4COG

Crystal structure of kynurenine formamidase from Burkholderia cenocepacia

Summary for 4COG

• Entry DOI: 10.2210/pdb4cog/pdb
• Related: 4CO9 4COB 4CZ1
• Descriptor: KYNURENINE FORMAMIDASE, ZINC ION, CADMIUM ION, ... (8 entities in total)
• Functional Keywords: hydrolase, kynurenine formamidase (kynb), ec 3.5.1.9, aerobic tryptophan degradation via anthranilate.
• Biological source: BURKHOLDERIA CENOCEPACIA
• Total number of polymer chains: 4
• Total formula weight: 94236.38

Authors

Diaz-Saez, L.,Srikannathasan, V.,Zoltner, M.,Hunter, W.N. (deposition date: 2014-01-28, release date: 2014-04-02, Last modification date: 2024-05-01)

Primary citation

Diaz-Saez, L.,Srikannathasan, V.,Zoltner, M.,Hunter, W.N.
Structure of Bacterial Kynurenine Formamidase Reveals a Crowded Binuclear-Zinc Catalytic Site Primed to Generate a Potent Nucleophile.
Biochem.J., 462:581-, 2014

PubMed Abstract: Tryptophan is an important precursor for chemical entities that ultimately support the biosynthesis of key metabolites. The second stage of tryptophan catabolism is catalysed by kynurenine formamidase, an enzyme that is different between eukaryotes and prokaryotes. In the present study, we characterize the catalytic properties and present the crystal structures of three bacterial kynurenine formamidases. The structures reveal a new amidase protein fold, a highly organized and distinctive binuclear Zn2+ catalytic centre in a confined, hydrophobic and relatively rigid active site. The structure of a complex with 2-aminoacetophenone delineates aspects of molecular recognition extending to the observation that the substrate itself may be conformationally restricted to assist binding in the confined space of the active site and for subsequent processing. The cations occupy a crowded environment, and, unlike most Zn2+-dependent enzymes, there is little scope to increase co-ordination number during catalysis. We propose that the presence of a bridging water/hydroxide ligand in conjunction with the placement of an active site histidine supports a distinctive amidation mechanism.

PubMed: 24942958
DOI: 10.1042/BJ20140511

Experimental method

X-RAY DIFFRACTION (1.6 Å)