Crystallographic and Calorimetric Analysis of Peptide Binding to OppA Protein

Sleigh, S.H.; Seavers, P.R.; Wilkinson, Anthony J.; Ladbury, John E.; Tame, J.R.H.

doi:10.1006/jmbi.1999.2929

Cited by 142 publications

(174 citation statements)

References 68 publications

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“…Because NADPH serves as an internal control, whatever effect causes the different behavior associated with DHF binding must lie in either the free ligand, free protein, or in the different mode of binding in the complexes. Clearly interfacial water contributes to binding plasticity in R67 DHFR and can provide hydrogen bonds either alone or in networks between ligand and protein (93)(94)(95)(96)(97). In other words, these osmolyte studies indicate that NADPH and R67 DHFR interact more directly, utilizing more protein contacts (i.e.…”

Section: Discussionmentioning

confidence: 94%

A Balancing Act between Net Uptake of Water during Dihydrofolate Binding and Net Release of Water upon NADPH Binding in R67 Dihydrofolate Reductase

Chopra

Dooling

Horner

et al. 2008

Journal of Biological Chemistry

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R67 dihydrofolate reductase (DHFR) catalyzes the reduction of dihydrofolate (DHF) to tetrahydrofolate using NADPH as a cofactor. This enzyme is a homotetramer possessing 222 symmetry, and a single active site pore traverses the length of the protein. A promiscuous binding surface can accommodate either DHF or NADPH, thus two nonproductive complexes can form (2NADPH or 2DHF) as well as a productive complex (NADPH⅐DHF). The role of water in binding was monitored using a number of different osmolytes. From isothermal titration calorimetry (ITC) studies, binding of NADPH is accompanied by the net release of 38 water molecules. In contrast, from both steady state kinetics and ITC studies, binding of DHF is accompanied by the net uptake of water. Although different osmolytes have similar effects on NADPH binding, variable results are observed when DHF binding is probed. Sensitivity to water activity can also be probed by an in vivo selection using the antibacterial drug, trimethoprim, where the water content of the media is decreased by increasing concentrations of sorbitol. The ability of wild type and mutant clones of R67 DHFR to allow host Escherichia coli to grow in the presence of trimethoprim plus added sorbitol parallels the catalytic efficiency of the DHFR clones, indicating water content strongly correlates with the in vivo function of R67 DHFR.R67 dihydrofolate reductase, a type II DHFR, 2 catalyzes the NADPH-dependent reduction of dihydrofolate (DHF) to tetrahydrofolate. The gene for this enzyme is carried by an R-plasmid, and its presence confers resistance to the antibiotic drug, trimethoprim (TMP). Trimethoprim is a competitive inhibitor of chromosomal DHFR with a picomolar K i (1). Although R67 DHFR is not a good catalyst, it is not inhibited by TMP very well, and thus it allows cell growth in the presence of this antibacterial drug (2, 3). R67 DHFR shares no homology in sequence or structure with chromosomal DHFR and has been proposed to be a good model of a primitive enzyme (4).R67 DHFR is a homotetramer with a single active site pore; the overall structure possesses 222 symmetry as seen in Fig. 1 (5). The symmetry of the active site results in overlapping binding sites for substrate, DHF, and cofactor, NADPH. This can be observed as R67 DHFR binds a total of two ligands as follows: either two NADPH molecules or two folate/DHF molecules or one NADPH plus one folate/DHF molecule (6). The first two complexes are dead-end (binary) complexes, whereas the third is the productive ternary complex. Because of the 222 symmetry, binding to either ligand is unlikely to be optimal.The active site pore of R67 DHFR is unusual in its hourglass shape as well as its large size (2938 Å 3 for apoR67 DHFR with hydrogens added, calculated by CASTp (4, 7)). Because of this large volume, DHF and NADPH cannot occupy all the space in the pore and must use water to mediate some contacts with the protein.How do substrate and cofactor bind to R67 DHFR? From NMR, crystallography, and docking studies, the pteridine ring of DHF/fo...

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Section: Discussionmentioning

confidence: 94%

A Balancing Act between Net Uptake of Water during Dihydrofolate Binding and Net Release of Water upon NADPH Binding in R67 Dihydrofolate Reductase

