Penicillin-binding proteins

Ribbon representation of the atomic structure of Penicillin Binding Protein 3 from Pseudomonas aeruginosa (PDB 3OC2), image created with PyMol.

Penicillin-binding protein, transpeptidase
Identifiers
Symbol	PCN-bd_Tpept
Pfam	PF00905
InterPro	IPR001460
OPM superfamily	195
OPM protein	5hlb
Membranome	541
Available protein structures: PDB   IPR001460 PF00905 (ECOD; PDBsum)   AlphaFold IPR001460 PF00905

Penicillin-binding protein, dimerisation domain
Identifiers
Symbol	PBP_dimer
Pfam	PF03717
InterPro	IPR005311
Available protein structures: PDB   PDB: 1k25​ PDB: 1mwr​ PDB: 1mws​ PDB: 1mwt​ PDB: 1mwu​ PDB: 1pmd​ PDB: 1pyy​ PDB: 1qme​ PDB: 1qmf​ PDB: 1rp5​ IPR005311 PF03717 (ECOD; PDBsum)   AlphaFold IPR005311 PF03717

PBPs normally catalyze the cross-linking of the bacterial cell wall, but they can be permanently inhibited by penicillin and other β-lactam antibiotics. (NAM = N-acetylmuramic acid; NAG = N-acetylglucosamine)

Penicillin-binding proteins (PBP) are a group of proteins that are characterized by their affinity for and binding of penicillin. They are a normal constituent of many bacteria; the name just reflects the way by which the protein was discovered. All β-lactam antibiotics (except for tabtoxinine-β-lactam, which inhibits glutamine synthetase) bind to PBPs, which are essential for bacterial cell wall synthesis. PBPs are members of a subgroup of transpeptidase enzymes called DD-transpeptidases.

Diversity

There are a large number of PBPs, usually several in each organism, and they are found as both membrane-bound and cytoplasmic proteins. For example, Spratt (1977) reports that six different PBPs are routinely detected in all strains of E. coli ranging in molecular weight from 40,000 to 91,000. The different PBPs occur in different numbers per cell and have varied affinities for penicillin. The PBPs are usually broadly classified into high-molecular-weight (HMW) and low-molecular-weight (LMW) categories. High Molecular Mass (HMM) PBP’s are essential for cell viability and they are divided between two classes. Class A enzymes catalyze both the polymerization of a peptidoglycan from disaccharide peptides (glycosyltransferase) and the cross-linking of muramyl peptides (transpeptidase). On the other hand, class B enzymes possess transpeptidase activity (only cross linking). Low Molecular-Mass (LMM) PBP’s are dispensable for normal cell growth and control how tightly the peptidoglycan chains are linked together. Proteins that have evolved from PBPs occur in many higher organisms and include the mammalian LACTB protein.

Function

PBPs are all involved in the final stages of the synthesis of peptidoglycan, which is the major component of bacterial cell walls. Bacterial cell wall synthesis is essential to growth, cell division (thus reproduction) and maintaining the cellular structure in bacteria. Inhibition of PBPs leads to defects in cell wall structure and irregularities in cell shape, for example filamentation, pseudomulticellular forms, lesions leading to spheroplast formation, and eventual cell death and lysis.

PBPs have been shown to catalyze a number of reactions involved in the process of synthesizing cross-linked peptidoglycan from lipid intermediates and mediating the removal of D-alanine from the precursor of peptidoglycan. Purified enzymes have been shown to catalyze the following reactions: D-alanine carboxypeptidase, peptidoglycan transpeptidase, and peptidoglycan endopeptidase. In all bacteria that have been studied, enzymes have been shown to catalyze more than one of the above reactions.