2ZC4

Penicillin-binding protein 2X (PBP 2X) acyl-enzyme complex (tebipenem) from Streptococcus pneumoniae

Summary for 2ZC4

• Entry DOI: 10.2210/pdb2zc4/pdb
• Related: 2ZC3 2ZC5 2ZC6
• Descriptor: Penicillin-binding protein 2X, (4R,5S)-3-(1-(4,5-dihydrothiazol-2-yl)azetidin-3-ylthio)-5-((2S,3R)-3-hydroxy-1-oxobutan-2-yl)-4-methyl-4,5- dihydro-1H-pyrrole-2-carboxylic acid, SULFATE ION, ... (6 entities in total)
• Functional Keywords: peptidoglycan synthesis, cell wall, penicillin-binding, antibiotics, tebipenem, antibiotic resistance, cell cycle, cell division, cell shape, cell wall biogenesis/degradation, membrane, secreted, transmembrane, biosynthetic protein
• Biological source: Streptococcus pneumoniae; More
• Cellular location: Cell membrane; Single-pass membrane protein: P59676 P59676 P59676
• Total number of polymer chains: 6
• Total formula weight: 149229.13

Authors

Yamada, M.,Watanabe, T.,Takeuchi, Y. (deposition date: 2007-11-02, release date: 2008-04-08, Last modification date: 2023-11-01)

Primary citation

Yamada, M.,Watanabe, T.,Baba, N.,Takeuchi, Y.,Ohsawa, F.,Gomi, S.
Crystal Structures of Biapenem and Tebipenem Complexed with Penicillin-Binding Proteins 2X and 1A from Streptococcus pneumoniae
Antimicrob.Agents Chemother., 52:2053-2060, 2008

PubMed Abstract: Biapenem is a parenteral carbapenem antibiotic that exhibits wide-ranging antibacterial activity, remarkable chemical stability, and extensive stability against human renal dehydropeptidase-I. Tebipenem is the active form of tebipenem pivoxil, a novel oral carbapenem antibiotic that has a high level of bioavailability in humans, in addition to the above-mentioned features. beta-lactam antibiotics, including carbapenems, target penicillin-binding proteins (PBPs), which are membrane-associated enzymes that play essential roles in peptidoglycan biosynthesis. To envisage the binding of carbapenems to PBPs, we determined the crystal structures of the trypsin-digested forms of both PBP 2X and PBP 1A from Streptococcus pneumoniae strain R6, each complexed with biapenem or tebipenem. The structures of the complexes revealed that the carbapenem C-2 side chains form hydrophobic interactions with Trp374 and Thr526 of PBP 2X and with Trp411 and Thr543 of PBP 1A. The Trp and Thr residues are conserved in PBP 2B. These results suggest that interactions between the C-2 side chains of carbapenems and the conserved Trp and Thr residues in PBPs play important roles in the binding of carbapenems to PBPs.

PubMed: 18391040
DOI: 10.1128/AAC.01456-07

Experimental method

X-RAY DIFFRACTION (2.8 Å)