DB code: D00257

CATH domain 3.90.1150.10 : Aspartate Aminotransferase, domain 1
3.40.640.10 : Aspartate Aminotransferase; domain 2 Catalytic domain
E.C. 4.1.99.1
CSA 1ax4
M-CSA 1ax4
MACiE

CATH domain Related DB codes (homologues)
3.40.640.10 : Aspartate Aminotransferase; domain 2 D00085 D00092 D00101 D00102 D00103 D00104 D00107 D00108 D00109 D00255 D00258 D00265 D00269 D00515 M00031 D00279
3.90.1150.10 : Aspartate Aminotransferase, domain 1 D00085 D00092 D00101 D00102 D00103 D00104 D00107 D00108 D00109 D00255 D00258 D00265 D00269 D00515 M00031 D00279

Uniprot Enzyme Name
UniprotKB Protein name Synonyms Pfam
P28796 Tryptophanase
EC 4.1.99.1
L-tryptophan indole-lyase
TNase
PF01212 (Beta_elim_lyase)
[Graphical View]

KEGG enzyme name
tryptophanase
L-tryptophanase
L-tryptophan indole-lyase (deaminating)

UniprotKB: Accession Number Entry name Activity Subunit Subcellular location Cofactor
P28796 TNAA_PROVU L-tryptophan + H(2)O = indole + pyruvate + NH(3). Homotetramer. Pyridoxal phosphate.

KEGG Pathways
Map code Pathways E.C.
MAP00380 Tryptophan metabolism
MAP00910 Nitrogen metabolism

Compound table
Cofactors Substrates Products Intermediates
KEGG-id C00018 C00238 C00078 C00001 C00463 C00022 C00014
E.C.
Compound Pyridoxal phosphate Potassium L-Tryptophan H2O Indole Pyruvate NH3
Type aromatic ring (with nitrogen atoms),phosphate group/phosphate ion univalent metal (Na+, K+) amino acids,aromatic ring (only carbon atom),aromatic ring (with nitrogen atoms) H2O aromatic ring (only carbon atom),aromatic ring (with nitrogen atoms) carbohydrate,carboxyl group amine group,organic ion
ChEBI 18405
 18405
 		29103
 29103
 		16828
 57912
 16828
 57912
 		15377
 15377
 		16881
 16881
 		32816
 32816
 		16134
 16134
PubChem 1051
 1051
 		813
 813
 		6305
 6923516
 6305
 6923516
 		22247451
 962
 22247451
 962
 		798
 798
 		1060
 1060
 		222
 222
1ax4A01 Unbound Unbound Unbound Unbound Unbound Unbound
1ax4B01 Unbound Unbound Unbound Unbound Unbound Unbound
1ax4C01 Unbound Unbound Unbound Unbound Unbound Unbound
1ax4D01 Unbound Unbound Unbound Unbound Unbound Unbound
1ax4A02 Analogue:LLP Bound:__K Unbound Unbound Unbound Unbound
1ax4B02 Analogue:LLP Bound:__K Unbound Unbound Unbound Unbound
1ax4C02 Analogue:LLP Bound:__K Unbound Unbound Unbound Unbound
1ax4D02 Analogue:LLP Bound:__K Unbound Unbound Unbound Unbound

Reference for Active-site residues
resource references E.C.
literature [17]

Active-site residues
PDB Catalytic residues Cofactor-binding residues Modified residues Main-chain involved in catalysis Comment
1ax4A01 GLY 53(Potassium binding)
1ax4B01 GLY 53(Potassium binding)
1ax4C01 GLY 53(Potassium binding)
1ax4D01 GLY 53(Potassium binding)
1ax4A02 ARG 226;LLP 266 GLU 70;ASN 271(Potassium binding) LLP 266(PLP-bound to Lys)
1ax4B02 ARG 226;LLP 266 GLU 70;ASN 271(Potassium binding) LLP 266(PLP-bound to Lys)
1ax4C02 ARG 226;LLP 266 GLU 70;ASN 271(Potassium binding) LLP 266(PLP-bound to Lys)
1ax4D02 ARG 226;LLP 266 GLU 70;ASN 271(Potassium binding) LLP 266(PLP-bound to Lys)

