1y3t | pdb_00001y3t
Crystal structure of YxaG, a dioxygenase from Bacillus subtilis
Structural highlights
Function[QDOI_BACSU] Performs the first step in the degradation of the flavonoid quercetin by a dioxygenase reaction. The enzyme catalyzes the cleavage of the O-heteroaromatic ring of the flavonol quercetin yielding the depside 2-protocatechuoyl-phloroglucinol carboxylic acid and carbon monoxide. This involves the remarkable dioxygenolytic cleavage of two carbon-carbon bonds.[1] Evolutionary Conservation Check, as determined by ConSurfDB. You may read the explanation of the method and the full data available from ConSurf. Publication Abstract from PubMedCommon structural motifs, such as the cupin domains, are found in enzymes performing different biochemical functions while retaining a similar active site configuration and structural scaffold. The soil bacterium Bacillus subtilis has 20 cupin genes (0.5% of the total genome) with up to 14% of its genes in the form of doublets, thus making it an attractive system for studying the effects of gene duplication. There are four bicupins in B. subtilis encoded by the genes yvrK, yoaN, yxaG, and ywfC. The gene products of yvrK and yoaN function as oxalate decarboxylases with a manganese ion at the active site(s), whereas YwfC is a bacitracin synthetase. Here we present the crystal structure of YxaG, a novel iron-containing quercetin 2,3-dioxygenase with one active site in each cupin domain. Yxag is a dimer, both in solution and in the crystal. The crystal structure shows that the coordination geometry of the Fe ion is different in the two active sites of YxaG. Replacement of the iron at the active site with other metal ions suggests modulation of enzymatic activity in accordance with the Irving-Williams observation on the stability of metal ion complexes. This observation, along with a comparison with the crystal structure of YvrK determined recently, has allowed for a detailed structure-function analysis of the active site, providing clues to the diversification of function in the bicupin family of proteins. The crystal structure of a quercetin 2,3-dioxygenase from Bacillus subtilis suggests modulation of enzyme activity by a change in the metal ion at the active site(s).,Gopal B, Madan LL, Betz SF, Kossiakoff AA Biochemistry. 2005 Jan 11;44(1):193-201. PMID:15628860[2] From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine. References
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