Related UniProtKB
[7]
Resource
Comments
Medline ID
PubMed ID 350274
Journal Biochemistry
Year 1978
Volume 17
Pages 1691-9
Authors Bhadra R, Datta P
Title Allosteric inhibition and catabolite inactivation of purified biodegradative threonine dehydratase of Salmonella typhimurium.
Related PDB
Related UniProtKB
[8]
Resource
Comments
Medline ID
PubMed ID 342520
Journal J Biol Chem
Year 1978
Volume 253
Pages 1245-51
Authors Hofler JG, Burns RO
Title Threonine deaminase from Salmonella typhimurium. Effect of regulatory ligands on the binding of substrates and substrate analogues to the active sites and the differentiation of the activator and inhibitor sites from the active sites.
Related PDB
Related UniProtKB
[9]
Resource
Comments
Medline ID
PubMed ID 438181
Journal J Biol Chem
Year 1979
Volume 254
Pages 4126-31
Authors Davis L
Title Functional and stereochemical specificity at the beta carbon atom of substrates in threonine dehydratase-catalyzed alpha,beta elimination reactions.
Related PDB
Related UniProtKB
[10]
Resource
Comments
Medline ID
PubMed ID 7016853
Journal J Biol Chem
Year 1981
Volume 256
Pages 5362-7
Authors Park LS, Datta P
Title Mechanism of catabolite inactivation of Escherichia coli biodegradative threonine dehydratase by glyoxylate.
Related PDB
Related UniProtKB
[11]
Resource
Comments
Medline ID
PubMed ID 3929853
Journal Biosci Rep
Year 1985
Volume 5
Pages 499-508
Authors Leoncini R, Pagani R, Casella A, Marinello E
Title Rat liver L-threonine deaminase: properties and purification.
Related PDB
Related UniProtKB
[12]
Resource
Comments
Medline ID
PubMed ID 3053659
Journal J Bacteriol
Year 1988
Volume 170
Pages 5352-9
Authors Goss TJ, Schweizer HP, Datta P
Title Molecular characterization of the tdc operon of Escherichia coli K-12.
Related PDB
Related UniProtKB
[13]
Resource
Comments
Medline ID
PubMed ID 2674117
Journal J Biol Chem
Year 1989
Volume 264
Pages 15818-23
Authors Ogawa H, Gomi T, Konishi K, Date T, Nakashima H, Nose K, Matsuda Y, Peraino C, Pitot HC, Fujioka M
Title Human liver serine dehydratase. cDNA cloning and sequence homology with hydroxyamino acid dehydratases from other sources.
Related PDB
Related UniProtKB
[14]
Resource
Comments
Medline ID
PubMed ID 2015295
Journal Biochim Biophys Acta
Year 1991
Volume 1077
Pages 233-40
Authors Pagani R, Ponticelli F, Terzuoli L, Leoncini R, Marinello E
Title The inhibition of rat liver threonine dehydratase by carbamoyl-phosphate. The formation of carbamoylpyridoxal 5'-phosphate.
Related PDB
Related UniProtKB
[15]
Resource
Comments
Medline ID
PubMed ID 8240316
Journal Bioessays
Year 1993
Volume 15
Pages 625-34
Authors Changeux JP
Title Allosteric proteins: from regulatory enzymes to receptors--personal recollections.
Related PDB
Related UniProtKB
[16]
Resource
Comments
Medline ID
PubMed ID 8407838
Journal J Bacteriol
Year 1993
Volume 175
Pages 6605-13
Authors Fisher KE, Eisenstein E
Title An efficient approach to identify ilvA mutations reveals an amino-terminal catalytic domain in biosynthetic threonine deaminase from Escherichia coli.
Related PDB
Related UniProtKB
[17]
Resource
Comments
Medline ID
PubMed ID 8413189
Journal Mol Gen Genet
Year 1993
Volume 240
Pages 395-402
Authors Ganduri YL, Sadda SR, Datta MW, Jambukeswaran RK, Datta P
Title TdcA, a transcriptional activator of the tdcABC operon of Escherichia coli, is a member of the LysR family of proteins.
Related PDB
Related UniProtKB
[18]
Resource
Comments
Medline ID
PubMed ID 7815942
Journal Mol Microbiol
Year 1994
Volume 13
Pages 833-42
Authors Mockel B, Eggeling L, Sahm H
Title Threonine dehydratases of Corynebacterium glutamicum with altered allosteric control: their generation and biochemical and structural analysis.
Related PDB
Related UniProtKB
[19]
Resource
Comments
Medline ID
PubMed ID 7703851
Journal Protein Sci
Year 1994
Volume 3
Pages 2055-63
Authors Matsuo Y, Nishikawa K
Title Protein structural similarities predicted by a sequence-structure compatibility method.
