PDBsum entry: 2oqx

Lyase

PDB id: 2oqx

Contents

Protein chain

465 a.a. *

Ligands

EPE

Metals

_CL

_MG

Waters ×364

* Residue conservation analysis

PDB id:

2oqx

Name:

Lyase

Title:

Crystal structure of the apo form of e. Coli tryptophanase a resolution

Structure:

Tryptophanase. Chain: a. Synonym: l-tryptophan indole-lyase, tnase. Ec: 4.1.99.1

Source:

Escherichia coli. Organism_taxid: 562

Resolution:

1.90Å R-factor: 0.203 R-free: 0.232

Authors:

Y.Goldgur,A.Kogan,G.Gdalevsky,A.Parola,R.Cohen-Luria,O.Almog

Key ref:

N.Tsesin et al. (2007). The structure of apo tryptophanase from Escherichia coli reveals a wide-open conformation. Acta Crystallogr D Biol Crystallogr, 63, 969-974. PubMed id: 17704565 DOI: 10.1107/S0907444907036396

Date:

01-Feb-07 Release date: 20-Feb-07

Protein chain

P0A853  (TNAA_ECOLI) -  Tryptophanase

Seq: 471 a.a.

Struc: 465 a.a.*

* PDB and UniProt seqs differ at 2 residue positions (black crosses)

Enzyme reactions

• Enzyme class: E.C.4.1.99.1 - Tryptophanase.
• Reaction: L-tryptophan + H₂O = indole + pyruvate + NH₃
• Cofactor: Potassium; Pyridoxal 5'-phosphate

Molecule diagrams generated from .mol files obtained from the KEGG ftp site

 Gene Ontology (GO) functional annotation 

• Cellular component: membrane (2 terms)
• Biological process: cellular amino acid metabolic process (4 terms)
• Biochemical function: catalytic activity (7 terms)

reference

DOI no: 10.1107/S0907444907036396

Acta Crystallogr D Biol Crystallogr 63:969-974 (2007)

PubMed id: 17704565

The structure of apo tryptophanase from Escherichia coli reveals a wide-open conformation.

N.Tsesin, A.Kogan, G.Y.Gdalevsky, J.P.Himanen, R.Cohen-Luria, A.H.Parola, Y.Goldgur, O.Almog.

ABSTRACT

The crystal structure of apo tryptophanase from Escherichia coli (space group F222, unit-cell parameters a = 118.4, b = 120.1, c = 171.2 A) was determined at 1.9 A resolution using the molecular-replacement method and refined to an R factor of 20.3% (R(free) = 23.2%). The structure revealed a significant shift in the relative orientation of the domains compared with both the holo form of Proteus vulgaris tryptophanase and with another crystal structure of apo E. coli tryptophanase, reflecting the internal flexibility of the molecule. Domain shifts were previously observed in tryptophanase and in the closely related enzyme tyrosine phenol-lyase, with the holo form found in an open conformation and the apo form in either an open or a closed conformation. Here, a wide-open conformation of the apo form of tryptophanase is reported. A conformational change is also observed in loop 297-303. The structure contains a hydrated Mg(2+) at the cation-binding site and a Cl(-) ion at the subunit interface. The enzyme activity depends on the nature of the bound cation, with smaller ions serving as inhibitors. It is hypothesized that this effect arises from variations of the coordination geometry of the bound cation.

Selected figure(s)

Figure 1.
Figure 1 (a) Superposition of Trpase monomers from P. vulgaris (holo form, shown in yellow) and E. coli (apoI structure, red; apoII structure, green) shown as ribbons. The apoI structure is found in the most closed conformation, while the apoII structure is the most open. (b) Space-filling models of the three structures, showing the variations in the catalytic cleft width.

Figure 2.
Figure 2 Loop 292-307. The conformation observed for the holo form is shown in magenta, which is nearly identical to the apoI crystal form. The same loop in the apoII structure is colored cyan. Cys298 forms a disulfide bond with a 2-mercaptoethanol molecule present in the crystallization mixture.

The above figures are reprinted by permission from the IUCr: Acta Crystallogr D Biol Crystallogr (2007, 63, 969-974) copyright 2007.

Figures were selected by an automated process.