1AX4

TRYPTOPHANASE FROM PROTEUS VULGARIS


Experimental Data Snapshot

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

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

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

  • DOI: 10.1006/jmbi.1997.1561

  • 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 (sp ...

    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.


    Related Citations: 
    • 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
    • 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


    Organizational Affiliation

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




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
TRYPTOPHANASE
A, B, C, D
467Proteus vulgarisGene Names: tnaA
EC: 4.1.99.1
Find proteins for P28796 (Proteus vulgaris)
Go to UniProtKB:  P28796
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
K
Query on K

Download SDF File 
Download CCD File 
A, B, C, D
POTASSIUM ION
K
NPYPAHLBTDXSSS-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
LLP
Query on LLP
A, B, C, D
L-PEPTIDE LINKINGC14 H22 N3 O7 PLYS
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 = 114.990α = 90.00
b = 118.230β = 90.00
c = 153.680γ = 90.00
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
REFMACrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

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