Experimental Data Snapshot
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(2000) J Mol Biology 299: 501
Penicillin-binding proteins (PBPs), the primary targets for beta-lactam antibiotics, are periplasmic membrane-attached proteins responsible for the construction and maintenance of the bacterial cell wall. Bacteria have developed several mechanisms of resistance, one of which is the mutation of the target enzymes to reduce their affinity for beta-lactam antibiotics. Here, we describe the structure of PBP2x from Streptococcus pneumoniae determined to 2.4 A. In addition, we also describe the PBP2x structure in complex with cefuroxime, a therapeutically relevant antibiotic, at 2.8 A. Surprisingly, two antibiotic molecules are observed: one as a covalent complex with the active-site serine residue, and a second one between the C-terminal and the transpeptidase domains. The structure of PBP2x reveals an active site similar to those of the class A beta-lactamases, albeit with an absence of unambiguous deacylation machinery. The structure highlights a few amino acid residues, namely Thr338, Thr550 and Gln552, which are directly related to the resistance phenomenon.
Laboratoire de Cristallographie Macromoléculaire, Institut de Biologie Structurale Jean-Pierre Ebel (CNRS-CEA), 41, rue Jules Horowitz, Grenoble, Cedex 1, 38027, France.
Explore in 3D: Structure |Sequence Annotations |Electron Density |Validation Report |Ligand Interaction (KEF)
Biological assembly 1 generated by PISA (software)
Macromolecule Content
Entity ID: 1 | |||||
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Molecule | Chains | Sequence Length | Organism | Details | Image |
PENICILLIN-BINDING PROTEIN 2X | 702 | Streptococcus pneumoniae | Mutation(s): 0 Gene Names: PBP2X | ![]() | |
UniProt | |||||
Find proteins for P14677 (Streptococcus pneumoniae serotype 4 (strain ATCC BAA-334 / TIGR4)) Explore P14677 Go to UniProtKB: P14677 | |||||
Entity Groups | |||||
Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
UniProt Group | P14677 | ||||
Sequence AnnotationsExpand | |||||
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Ligands 2 Unique | |||||
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ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
KEF Query on KEF Download Ideal Coordinates CCD File | C [auth A] | CEFUROXIME (OCT-3-ENE FORM) C16 H16 N4 O8 S AIEMBSSBMKFDGU-HPUGUEDKSA-N | |||
CES Query on CES Download Ideal Coordinates CCD File | B [auth A] | 2-[CARBOXY-(2-FURAN-2-YL-2-METHOXYIMINO-ACETYLAMINO)-METHYL]-5-METHYL-3,6-DIHYDRO-2H-[1,3]THIAZINE-4-CARBOXYLIC ACID C15 H17 N3 O7 S XTOFBDKWRLNHGR-LHLQUDMSSA-N |
Length ( Å ) | Angle ( ˚ ) |
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a = 129.91 | α = 90 |
b = 129.91 | β = 90 |
c = 139.86 | γ = 90 |
Software Name | Purpose |
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CNS | refinement |
DENZO | data reduction |
SCALA | data scaling |
CNS | phasing |
RCSB PDB Core Operations are funded by theU.S. National Science Foundation (DBI-2321666), theUS Department of Energy (DE-SC0019749), and theNational Cancer Institute,National Institute of Allergy and Infectious Diseases, andNational Institute of General Medical Sciences of theNational Institutes of Health under grant R01GM157729.