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1z6f
From Proteopedia
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| - | [[Image:1z6f.gif|left|200px]] | + | [[Image:1z6f.gif|left|200px]] |
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| - | '''Crystal structure of penicillin-binding protein 5 from E. coli in complex with a boronic acid inhibitor''' | + | {{Structure |
| + | |PDB= 1z6f |SIZE=350|CAPTION= <scene name='initialview01'>1z6f</scene>, resolution 1.60Å | ||
| + | |SITE= | ||
| + | |LIGAND= <scene name='pdbligand=BO9:N1-[(1R)-1-(DIHYDROXYBORYL)ETHYL]-N2-[(TERT-BUTOXYCARBONYL)-D-GAMMA-GLUTAMYL]-N6-[(BENZYLOXY)CARBONYL-L-LYSINAMIDE'>BO9</scene> and <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene> | ||
| + | |ACTIVITY= [http://en.wikipedia.org/wiki/Serine-type_D-Ala-D-Ala_carboxypeptidase Serine-type D-Ala-D-Ala carboxypeptidase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.4.16.4 3.4.16.4] | ||
| + | |GENE= dacA, pfv ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=562 Escherichia coli]) | ||
| + | }} | ||
| + | |||
| + | '''Crystal structure of penicillin-binding protein 5 from E. coli in complex with a boronic acid inhibitor''' | ||
| + | |||
==Overview== | ==Overview== | ||
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==About this Structure== | ==About this Structure== | ||
| - | 1Z6F is a [ | + | 1Z6F is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1Z6F OCA]. |
==Reference== | ==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:[http:// | + | 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:[http://www.ncbi.nlm.nih.gov/pubmed/15938610 15938610] |
[[Category: Escherichia coli]] | [[Category: Escherichia coli]] | ||
[[Category: Serine-type D-Ala-D-Ala carboxypeptidase]] | [[Category: Serine-type D-Ala-D-Ala carboxypeptidase]] | ||
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[[Category: peptidoglycan synthesis]] | [[Category: peptidoglycan synthesis]] | ||
| - | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu | + | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Mar 20 15:31:41 2008'' |
Revision as of 13:31, 20 March 2008
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| , resolution 1.60Å | |||||||
|---|---|---|---|---|---|---|---|
| Ligands: | and | ||||||
| Gene: | dacA, pfv (Escherichia coli) | ||||||
| Activity: | Serine-type D-Ala-D-Ala carboxypeptidase, with EC number 3.4.16.4 | ||||||
| Coordinates: | save as pdb, mmCIF, xml | ||||||
Crystal structure of penicillin-binding protein 5 from E. coli in complex with a boronic acid inhibitor
Overview
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.
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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