BindingDB, www.bindingdb.org, is a publicly accessible database of experimental protein-small molecule interaction data. Its collection of over a million data entries derives primarily from scientific articles and, increasingly, US patents. BindingDB provides many ways to browse and search for data of interest, including an advanced search tool, which can cross searches of multiple query types, including text, chemical structure, protein sequence and numerical affinities. The PDB and PubMed provide links to data in BindingDB, and vice versa; and BindingDB provides links to pathway information, the ZINC catalog of available compounds, and other resources. The BindingDB website offers specialized tools that take advantage of its large data collection, including ones to generate hypotheses for the protein targets bound by a bioactive compound, and for the compounds bound by a new protein of known sequence; and virtual compound screening by maximal chemical similarity, binary kernel discrimination, and support vector machine methods. Specialized data sets are also available, such as binding data for hundreds of congeneric series of ligands, drawn from BindingDB and organized for use in validating drug design methods. BindingDB offers several forms of programmatic access, and comes with extensive background material and documentation. Here, we provide the first update of BindingDB since 2007, focusing on new and unique features and highlighting directions of importance to the field as a whole.
1 Cross-linking of the peptide chains confers rigidity to the peptidoglycan and viability to the bacterial cell. The related carboxypeptidases, which hydrolyze the C-terminal D-Ala moiety from the peptide chain, may modulate the degree of cross-linking.In E. coli at least 10 PBPs have been identified. These enzymes fall into two categories: the high molecular mass PBPs, which are essential for cell viability and catalyze transpeptidase and sometimes transglycosylase activity, and the low molecular mass PBPs, which are non-essential and catalyze D,D-carboxypeptidase (CPase) and sometimes D,D-endopeptidase activity (1). Regardless of the type of PBP, all of these enzymes react with peptide substrates and -lactam antibiotics by a similar mechanism. The initial step in the reaction of PBPs with their peptide substrates is a nucleophilic attack of the D-Ala-D-Ala peptide bond by a conserved serine residue, leading to acylation of the serine hydroxyl side chain and the concomitant release of the C-terminal D-Ala. In the subsequent deacylation step, the acyl-enzyme complex can react with either an amino group (from m-DAP) of another peptide to form a cross-link (transpeptidation) or it can react with water to release the peptide (carboxypeptidation). Penicillin and other -lactam antibiotics inactivate these enzymes by mimicking the structure of the D-Ala-D-Ala C terminus of the peptide chain (2, 3) and reacting with the same serine nucleophile to form an analogous acyl-enzyme complex (4). Unlike the complex formed with peptide substrates, however, the -lactam-PBP complex is long-lived and renders the enzyme inactive.PBPs and other penicillin-interacting enzymes (e.g. class A -lactamases) are characterized by a set of conserved motifs that are clustered in their respective active sites (5). These motifs include the Ser-X-X-Lys (SXXK) tetrad that contains the serine nucleophile, the Ser-X-Asn (SXN) triad, and the LysThr(Ser)-Gly (KTG) triad. In all serine-based PBPs and -lactamases of known structure, these motifs adopt a strikingly similar conformation to the extent that the active site of one PBP or -lactamase can look very much like another. In addition to these three motifs, class A -lactamases have a fourth motif, Glu-X-X-X-Asn, present on the so-called ⍀ loop, that is responsible for the extremely high rates of deacylation of the * This work was supported by National Institutes of Health Grants AI36901 (to R. A. N.) and GM66861 (to C. D.). The costs of publication of this article were defrayed in part by the payment of page charges. This article must therefore be hereby marked "advertisement" in accordance with 18 U.S.C. Section 1734 solely to indicate this fact.§ To whom correspondence may be addressed: Dept.
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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