Protein Recognition of Adenylate: An Example of a Fuzzy Recognition Template

Moodie, Stuart; Mitchell, John B. O.; Thornton, Janet M.

doi:10.1006/jmbi.1996.0591

Cited by 125 publications

(106 citation statements)

References 28 publications

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“…lb, double-underlined), is interrupted by a nonapeptide present only in the AprA sequences. In accordance with the observations of Moodie et al (1996) , this nonapeptide contains strictly conserved glycine, arginine, tryptophan and tyrosine residues (residues 212-220). It is, therefore, tempting to assume that both this nonapeptide and the strictly conserved undecapeptide mentioned above are involved in APS binding.…”

Section: Aps Reductases Speich Et Al (1994) Found a Highsupporting

confidence: 85%

“…Due to its agreement with the 'core' fingerprint for ADP-binding folds (Wierenga et al, 1986) (Lys-263), however, does not favour an ADP-binding fold (Wierenga et al, 1986) and none of the programs used in this study predicted a suitable secondary structure. Recently, Moodie et al (1996) stated that adenylate binding can be achieved by a large number of alternative arrangements. Adenylate-binding regions showed high frequencies of arginine, tyrosine and glycine, whereas glutamate rarely occurred.…”

Section: Aps Reductases Speich Et Al (1994) Found a Highmentioning

confidence: 99%

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Towards the phylogeny of APS reductases and sirohaem sulfite reductases in sulfate-reducing and sulfur-oxidizing prokaryotes

et al. 1997

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The genes for adenosine-5'-phosphosulfate (APS) reductase, aprBA, and sirohaem sulf ite reductase, dsrAB, from the sulfur-oxidizing phototrophic bacterium Chmmatium winosum strain D (DSMZ 1803 were cloned and sequenced. Statistically significant sequence similarities and similar physicochemical properties suggest that the aprBA and dsrAB gene products from Chr. winosum are true homologues of their counterparts from the sulfatereducing chemotrophic archaeon Amhaeoglobus filgidus and the sulfatereducing chemotrophic bacterium Desulfowibrio wlgaris. Evidence for the proposed duplication of a common ancestor of the dsrAB genes is provided. Phylogenetic analyses revealed a greater evolutionary distance between the enzymes from Chr. winosum and D. vulgaris than between those from A. fulgidus and D. wlgaris. The data reported in this study are most consistent with the concept of common ancestral protogenotic genes both for dissimilatory sirohaem sulfite reductases and for APS reductases. The aprA gene was demonstrated to be a suitable DNA probe for the identification of apr genes from organisms of different phylogenetic positions. PCR primers and conditions for the amplification of apr homologous regions are described.

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Section: Aps Reductases Speich Et Al (1994) Found a Highsupporting

confidence: 85%

Section: Aps Reductases Speich Et Al (1994) Found a Highmentioning

confidence: 99%

Towards the phylogeny of APS reductases and sirohaem sulfite reductases in sulfate-reducing and sulfur-oxidizing prokaryotes

et al. 1997

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“…The affinity grids demonstrate that this pocket is a satisfactory position for an aromatic amine in the nonionized state. This feature has been observed in other proteins bound to adenine-containing ligands (24). Although the adenine does form hydrogen bonds in some of the structures studied here, there is no consistent or conserved pattern.…”

Section: Discussionsupporting

confidence: 47%

“…In some of the structures, the adenine forms hydrogen bonds with protein residues and in others it does not; there is no consistent pattern. The affinity grid method showed that the adenine ring is always involved in hydrophobic interactions as has been observed previously in analyses of structures containing adenine cofactors or ligands (24). Analysis of the structures allowed us to identify the nature of the interactions.…”

Section: Methodsmentioning

confidence: 76%

The cAMP binding domain: An ancient signaling module

Berman

Eyck

Goodsell

et al. 2004

Proc. Natl. Acad. Sci. U.S.A.

