6EEJ image
Entry Detail
PDB ID:
6EEJ
Keywords:
Title:
Streptomyces bingchenggensis Aldolase-Dehydratase in covalent complex with dienone product.
Biological Source:
PDB Version:
Deposition Date:
2018-08-14
Release Date:
2019-08-14
Method Details:
Experimental Method:
Resolution:
1.89 Å
R-Value Free:
0.18
R-Value Work:
0.16
R-Value Observed:
0.16
Space Group:
P 21 21 2
Macromolecular Entities
Polymer Type:polypeptide(L)
Description:Acetoacetate decarboxylase
Mutations:Y252F
Chain IDs:A, B, C, D
Chain Length:265
Number of Molecules:4
Biological Source:Streptomyces bingchenggensis (strain BCW-1)
Primary Citation
Mechanistic Studies of theStreptomyces bingchenggensisAldolase-Dehydratase: Implications for Substrate and Reaction Specificity in the Acetoacetate Decarboxylase-like Superfamily.
Biochemistry 58 4136 4147 (2019)
PMID: 31524380 DOI: 10.1021/acs.biochem.9b00652

Abstact

The acetoacetate decarboxylase-like superfamily (ADCSF) is a little-explored group of enzymes that may contain new biocatalysts. The low level of sequence identity (∼20%) between many ADCSF enzymes and the confirmed acetoacetate decarboxylases led us to investigate the degree of diversity in the reaction and substrate specificity of ADCSF enzymes. We have previously reported on Sbi00515, which belongs to Family V of the ADCSF and functions as an aldolase-dehydratase. Here, we more thoroughly characterize the substrate specificity of Sbi00515 and find that aromatic, unsaturated aldehydes yield lower KM and higher kcat values compared to those of other small electrophilic substrates in the condensation reaction. The roles of several active site residues were explored by site-directed mutagenesis and steady state kinetics. The lysine-glutamate catalytic dyad, conserved throughout the ADCSF, is required for catalysis. Tyrosine 252, which is unique to Sbi00515, is hypothesized to orient the incoming aldehyde in the condensation reaction. Transient state kinetics and an intermediate-bound crystal structure aid in completing a proposed mechanism for Sbi00515.

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