Structural basis for the recognition of muramyltripeptide by Helicobacter pylori Csd4, a D,L-carboxypeptidase controlling the helical cell shape.
Helicobacter pylori infection causes a variety of gastrointestinal diseases, including peptic ulcers and gastric cancer. Its colonization of the gastric mucosa of the human stomach is a prerequisite for survival in the stomach. Colonization depends on its motility, which is facilitated by the helical shape of the bacterium. In H. pylori, cross-linking relaxation or trimming of peptidoglycan muropeptides affects the helical cell shape. Csd4 has been identified as one of the cell shape-determining peptidoglycan hydrolases in H. pylori. It is a Zn(2+)-dependent D,L-carboxypeptidase that cleaves the bond between the γ-D-Glu and the mDAP of the non-cross-linked muramyltripeptide (muramyl-L-Ala-γ-D-Glu-mDAP) of the peptidoglycan to produce the muramyldipeptide (muramyl-L-Ala-γ-D-Glu) and mDAP. Here, the crystal structure of H. pylori Csd4 (HP1075 in strain 26695) is reported in three different states: the ligand-unbound form, the substrate-bound form and the product-bound form. H. pylori Csd4 consists of three domains: an N-terminal D,L-carboxypeptidase domain with a typical carboxypeptidase fold, a central β-barrel domain with a novel fold and a C-terminal immunoglobulin-like domain. The D,L-carboxypeptidase domain recognizes the substrate by interacting primarily with the terminal mDAP moiety of the muramyltripeptide. It undergoes a significant structural change upon binding either mDAP or the mDAP-containing muramyltripeptide. It it also shown that Csd5, another cell-shape determinant in H. pylori, is capable of interacting not only with H. pylori Csd4 but also with the dipeptide product of the reaction catalyzed by Csd4.
Research Institute of Pharmaceutical Sciences, College of Pharmacy, Seoul National University, Seoul 151-742, Republic of Korea.
Hyoun Sook
HS
Kim
Department of Biophysics and Chemical Biology, College of Natural Sciences, Seoul National University, Seoul 151-742, Republic of Korea.
Jieun
J
Kim
Department of Biophysics and Chemical Biology, College of Natural Sciences, Seoul National University, Seoul 151-742, Republic of Korea.
Ha Na
HN
Im
Department of Biophysics and Chemical Biology, College of Natural Sciences, Seoul National University, Seoul 151-742, Republic of Korea.
Doo Ri
DR
An
Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, IN 46556, USA.
Mijoon
M
Lee
Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, IN 46556, USA.
Dusan
D
Hesek
Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, IN 46556, USA.
Shahriar
S
Mobashery
Division of Mass Spectrometry, Korea Basic Science Institute, Chungbuk 363-883, Republic of Korea.
Jin Young
JY
Kim
Division of Mass Spectrometry, Korea Basic Science Institute, Chungbuk 363-883, Republic of Korea.
Kun
K
Cho
Department of Chemistry, College of Natural Sciences, Seoul National University, Seoul 151-742, Republic of Korea.
Hye Jin
HJ
Yoon
Research Institute of Pharmaceutical Sciences, College of Pharmacy, Seoul National University, Seoul 151-742, Republic of Korea.
Byung Woo
BW
Han
Biomolecular Function Research Branch, Division of Convergence Technology, Research Institute, National Cancer Center, Gyeonggi 410-769, Republic of Korea.
Byung Il
BI
Lee
Department of Chemistry, College of Natural Sciences, Seoul National University, Seoul 151-742, Republic of Korea.
Se Won
SW
Suh
D000595:Amino Acid Sequence; D001426:Bacterial Proteins / Q000737:chemistry* / Q000378:metabolism; D001665:Binding Sites; D002268:Carboxypeptidases / Q000737:chemistry* / Q000378:metabolism; D018360:Crystallography, X-Ray; D016481:Helicobacter Infections / Q000382:microbiology*; D016480:Helicobacter pylori / Q000737:chemistry* / Q000378:metabolism; D006801:Humans; D008958:Models, Molecular; D008969:Molecular Sequence Data; D009112:Muramic Acids / Q000737:chemistry / Q000378:metabolism; D009842:Oligopeptides / Q000737:chemistry / Q000378:metabolism*; D011485:Protein Binding; D011487:Protein Conformation; D017434:Protein Structure, Tertiary; D016415:Sequence Alignment
D001426:Bacterial Proteins; D009112:Muramic Acids; D009842:Oligopeptides; D002268:Carboxypeptidases; C055587:carboxypeptidase L
HP1075; Helicobacter pylori; cell shape; csd4; csd5; d,l-carboxypeptidase; meso-diaminopimelate; peptidoglycan; pgp1