1XP4

Crystal structure of a peptidoglycan synthesis regulatory factor (PBP3) from Streptococcus pneumoniae

Summary for 1XP4

• Entry DOI: 10.2210/pdb1xp4/pdb
• Descriptor: D-alanyl-D-alanine carboxypeptidase, SULFATE ION, IODIDE ION, ... (4 entities in total)
• Functional Keywords: five-stranded antiparallel beta-sheet, omega-like loop, hydrolase
• Biological source: Streptococcus pneumoniae R6
• Total number of polymer chains: 4
• Total formula weight: 168678.98

Authors

Morlot, C.,Pernot, L.,Le Gouellec, A.,Di Guilmi, A.M.,Vernet, T.,Dideberg, O.,Dessen, A. (deposition date: 2004-10-08, release date: 2004-11-09, Last modification date: 2023-11-15)

Primary citation

Morlot, C.,Pernot, L.,Le Gouellec, A.,Di Guilmi, A.M.,Vernet, T.,Dideberg, O.,Dessen, A.
Crystal structure of a peptidoglycan synthesis regulatory factor (PBP3) from Streptococcus pneumoniae
J.Biol.Chem., 280:15984-15991, 2005

PubMed Abstract: Penicillin-binding proteins (PBPs) are membrane-associated enzymes which perform critical functions in the bacterial cell division process. The single d-Ala,d-Ala (d,d)-carboxypeptidase in Streptococcus pneumoniae, PBP3, has been shown to play a key role in control of availability of the peptidoglycal substrate during cell growth. Here, we have biochemically characterized and solved the crystal structure of a soluble form of PBP3 to 2.8 A resolution. PBP3 folds into an NH(2)-terminal, d,d-carboxypeptidase-like domain, and a COOH-terminal, elongated beta-rich region. The carboxypeptidase domain harbors the classic signature of the penicilloyl serine transferase superfamily, in that it contains a central, five-stranded antiparallel beta-sheet surrounded by alpha-helices. As in other carboxypeptidases, which are present in species whose peptidoglycan stem peptide has a lysine residue at the third position, PBP3 has a 14-residue insertion at the level of its omega loop, a feature that distinguishes it from carboxypeptidases from bacteria whose peptidoglycan harbors a diaminopimelate moiety at this position. PBP3 performs substrate acylation in a highly efficient manner (k(cat)/K(m) = 50,500 M(-1) x s(-1)), an event that may be linked to role in control of pneumococcal peptidoglycan reticulation. A model that places PBP3 poised vertically on the bacterial membrane suggests that its COOH-terminal region could act as a pedestal, placing the active site in proximity to the peptidoglycan and allowing the protein to "skid" on the surface of the membrane, trimming pentapeptides during the cell growth and division processes.

PubMed: 15596446
DOI: 10.1074/jbc.M408446200

Experimental method

X-RAY DIFFRACTION (2.8 Å)