Related PDB
Related UniProtKB
[20]
Resource
Comments
Medline ID
PubMed ID 7840631
Journal Arch Biochem Biophys
Year 1995
Volume 316
Pages 311-8
Authors Eisenstein E
Title Allosteric regulation of biosynthetic threonine deaminase from Escherichia coli: effects of isoleucine and valine on active-site ligand binding and catalysis.
Related PDB
Related UniProtKB
[21]
Resource
Comments
Medline ID
PubMed ID 8659901
Journal Ann N Y Acad Sci
Year 1996
Volume 782
Pages 25-39
Authors Sahm H, Eggeling L, Eikmanns B, Kramer R
Title Construction of L-lysine-, L-threonine-, and L-isoleucine-overproducing strains of Corynebacterium glutamicum.
Related PDB
Related UniProtKB
[22]
Resource
Comments
Medline ID
PubMed ID 9761930
Journal Acta Crystallogr D Biol Crystallogr
Year 1998
Volume 54
Pages 467-9
Authors Gallagher DT, Eisenstein E, Fisher KE, Zondlo J, Chinchilla D, Yu HD, Dill J, Winborne E, Ducote K, Xiao G, Gilliland GL
Title Polymorphous crystallization and diffraction of threonine deaminase from Escherichia coli.
Related PDB
Related UniProtKB
[23]
Resource
Comments
Medline ID
PubMed ID 9722552
Journal J Biol Chem
Year 1998
Volume 273
Pages 23219-24
Authors Chinchilla D, Schwarz FP, Eisenstein E
Title Amino acid substitutions in the C-terminal regulatory domain disrupt allosteric effector binding to biosynthetic threonine deaminase from Escherichia coli.
Related PDB
Related UniProtKB
[24]
Resource
Comments X-RAY CRYSTALLOGRAPHY (2.8 ANGSTROMS)
Medline ID 98230745
PubMed ID 9562556
Journal Structure
Year 1998
Volume 6
Pages 465-75
Authors Gallagher DT, Gilliland GL, Xiao G, Zondlo J, Fisher KE, Chinchilla D, Eisenstein E
Title Structure and control of pyridoxal phosphate dependent allosteric threonine deaminase.
Related PDB 1tdj
Related UniProtKB P04968
[25]
Resource
Comments
Medline ID
PubMed ID 9914259
Journal Curr Opin Struct Biol
Year 1998
Volume 8
Pages 759-69
Authors Jansonius JN
Title Structure, evolution and action of vitamin B6-dependent enzymes.
Related PDB
Related UniProtKB
[26]
Resource
Comments
Medline ID
PubMed ID 11106492
Journal Biochemistry
Year 2000
Volume 39
Pages 15136-43
Authors Wessel PM, Graciet E, Douce R, Dumas R
Title Evidence for two distinct effector-binding sites in threonine deaminase by site-directed mutagenesis, kinetic, and binding experiments.
Related PDB
Related UniProtKB
[27]
Resource
Comments
Medline ID
PubMed ID 10673430
Journal Structure Fold Des
Year 2000
Volume 8
Pages R1-6
Authors Schneider G, Kack H, Lindqvist Y
Title The manifold of vitamin B6 dependent enzymes.
Related PDB
Related UniProtKB
[28]
Resource
Comments
Medline ID
PubMed ID 11389597
Journal Biochemistry
Year 2001
Volume 40
Pages 6836-44
Authors Lee YT, Duggleby RG
Title Identification of the regulatory subunit of Arabidopsis thaliana acetohydroxyacid synthase and reconstitution with its catalytic subunit.
Related PDB
Related UniProtKB
[29]
Resource
Comments
Medline ID
PubMed ID 11751050
Journal Curr Opin Struct Biol
Year 2001
Volume 11
Pages 694-700
Authors Chipman DM, Shaanan B
Title The ACT domain family.
Related PDB
Related UniProtKB
[30]
Resource
Comments
Medline ID
PubMed ID 12427039
Journal Biochemistry
Year 2002
Volume 41
Pages 13767-73
Authors Halgand F, Wessel PM, Laprevote O, Dumas R
Title Biochemical and mass spectrometric evidence for quaternary structure modifications of plant threonine deaminase induced by isoleucine.
Related PDB
Related UniProtKB

Comments
This enzyme was transferred from 4.2.1.16 to 4.3.1.19.
This enzyme belongs to type-II PLP-dependent enzyme superfamily (or Tryptophan synthase beta-subunit family), according to the literature [25] & [27].
Although the catalytic mechanism of this enzyme has not been elucidated, this enzyme probably catalyzes the following reactions, considering those of other PLP-dependent enzymes (see [25]):
(A) Formation of external aldimine (with amine group of Threonine substrate),
(B) Isomerization (change in the position of double-bond),
(C) Elimination of hydroxyl group, forming double bonded carbon atoms, leading to aminoacrylate intermediate,
(D) Formation of internal aldimine, leading to the elimination of imine intermediate from PLP,
(E) Schiff-base deforming of the imine product (by hydration), producing ammonia and oxobutanoate.

Created Updated
2004-06-07 2009-02-26