References for Catalytic Mechanism
References Sections No. of steps in catalysis
[7]
SCHEME 2A
[8]
Fig.5, p.7343 3
[12]
SCHEME I
[14]
Fig.1
[17]
Figure 1 p.604
[19]
Fig. 3
[20]
Scheme 3, p.21595-21597 3

References
[1]
Resource
Comments
Medline ID
PubMed ID 4575958
Journal Biochem Biophys Res Commun
Year 1973
Volume 52
Pages 482-8
Authors Ikeda S, Fukui S
Title Preparation of pyridoxal 5'-phosphate-bound sepharose and its use for immobilization of tryptophanase.
Related PDB
Related UniProtKB
[2]
Resource
Comments
Medline ID
PubMed ID 20936
Journal Biochemistry
Year 1977
Volume 16
Pages 4584-90
Authors Ritchey JM, Gibbons I, Schachman HK
Title Reactivation of enzymes by light-stimulated cleavage of reduced pyridoxal 5'-phosphate-enzyme complexes.
Related PDB
Related UniProtKB
[3]
Resource
Comments
Medline ID
PubMed ID 6339506
Journal J Biol Chem
Year 1983
Volume 258
Pages 4839-41
Authors Schnackerz KD, Snell EE
Title Phosphorus 31 nuclear magnetic resonance study of tryptophanase. Pyridoxal phosphate-binding site.
Related PDB
Related UniProtKB
[4]
Resource
Comments
Medline ID
PubMed ID 6728845
Journal Prog Clin Biol Res
Year 1984
Volume 144A
Pages 195-208
Authors Schnackerz KD
Title Phosphorus-31 nuclear magnetic resonance studies on four pyridoxal 5'-phosphate dependent enzymes.
Related PDB
Related UniProtKB
[5]
Resource
Comments
Medline ID
PubMed ID 3888623
Journal Eur J Biochem
Year 1985
Volume 149
Pages 129-33
Authors Nihira T, Yasuda T, Kakizono T, Taguchi H, Ichikawa M, Toraya T, Fukui S
Title Functional role of cysteinyl residues in tryptophanase.
Related PDB
Related UniProtKB
[6]
Resource
Comments
Medline ID
PubMed ID 3524569
Journal Biochem Biophys Res Commun
Year 1986
Volume 137
Pages 964-9
Authors Kakizono T, Nihira T, Taguchi H
Title Catalytic function of a tyrosyl residue in tryptophanase.
Related PDB
Related UniProtKB
[7]
Resource
Comments
Medline ID
PubMed ID 3111376
Journal Arch Biochem Biophys
Year 1987
Volume 256
Pages 302-10
Authors Phillips RS
Title Reactions of O-acyl-L-serines with tryptophanase, tyrosine phenol-lyase, and tryptophan synthase.
Related PDB
Related UniProtKB
[8]
Resource
Comments
Medline ID
PubMed ID 3061452
Journal Biochemistry
Year 1988
Volume 27
Pages 7339-44
Authors Kiick DM, Phillips RS
Title Mechanistic deductions from multiple kinetic and solvent deuterium isotope effects and pH studies of pyridoxal phosphate dependent carbon-carbon lyases: Escherichia coli tryptophan indole-lyase.
Related PDB
Related UniProtKB
[9]
Resource
Comments
Medline ID
PubMed ID 2178632
Journal Biotechnol Appl Biochem
Year 1990
Volume 12
Pages 28-33
Authors Tani S, Tsujimoto N, Kawata Y, Tokushige M
Title Overproduction and crystallization of tryptophanase from recombinant cells of Escherichia coli.
Related PDB
Related UniProtKB
[10]
Resource
Comments
Medline ID
PubMed ID 2069576
Journal Biochem Biophys Res Commun
Year 1991
Volume 178
Pages 385-92
Authors Metzler CM, Metzler DE, Kintanar A, Scott RD, Marceau M
Title NMR spectra of exchangeable protons of pyridoxal phosphate-dependent enzymes.
Related PDB
Related UniProtKB
[11]
Resource
Comments
Medline ID
PubMed ID 2060649
Journal FEBS Lett
Year 1991
Volume 284
Pages 270-2
Authors Kawata Y, Tani S, Sato M, Katsube Y, Tokushige M
Title Preliminary X-ray crystallographic analysis of tryptophanase from Escherichia coli.
Related PDB
Related UniProtKB
[12]
Resource
Comments
Medline ID
PubMed ID 1632641
Journal Arch Biochem Biophys
Year 1992
Volume 296
Pages 489-96
