Structural and Mutational Studies on the Unusual Substrate Specificity of meso-Diaminopimelate Dehydrogenase from Symbiobacterium thermophilum

Wild‐type meso‐diaminopimelate dehydrogenase (DAPDH) is usually specific to the native substrate, meso‐2,6‐diaminopimelate. Recently, a DAPDH from Symbiobacterium thermophilum (StDAPDH) was found to exhibit expanded substrate specificity. As such, its crystal structures in apo form and in complex wi...

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Published in:Chembiochem : a European journal of chemical biology 2014-01, Vol.15 (2), p.217-222
Main Authors: Liu, Weidong, Li, Zhe, Huang, Chun-Hsiang, Guo, Rey-Ting, Zhao, Leiming, Zhang, Dalong, Chen, Xi, Wu, Qiaqing, Zhu, Dunming
Format: Article
Language:English
Subjects:
amination
Amino Acid Oxidoreductases - chemistry
Amino Acid Oxidoreductases - genetics
Amino Acid Oxidoreductases - metabolism
Crystal structure
Dehydrogenases
enzyme catalysis
Gammaproteobacteria - enzymology
meso-diaminopimelate dehydrogenase
Models, Molecular
Mutagenesis
Mutation
Protein Conformation
protein structure
Substrate Specificity
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Summary:Wild‐type meso‐diaminopimelate dehydrogenase (DAPDH) is usually specific to the native substrate, meso‐2,6‐diaminopimelate. Recently, a DAPDH from Symbiobacterium thermophilum (StDAPDH) was found to exhibit expanded substrate specificity. As such, its crystal structures in apo form and in complex with NADP+ and both NADPH and meso‐DAP were investigated to reveal the structural basis of its unique catalytic properties. Structural analysis results show that StDAPDH should prefer an ordered kinetic catalytic mechanism. A second substrate entrance tunnel with Met152 at its bottleneck was found, through which pyruvate/D‐alanine might bind and enter the catalytic cavity, providing some structural insights into its high activity toward pyruvate. The side chain of Met152 might interact with Asp92 and Asn253, thus affecting the domain motion and catalysis. These results offer useful information for understanding the unique catalytic properties of StDAPDH and guiding further engineering of this enzyme. Structure and specificity: Structural analysis of a meso‐diaminopimelate dehydrogenase from Symbiobacterium thermophilum revealed a second substrate entrance tunnel with Met152 at its bottleneck, possibly responsible for its unusual substrate profile for small substrates. Structural and site‐specific mutagenesis showed that the Met152 side chain might interact with Asp92 and Asn253 to affect domain motion and catalysis.
ISSN:1439-4227
1439-7633
DOI:10.1002/cbic.201300691