Biological Assembly 1  

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Global Symmetry: Dihedral - D2  (3D View)
Global Stoichiometry: Homo 4-mer - A4 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 211304.80 
• Atom Count: 14775 
• Residue Count: 1868 
• Unique protein chains: 1

1AX4

TRYPTOPHANASE FROM PROTEUS VULGARIS

• DOI: 10.2210/pdb1AX4/pdb

• Classification: TRYPTOPHAN BIOSYNTHESIS
• Organism(s): Proteus vulgaris
• Expression System: Escherichia coli


• Deposited: 1997-10-28 Released: 1998-01-28 
• Deposition Author(s): Isupov, M.N., Antson, A.A., Dodson, E.J., Dodson, G.G., Dementieva, I.S., Zakomirdina, L.N., Wilson, K.S., Dauter, Z., Lebedev, A.A., Harutyunyan, E.H.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.1 Å
• R-Value Free: 0.227 
• R-Value Work: 0.187 

Literature

Crystal structure of tryptophanase.

Isupov, M.N., Antson, A.A., Dodson, E.J., Dodson, G.G., Dementieva, I.S., Zakomirdina, L.N., Wilson, K.S., Dauter, Z., Lebedev, A.A., Harutyunyan, E.H.

(1998) J.Mol.Biol. 276: 603-623

• PubMed: 9551100 
• DOI: 10.1006/jmbi.1997.1561
• Also Cited By: 5W19


• PubMed Abstract: 
  

The X-ray structure of tryptophanase (Tnase) reveals the interactions responsible for binding of the pyridoxal 5'-phosphate (PLP) and atomic details of the K+ binding site essential for catalysis. The structure of holo Tnase from Proteus vulgaris (space group P2(1)2(1)2(1) with a = 115.0 A, b = 118.2 A, c = 153.7 A) has been determined at 2.1 A resolution by molecular replacement using tyrosine phenol-lyase (TPL) coordinates. The final model of Tnase, refined to an R-factor of 18.7%, (Rfree = 22.8%) suggests that the PLP-enzyme from observed in the structure is a ketoenamine. PLP is bound in a cleft formed by both the small and large domains of one subunit and the large domain of the adjacent subunit in the so-called "catalytic" dimer. The K+ cations are located on the interface of the subunits in the dimer. The structure of the catalytic dimer and mode of PLP binding in Tnase resemble those found in aspartate amino-transferase, TPL, omega-amino acid pyruvate aminotransferase, dialkylglycine decarboxylase (DGD), cystathionine beta-lyase and ornithine decarboxylase. No structural similarity has been detected between Tnase and the beta 2 dimer of tryptophan synthase which catalyses the same beta-replacement reaction. The single monovalent cation binding site of Tnase is similar to that of TPL, but differs from either of those in DGD.

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Related Citations: 

• X-Ray Study of Tryptophanase at 2.1 Angstrom Resolution
  Isupov, M.,Dementieva, I.,Zakomirdina, L.,Wilson, K.S.,Dauter, Z.,Antson, A.A.,Dodson, G.G.,Harutyunyan, E.H.
  (1994) Biochemistry of Vitamin B6 and Pqq --: 183
• Crystallization and Preliminary X-Ray Investigation of Holotryptophanases from Escherichia Coli and Proteus Vulgaris
  Dementieva, I.S.,Zakomirdina, L.N.,Sinitzina, N.I.,Antson, A.A.,Wilson, K.S.,Isupov, M.N.,Lebedev, A.A.,Harutyunyan, E.H.
  (1994) J.Mol.Biol. 235: 783




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Organizational Affiliation: 

Shubnikov Institute of Crystallography, Russian Academy of Sciences, Moscow, Russia.

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
TRYPTOPHANASE	A, B, C, D	467	Proteus vulgaris	Mutation(s): 0  Gene Names: tnaA EC: 4.1.99.1
Find proteins for P28796 (Proteus vulgaris) Go to UniProtKB:  P28796

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram & Interactions
K	A, B, C, D	POTASSIUM ION K NPYPAHLBTDXSSS-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
LLP	A, B, C, D	L-PEPTIDE LINKING	C14 H22 N3 O7 P		LYS

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.1 Å
• R-Value Free: 0.227 
• R-Value Work: 0.187 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length (Å)	Angle (°)
a = 114.990	α = 90.00
b = 118.230	β = 90.00
c = 153.680	γ = 90.00

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
AMoRE	phasing
REFMAC	refinement

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 1997-10-28 
• Released Date: 1998-01-28 
• Deposition Author(s): Isupov, M.N., Antson, A.A., Dodson, E.J., Dodson, G.G., Dementieva, I.S., Zakomirdina, L.N., Wilson, K.S., Dauter, Z., Lebedev, A.A., Harutyunyan, E.H.

Revision History 

• Version 1.0: 1998-01-28
  Type: Initial release
• Version 1.1: 2008-03-24
  Type: Version format compliance
• Version 1.2: 2011-07-13
  Type: Version format compliance