Chopra

Dooling

Horner

et al. 2008

Journal of Biological Chemistry

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“…The resulting binding sites typically form extensive specific interactions with their cognate ligands, enabling highly specific discrimination between anomeric or epimeric carbohydrates (15), differently sized carbohydrates (15,16), or chemically similar anions (17). By contrast, group II di/oligopeptide-binding proteins (OpBPs), which bind peptides that range from two to nine amino acids (18,19), are semispecific and show little discrimination between side chains of bound peptides (20). In these proteins, recognition is mediated primarily through hydrogen bonds to the peptide main chain atoms, whereas the side chains are placed in nonspecific pockets that accommodate both polar and non-polar amino acid side chains through interactions with differentially ordered water molecules (19 -21).…”

mentioning

confidence: 99%

“…In these proteins, recognition is mediated primarily through hydrogen bonds to the peptide main chain atoms, whereas the side chains are placed in nonspecific pockets that accommodate both polar and non-polar amino acid side chains through interactions with differentially ordered water molecules (19 -21). Any of the 20 amino acids are bound by OpBPs with little sequence-dependent variations in dissociation constants (K d ) (19).…”

mentioning

confidence: 99%

“…X-ray crystallographic structural analysis revealed that only the first two sugar rings are recognized specifically though hydrogen bonds and van der Waals interactions with the protein. Additional rings are placed into a large solvent-filled cavity in the interior of the binding pocket, where there is little specific recognition of the ligand polar and non-polar groups, in a manner similar to the recognition of peptides in the OpBP fold (19). Comparison of superimposed apo-1VR5 with ligand-bound tmCBP suggests that the former possesses similar adaptations to bind its cognate ligand(s).…”

mentioning

confidence: 99%

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Structural Analysis of Semi-specific Oligosaccharide Recognition by a Cellulose-binding Protein of Thermotoga maritima Reveals Adaptations for Functional Diversification of the Oligopeptide Periplasmic Binding Protein Fold

Cuneo

Beese

Hellinga

2009

Journal of Biological Chemistry

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Periplasmic binding proteins (PBPs) constitute a protein superfamily that binds a wide variety of ligands. In prokaryotes, PBPs function as receptors for ATP-binding cassette or tripartite ATP-independent transporters and chemotaxis systems. In many instances, PBPs bind their cognate ligands with exquisite specificity, distinguishing, for example, between sugar epimers or structurally similar anions. By contrast, oligopeptide-binding proteins bind their ligands through interactions with the peptide backbone but do not distinguish between different side chains. The extremophile Thermotoga maritima possesses a remarkable array of carbohydrate-processing metabolic systems, including the hydrolysis of cellulosic polymers. Here, we present the crystal structure of a T. maritima cellobiose-binding protein (tm0031) that is homologous to oligopeptide-binding proteins. T. maritima cellobiose-binding protein binds a variety of lengths of ␤(134)-linked glucose oligomers, ranging from two rings (cellobiose) to five (cellopentaose). The structure reveals that binding is semi-specific. The disaccharide at the nonreducing end binds specifically; the other rings are located in a large solvent-filled groove, where the reducing end makes several contacts with the protein, thereby imposing an upper limit of the oligosaccharides that are recognized. Semi-specific recognition, in which a molecular class rather than individual species is selected, provides an efficient solution for the uptake of complex mixtures.

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“…The water molecules act as flexible adapters, matching the hydrogen-bonding requirements of the protein and the ligand, and shielding charges on the buried ligand. The hydrogen bonds and salt bridges formed by the peptide backbone alone can drive binding and there is only a small contribution of the amino acid side chains to the binding affinity [51]. Although this binding mechanism is also observed for the dipeptide binding protein, DppA, of Escherichia coli, recent studies with OppA protein of L. lactis indicate that oligopeptide binding to this receptor is more complicated than suggested by the crystallographic studies.…”

Section: Introductionmentioning

confidence: 86%

Peptides and ATP binding cassette peptide transporters

Detmers

Lanfermeijer

Poolman

2001

Research in Microbiology

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-In this review our knowledge of ATP binding cassette (ABC) transporters specific for peptides is discussed. Besides serving a role in nutrition of the cell, the systems participate in various signaling processes that allow (micro)organisms to monitor the local environment. In bacteria, these include regulation of gene expression, competence development, sporulation, DNA transfer by conjugation, chemotaxis, and virulence development, and the role of ABC transporters in each of these processes is discussed. Particular attention is paid to the specificity determinants of peptide receptors and transporters in relation to their structure and to the mechanisms of peptide binding.

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Crystallographic and Calorimetric Analysis of Peptide Binding to OppA Protein

Cited by 142 publications

References 68 publications

A Balancing Act between Net Uptake of Water during Dihydrofolate Binding and Net Release of Water upon NADPH Binding in R67 Dihydrofolate Reductase

A Balancing Act between Net Uptake of Water during Dihydrofolate Binding and Net Release of Water upon NADPH Binding in R67 Dihydrofolate Reductase

Structural Analysis of Semi-specific Oligosaccharide Recognition by a Cellulose-binding Protein of Thermotoga maritima Reveals Adaptations for Functional Diversification of the Oligopeptide Periplasmic Binding Protein Fold

Peptides and ATP binding cassette peptide transporters

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