title: Structural and biochemical analyses of the Streptococcus pneumonia L,D-carboxypeptidase DacB.
abstract: The L,D-carboxypeptidase DacB plays a key role in the remodelling of Streptococcus pneumoniae peptidoglycan during cell division. In order to decipher its substrate-binding properties and catalytic mechanism, the 1.71 Å resolution crystal structure of DacB from S. pneumoniae TIGR4 is reported. Structural analyses in combination with comparisons with the recently reported structures of DacB from S. pneumoniae D39 and R6 clearly demonstrate that DacB adopts a zinc-dependent carboxypeptidase fold and belongs to the metallopeptidase M15B subfamily. In addition, enzymatic activity assays further confirm that DacB indeed acts as an L,D-carboxypeptidase towards the tetrapeptide L-Ala-D-iGln-L-Lys-D-Ala of the peptidoglycan stem, with Km and kcat values of 2.84 ± 0.37 mM and 91.49 ± 0.05 s(-1), respectively. Subsequent molecular docking and site-directed mutagenesis enable the assignment of the key residues that bind to the tetrapeptide. Altogether, these findings provide structural insights into substrate recognition in the metallopeptidase M15B subfamily.
authors: Hefei National Laboratory for Physical Sciences at the Microscale and School of Life Sciences, University of Science and Technology of China, Hefei 230027, People's Republic of China.
authors: Juan
authors: J
authors: Zhang
authors: Hefei National Laboratory for Physical Sciences at the Microscale and School of Life Sciences, University of Science and Technology of China, Hefei 230027, People's Republic of China.
authors: Yi-Hu
authors: YH
authors: Yang
authors: Hefei National Laboratory for Physical Sciences at the Microscale and School of Life Sciences, University of Science and Technology of China, Hefei 230027, People's Republic of China.
authors: Yong-Liang
authors: YL
authors: Jiang
authors: Hefei National Laboratory for Physical Sciences at the Microscale and School of Life Sciences, University of Science and Technology of China, Hefei 230027, People's Republic of China.
authors: Cong-Zhao
authors: CZ
authors: Zhou
authors: Hefei National Laboratory for Physical Sciences at the Microscale and School of Life Sciences, University of Science and Technology of China, Hefei 230027, People's Republic of China.
authors: Yuxing
authors: Y
authors: Chen
mesh_terms: D000595:Amino Acid Sequence; D002268:Carboxypeptidases / Q000737:chemistry* / Q000378:metabolism; D018360:Crystallography, X-Ray; D006801:Humans; D062105:Molecular Docking Simulation; D010457:Peptidoglycan / Q000737:chemistry / Q000378:metabolism; D011008:Pneumococcal Infections / Q000382:microbiology; D013296:Streptococcus pneumoniae / Q000737:chemistry / Q000201:enzymology* / Q000378:metabolism; D013379:Substrate Specificity
chemical_list: D010457:Peptidoglycan; D002268:Carboxypeptidases; C055587:carboxypeptidase L; C078874:carboxypeptidase D
keywords: Streptococcus pneumoniae; l,d-carboxypeptidase; molecular docking; peptidoglycan