3WBF

Crystal Structure of meso-diaminopimelate dehydrogenase from Symbiobacterium thermophilum co-crystallized with NADP+ and DAP

Summary for 3WBF

• Entry DOI: 10.2210/pdb3wbf/pdb
• Related: 3WB9 3WBB
• Descriptor: Diaminopimelate dehydrogenase, 2,6-DIAMINOPIMELIC ACID, GLYCEROL, ... (5 entities in total)
• Functional Keywords: domain motion, thermo-stable, d-amino acid dehydrogenase, oxidoreductase
• Biological source: Symbiobacterium thermophilum
• Total number of polymer chains: 3
• Total formula weight: 104211.54

Authors

Liu, W.D.,Li, Z.,Huang, C.H.,Guo, R.T.,Wu, Q.Q.,Zhu, D.M. (deposition date: 2013-05-15, release date: 2014-03-26, Last modification date: 2023-11-15)

Primary citation

Liu, W.,Li, Z.,Huang, C.H.,Guo, R.T.,Zhao, L.,Zhang, D.,Chen, X.,Wu, Q.,Zhu, D.
Structural and mutational studies on the unusual substrate specificity of meso-diaminopimelate dehydrogenase from Symbiobacterium thermophilum.
Chembiochem, 15:217-222, 2014

PubMed Abstract: 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.

PubMed: 24339368
DOI: 10.1002/cbic.201300691

Experimental method

X-RAY DIFFRACTION (2.12 Å)