3ZVW

Unexpected tricovalent binding mode of boronic acids within the active site of a penicillin binding protein

Replaces:  2Y5O

Summary for 3ZVW

• Entry DOI: 10.2210/pdb3zvw/pdb
• Related: 1W79 1W8Q 1W8Y 2VGJ 2VGK 2WKE 2XDM 2XK1 2XLN 2Y4A 2Y55 2Y59 3ZVT
• Descriptor: D-ALANYL-D-ALANINE CARBOXYPEPTIDASE, SULFATE ION, MAGNESIUM ION, ... (8 entities in total)
• Functional Keywords: hydrolase, peptidoglycan, penicillin-binding, tetravalent boron
• Biological source: ACTINOMADURA SP. R39
• Cellular location: Secreted: P39045
• Total number of polymer chains: 4
• Total formula weight: 193559.18

Authors

Sauvage, E.,Zervosen, A.,Herman, R.,Kerff, F.,Rocaboy, M.,Charlier, P. (deposition date: 2011-07-28, release date: 2012-02-29, Last modification date: 2023-12-20)

Primary citation

Zervosen, A.,Herman, R.,Kerff, F.,Herman, A.,Bouillez, A.,Prati, F.,Pratt, R.F.,Frere, J.M.,Joris, B.,Luxen, A.,Charlier, P.,Sauvage, E.
Unexpected Tricovalent Binding Mode of Boronic Acids within the Active Site of a Penicillin- Binding Protein.
J.Am.Chem.Soc., 133:10839-, 2011

PubMed Abstract: Boronic acids bearing appropriate side chains are good inhibitors of serine amidohydrolases. The boron usually adopts a tetrahedral conformation, bound to the nucleophilic serine of the active site and mimicking the transition state of the enzymatic reaction. We have solved the structures of complexes of a penicillin-binding protein, the DD-peptidase from Actinomadura sp. R39, with four amidomethylboronic acids (2,6-dimethoxybenzamidomethylboronic acid, phenylacetamidomethylboronic acid, 2-chlorobenzamidomethylboronic acid, and 2-nitrobenzamidomethylboronic acid) and the pinacol ester derived from phenylacetamidomethylboronic acid. We found that, in each case, the boron forms a tricovalent adduct with Oγ of Ser49, Ser298, and the terminal amine group of Lys410, three key residues involved in the catalytic mechanism of penicillin-binding proteins. This represents the first tricovalent enzyme-inhibitor adducts observed by crystallography. In two of the five R39-boronate structures, the boronic acid is found as a tricovalent adduct in two monomers of the asymmetric unit and as a monocovalent adduct with the active serine in the two remaining monomers of the asymmetric unit. Formation of the tricovalent complex from a classical monocovalent complex may involve rotation around the Ser49 Cα-Cβ bond to place the boron in a position to interact with Ser298 and Lys410, and a twisting of the side-chain amide such that its carbonyl oxygen is able to hydrogen bond to the oxyanion hole NH of Thr413. Biphasic kinetics were observed in three of the five cases, and details of the reaction between R39 and 2,6-dimethoxybenzamidomethylboronic acid were studied. Observation of biphasic kinetics was not, however, thought to be correlated to formation of tricovalent complexes, assuming that the latter do form in solution. On the basis of the crystallographic and kinetic results, a reaction scheme for this unexpected inhibition by boronic acids is proposed.

PubMed: 21574608
DOI: 10.1021/JA200696Y

Experimental method

X-RAY DIFFRACTION (2 Å)