2EX9

Crystal structure of penicillin binding protein 4 (dacB) from Escherichia coli, complexed with penicillin-V

Summary for 2EX9

• Entry DOI: 10.2210/pdb2ex9/pdb
• Related: 2EX2 2EX6 2EX8 2EXA 2EXB
• Descriptor: Penicillin-binding protein 4, (2R,4S)-5,5-dimethyl-2-{(1R)-2-oxo-1-[(phenoxyacetyl)amino]ethyl}-1,3-thiazolidine-4-carboxylic acid, GLYCEROL, ... (4 entities in total)
• Functional Keywords: penicillin-binding protein, penicillin-v, cephem, penem, d-alanyl-d-alanine-carboxypeptidase, d-alanyl-d-alanine-endopeptidase, hydrolase
• Biological source: Escherichia coli
• Cellular location: Periplasm : P24228
• Total number of polymer chains: 1
• Total formula weight: 50241.21

Authors

Kishida, H.,Unzai, S.,Roper, D.I.,Lloyd, A.,Park, S.-Y.,Tame, J.R.H. (deposition date: 2005-11-08, release date: 2006-06-13, Last modification date: 2024-11-06)

Primary citation

Kishida, H.,Unzai, S.,Roper, D.I.,Lloyd, A.,Park, S.-Y.,Tame, J.R.H.
Crystal structure of penicillin binding protein 4 (dacB) from Escherichia coli, both in the native form and covalently linked to various antibiotics
Biochemistry, 45:783-792, 2006

PubMed Abstract: The crystal structure of penicillin binding protein 4 (PBP4) from Escherichia coli, which has both DD-endopeptidase and DD-carboxypeptidase activity, is presented. PBP4 is one of 12 penicillin binding proteins in E. coli involved in the synthesis and maintenance of the cell wall. The model contains a penicillin binding domain similar to known structures, but includes a large insertion which folds into domains with unique folds. The structures of the protein covalently attached to five different antibiotics presented here show the active site residues are unmoved compared to the apoprotein, but nearby surface loops and helices are displaced in some cases. The altered geometry of conserved active site residues compared with those of other PBPs suggests a possible cause for the slow deacylation rate of PBP4.

PubMed: 16411754
DOI: 10.1021/bi051533t

Experimental method

X-RAY DIFFRACTION (1.65 Å)