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1z6f

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{{STRUCTURE_1z6f| PDB=1z6f | SCENE= }}
{{STRUCTURE_1z6f| PDB=1z6f | SCENE= }}
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'''Crystal structure of penicillin-binding protein 5 from E. coli in complex with a boronic acid inhibitor'''
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===Crystal structure of penicillin-binding protein 5 from E. coli in complex with a boronic acid inhibitor===
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==Overview==
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Penicillin-binding protein 5 (PBP 5) from Escherichia coli is a well-characterized d-alanine carboxypeptidase that serves as a prototypical enzyme to elucidate the structure, function, and catalytic mechanism of PBPs. A comprehensive understanding of the catalytic mechanism underlying d-alanine carboxypeptidation and antibiotic binding has proven elusive. In this study, we report the crystal structure at 1.6 A resolution of PBP 5 in complex with a substrate-like peptide boronic acid, which was designed to resemble the transition-state intermediate during the deacylation step of the enzyme-catalyzed reaction with peptide substrates. In the structure of the complex, the boron atom is covalently attached to Ser-44, which in turn is within hydrogen-bonding distance to Lys-47. This arrangement further supports the assignment of Lys-47 as the general base that activates Ser-44 during acylation. One of the two hydroxyls in the boronyl center (O2) is held by the oxyanion hole comprising the amides of Ser-44 and His-216, while the other hydroxyl (O3), which is analogous to the nucleophilic water for hydrolysis of the acyl-enzyme intermediate, is solvated by a water molecule that bridges to Ser-110. Lys-47 is not well-positioned to act as the catalytic base in the deacylation reaction. Instead, these data suggest a mechanism of catalysis for deacylation that uses a hydrogen-bonding network, involving Lys-213, Ser-110, and a bridging water molecule, to polarize the hydrolytic water molecule.
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(as it appears on PubMed at http://www.pubmed.gov), where 15938610 is the PubMed ID number.
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{{ABSTRACT_PUBMED_15938610}}
==About this Structure==
==About this Structure==
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[[Category: Penicillin-binding protein]]
[[Category: Penicillin-binding protein]]
[[Category: Peptidoglycan synthesis]]
[[Category: Peptidoglycan synthesis]]
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''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Tue Jul 29 05:38:08 2008''

Revision as of 02:38, 29 July 2008

Image:1z6f.png

Template:STRUCTURE 1z6f

Crystal structure of penicillin-binding protein 5 from E. coli in complex with a boronic acid inhibitor

Template:ABSTRACT PUBMED 15938610

About this Structure

1Z6F is a Single protein structure of sequence from Escherichia coli. Full crystallographic information is available from OCA.

Reference

Crystal structure of Escherichia coli penicillin-binding protein 5 bound to a tripeptide boronic acid inhibitor: a role for Ser-110 in deacylation., Nicola G, Peddi S, Stefanova M, Nicholas RA, Gutheil WG, Davies C, Biochemistry. 2005 Jun 14;44(23):8207-17. PMID:15938610

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