Structural Comparison and Simulation of Pneumococcal Peptidoglycan Hydrolase LytB.
Three-dimensional structural determination combined with comprehensive comparisons with the homologs is a straightforward strategy to decipher the molecular function of an enzyme. However, in many cases it's difficult to obtain the complex structure with the substrate/ligand. Structure-based molecular simulation provides an alternative solution to predict the binding pattern of a substrate/ligand to the enzyme. The Streptococcus pneumoniae LytB is a peptidoglycan hydrolase that cleaves the glycosidic bond and therefore involves the cell division; however, the details of catalytic mechanism remain unknown. Based on the crystal structure of the catalytic domain of LytB (termed LytBCAT), we describe here how to assign the molecular functions of three LytBCAT modules: SH3b, WW, and GH73, using structural comparisons. Moreover, we dock a putative tetrasaccharide-pentapeptide substrate of peptidoglycan onto LytBCAT to provide the details of substrate binding pattern. The tetrasaccharide-pentapeptide is well accommodated in a T-shaped substrate binding pocket formed by the three modules. The conclusions deduced from structural comparison and simulation are further proved by the hydrolytic activity assays in combination with site-directed mutagenesis.
Hefei National Laboratory for Physical Sciences at the Microscale and School of Life Sciences, University of Science and Technology of China, Hefei, Anhui, 230027, People's Republic of China.|College of Life and Environment Science, Huangshan University, Huangshan, Anhui, 245041, People's Republic of China.
Xiao-Hui
XH
Bai
Hefei National Laboratory for Physical Sciences at the Microscale and School of Life Sciences, University of Science and Technology of China, Hefei, Anhui, 230027, People's Republic of China.
Qiong
Q
Li
Hefei National Laboratory for Physical Sciences at the Microscale and School of Life Sciences, University of Science and Technology of China, Hefei, Anhui, 230027, People's Republic of China.
Yong-Liang
YL
Jiang
Center for Infectious Disease Research, School of Medicine, Tsinghua University, Beijing, 100084, People's Republic of China. zhanglab@tsinghua.edu.cn.
Jing-Ren
JR
Zhang
Hefei National Laboratory for Physical Sciences at the Microscale and School of Life Sciences, University of Science and Technology of China, Hefei, Anhui, 230027, People's Republic of China. cyxing@ustc.edu.cn.
Yuxing
Y
Chen
Hefei National Laboratory for Physical Sciences at the Microscale and School of Life Sciences, University of Science and Technology of China, Hefei, Anhui, 230027, People's Republic of China. zcz@ustc.edu.cn.
Cong-Zhao
CZ
Zhou
D001426:Bacterial Proteins / Q000737:chemistry / Q000235:genetics / Q000378:metabolism; D020134:Catalytic Domain; D003198:Computer Simulation; D018360:Crystallography, X-Ray; D008958:Models, Molecular; D062105:Molecular Docking Simulation; D016297:Mutagenesis, Site-Directed; D009238:N-Acetylmuramoyl-L-alanine Amidase / Q000737:chemistry* / Q000235:genetics / Q000378:metabolism*; D009842:Oligopeptides / Q000737:chemistry / Q000378:metabolism*; D011485:Protein Binding; D011487:Protein Conformation; D013296:Streptococcus pneumoniae / Q000737:chemistry / Q000201:enzymology* / Q000235:genetics; D040681:Structural Homology, Protein; D013379:Substrate Specificity
D001426:Bacterial Proteins; D009842:Oligopeptides; D009238:N-Acetylmuramoyl-L-alanine Amidase
Hydrolytic activity assay; LytB; Peptidoglycan; Peptidoglycan hydrolase; Simulation; Streptococcus pneumoniae; Structural comparison