1AX4

TRYPTOPHANASE FROM PROTEUS VULGARIS

PDB DOI: 10.2210/pdb1AX4/pdb

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

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.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.10 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

PubMed: 9551100 Search on PubMed
DOI: 10.1006/jmbi.1997.1561
Primary Citation of Related Structures:
1AX4

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.

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

Organizational Affiliation:

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

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
TRYPTOPHANASE	A, B, C, D	467	Proteus vulgaris	Mutation(s): 1 Gene Names: tnaA EC: 4.1.99.1
UniProt
Find proteins for P28796 (Proteus vulgaris) Explore P28796 Go to UniProtKB: P28796
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P28796
Protein Feature View Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
K Query on K Download Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain F [auth B] SDF format, chain G [auth C] SDF format, chain H [auth D] MOL2 format, chain E [auth A] MOL2 format, chain F [auth B] MOL2 format, chain G [auth C] MOL2 format, chain H [auth D]	E [auth A], F [auth B], G [auth C], H [auth D]	POTASSIUM ION K NPYPAHLBTDXSSS-UHFFFAOYSA-N		Ligand Interaction