Authors Phillips RS, Dua RK
Title Indole protects tryptophan indole-lyase, but not tryptophan synthase, from inactivation by trifluoroalanine.
Related PDB
Related UniProtKB
[13]
Resource
Comments
Medline ID
PubMed ID 1372930
Journal J Gen Microbiol
Year 1992
Volume 138
Pages 211-6
Authors Hart S, Koch KR, Woods DR
Title Identification of indigo-related pigments produced by Escherichia coli containing a cloned Rhodococcus gene.
Related PDB
Related UniProtKB
[14]
Resource
Comments
Medline ID
PubMed ID 7849621
Journal Biochem Mol Biol Int
Year 1994
Volume 34
Pages 209-16
Authors Faleev NG, Dementieva IS, Zakomirdina LN, Gogoleva OI, Belikov VM
Title Tryptophanase from Escherichia coli: catalytic and spectral properties in water-organic solvents.
Related PDB
Related UniProtKB
[15]
Resource
Comments
Medline ID
PubMed ID 8289300
Journal J Mol Biol
Year 1994
Volume 235
Pages 783-6
Authors Dementieva IS, Zakomirdina LN, Sinitzina NI, Antson AA, Wilson KS, Isupov MN, Lebedev AA, Harutyunyan EH
Title Crystallization and preliminary X-ray investigation of holotryptophanases from Escherichia coli and Proteus vulgaris.
Related PDB
Related UniProtKB
[16]
Resource
Comments
Medline ID
PubMed ID 9485457
Journal Biochemistry
Year 1998
Volume 37
Pages 3043-52
Authors Ikushiro H, Hayashi H, Kawata Y, Kagamiyama H
Title Analysis of the pH- and ligand-induced spectral transitions of tryptophanase: activation of the coenzyme at the early steps of the catalytic cycle.
Related PDB
Related UniProtKB
[17]
Resource
Comments X-RAY CRYSTALLOGRAPHY (2.1 ANGSTROMS).
Medline ID 98212457
PubMed ID 9551100
Journal J Mol Biol
Year 1998
Volume 276
Pages 603-23
Authors Isupov MN, Antson AA, Dodson EJ, Dodson GG, Dementieva IS, Zakomirdina LN, Wilson KS, Dauter Z, Lebedev AA, Harutyunyan EH
Title Crystal structure of tryptophanase.
Related PDB 1ax4
Related UniProtKB P28796
[18]
Resource
Comments
Medline ID
PubMed ID 10469830
Journal Protein Eng
Year 1999
Volume 12
Pages 687-92
Authors Kudo H, Natsume R, Nishiyama M, Horinouchi S
Title Analysis of stability and catalytic properties of two tryptophanases from a thermophile.
Related PDB
Related UniProtKB
[19]
Resource
Comments
Medline ID
PubMed ID 11011151
Journal J Biochem (Tokyo)
Year 2000
Volume 128
Pages 679-86
Authors Jhee KH, Yoshimura T, Miles EW, Takeda S, Miyahara I, Hirotsu K, Soda K, Kawata Y, Esaki N
Title Stereochemistry of the transamination reaction catalyzed by aminodeoxychorismate lyase from Escherichia coli: close relationship between fold type and stereochemistry.
Related PDB
Related UniProtKB
[20]
Resource
Comments
Medline ID
PubMed ID 11934889
Journal J Biol Chem
Year 2002
Volume 277
Pages 21592-7
Authors Phillips RS, Demidkina TV, Zakomirdina LN, Bruno S, Ronda L, Mozzarelli A
Title Crystals of tryptophan indole-lyase and tyrosine phenol-lyase form stable quinonoid complexes.
Related PDB
Related UniProtKB

Comments
Although this enzyme binds potassium ion, it is too distant from the active site to be involved in catalysis directly (see [17]).
According to the literature [17], this enzyme catalyzes five reactions:
(A) Formation of external aldimine (Schiff-base between PLP & substrate amino group),
(B) Elimination of indole ring from the external aldimine complex,
(C) Addition of water to double-bonded carbon atom (or Hydration),
(D) Elimination of imine group from the product,
(E) Formation of internal aldimine (Schiff-base between PLP & catalytic lysine).

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