PDBsum entry 4d0y

Hydrolase

PDB id: 4d0y

Contents

Protein chains

184 a.a.

Ligands

PO4 ×2

Metals

_ZN ×13

Waters ×479

PDB id:

4d0y

Name:

Hydrolase

Title:

Crystal structure of dacb from streptococcus pneumoniae d39

Structure:

Dacb. Chain: a, b. Fragment: catalytic domain, residues 55-238. Synonym: lipoprotein, putative. Engineered: yes

Source:

Streptococcus pneumoniae d39. Organism_taxid: 373153. Expressed in: escherichia coli. Expression_system_taxid: 511693.

Resolution:

2.00Å R-factor: 0.184 R-free: 0.243

Authors:

J.Gutierrez-Fernandez,J.A.Hermoso

Key ref:

M.R.Abdullah et al. (2014). Structure of the pneumococcal l,d-carboxypeptidase DacB and pathophysiological effects of disabled cell wall hydrolases DacA and DacB. Mol Microbiol, 93, 1183-1206. PubMed id: 25060741 DOI: 10.1111/mmi.12729

Date:

30-Apr-14 Release date: 06-Aug-14

Protein chains

A0A0H2ZP28  (A0A0H2ZP28_STRP2) -  Lipoprotein, putative from Streptococcus pneumoniae serotype 2 (strain D39 / NCTC 7466)

Seq: 238 a.a.

Struc: 184 a.a.

Enzyme reactions

• Enzyme class: E.C.3.4.17.13 - muramoyltetrapeptide carboxypeptidase.
• Reaction: N-acetyl-D-glucosaminyl-N-acetylmuramoyl-L-alanyl-meso-2,6- diaminoheptanedioyl-D-alanine + H2O = N-acetyl-D-glucosaminyl-N- acetylmuramoyl-L-alanyl-meso-2,6-diaminoheptanedioate + D-alanine

Molecule diagrams generated from .mol files obtained from the KEGG ftp site

Key reference

DOI no: 10.1111/mmi.12729

Mol Microbiol 93:1183-1206 (2014)

PubMed id: 25060741

Structure of the pneumococcal l,d-carboxypeptidase DacB and pathophysiological effects of disabled cell wall hydrolases DacA and DacB.

M.R.Abdullah, J.Gutiérrez-Fernández, T.Pribyl, N.Gisch, M.Saleh, M.Rohde, L.Petruschka, G.Burchhardt, D.Schwudke, J.A.Hermoso, S.Hammerschmidt.

ABSTRACT

Bacterial cell wall hydrolases are essential for peptidoglycan turnover and crucial to preserve cell shape. The d,d-carboxypeptidase DacA and l,d-carboxypeptidase DacB of Streptococcus pneumoniae function in a sequential manner. Here, we determined the structure of the surface-exposed lipoprotein DacB. The crystal structure of DacB, radically different to that of DacA, contains a mononuclear Zn(2+) catalytic centre located in the middle of a large and fully exposed groove. Two different conformations were found presenting a different arrangement of the active site topology. The critical residues for catalysis and substrate specificity were identified. Loss-of-function of DacA and DacB altered the cell shape and this was consistent with a modified peptidoglycan peptide composition in dac mutants. Contrary, an lgt mutant lacking lipoprotein diacylglyceryl transferase activity required for proper lipoprotein maturation retained l,d-carboxypeptidase activity and showed an intact murein sacculus. In addition we demonstrated pathophysiological effects of disabled DacA or DacB activities. Real-time bioimaging of intranasal infected mice indicated a substantial attenuation of ΔdacB and ΔdacAΔdacB pneumococci, while ΔdacA had no significant effect. In addition, uptake of these mutants by professional phagocytes was enhanced, while the adherence to lung epithelial cells was decreased. Thus, structural and functional studies suggest DacA and DacB as optimal drug targets.