195

213

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cAMP-binding domains from several different proteins were analyzed to determine the properties and interactions of this recognition motif. Systematic computational analyses, including structure-based sequence comparison, surface matching, affinity grid analysis, and analyses of the ligand protein interactions were carried out. These analyses show distinctive roles of the sugar phosphate and the adenine in the cAMP-binding module. We propose that the cAMPbinding regulatory proteins function by providing an allosteric system in which the presence or absence of cAMP produces a substantial structural change through the loss of hydrophobic interactions with the adenine ring and consequent repositioning of the C helix. The modified positioning of the helix in turn is recognized by a proteinbinding event, completing the allostery.allostery ͉ conserved cyclic nucleotide-binding motif C yclic AMP (cAMP) (Fig. 1a) is an ancient signaling molecule that serves as an indicator of stress from the most primitive bacteria to humans. The module that binds cAMP and translates the signal into a biological response, the cyclic nucleotidebinding (CNB) domain, is also ancient. Although the best-known bacterial CNB domain is associated with the catabolite activator protein (CAP), is linked to a DNA binding domain, and mediates gene transcription in the absence of glucose, the elucidation of many bacterial genomes indicates that this module is much more diverse. There are literally hundreds of proteins that are linked to CNB domains, and these proteins mediate many types of stress responses (1).The CNB domain is a small module, typically Ϸ120 aa, comprised of both ␤ strands and helical elements. The general organization of secondary structure of the essential cAMPbinding site is an eight-stranded ␤ barrel that functions as a basket. The cyclic nucleotide phosphate lies at the base of the ␤ barrel where it is well shielded from solvent and protected from phosphodiesterases (2). The most conserved feature of the ␤ barrel is the phosphate binding cassette (PBC) comprised of ␤ strand 6, a short turn of helix, and ␤ strand 7. A conserved feature of this PBC is a buried arginine that binds to the exocyclic phosphate of cAMP and a glutamate that binds the ribose 2Ј-OH. In addition to the ␤ barrel, the CNB module has a helical subdomain. The A helix precedes the ␤ barrel and is in an antiparallel manner with the B helix that immediately follows ␤ strand 8. The most variable feature of the domain is the C helix ( Fig. 1 b and c).The structure of the CNB domain was first revealed when the structure of CAP was determined (3). Based on sequence similarities, it was predicted that the fold would be conserved in the CNB domains associated with mammalian protein kinases (4), protein kinase A (PKA) and cGMP-dependent protein kinase (5). This prediction was confirmed when the structure of a deletion mutant of the RI␣ subunit of PKA was determined (6). RI␣ has two tandem CNB domains, each with a fold that resembles the CNB domain of CAP. The subsequent ...

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“…Therefore, we employ a function for determining propensities that considers H-bond numbers, number of amino acids on the surface, nucleotide numbers and explosion values. The propensity function is based on that reported by Moodie et al (1996), but we modified their function to determine the interaction propensities of amino acids and nucleotides pair on the surface of a complex. Amino acids are considered to be on the surface if their relative accessibility exceeds 5% according to the NACCESS program (Hubbard and Thornton 1993).…”

Section: Binding Propensitymentioning

confidence: 99%

Mining Molecular Structure Data for the Patterns of Interactions Between Protein and RNA

Han

Nepal

2007

Computational Science – ICCS 2007

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Abstract. Mining useful information from a large amount of biological data is becoming important, but most data mining research in bioinformatics is limited to molecular sequence data. We have developed a set of algorithms for analyzing hydrogen bond and van der Waals interactions between protein and RNA. Analysis of the most representative set of protein-RNA complexes revealed several interesting observations: (1) in both hydrogen bond and van der Waals interactions, arginine has the highest interaction propensity, whereas cytosine has the lowest interaction propensity; (2) side chain contacts are more frequent than main chain contacts in amino acids, whereas backbone contacts are more frequent than base contacts in nucleotides; (3) amino acids, in which side chain contacts are dominant, reveal more diverse interaction propensities than nucleotides; and (4) valine rarely binds to any nucleotide. The interaction patterns found in this study should prove useful for determining binding sites in protein-RNA complexes.

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Protein Recognition of Adenylate: An Example of a Fuzzy Recognition Template

Cited by 125 publications

References 28 publications

Towards the phylogeny of APS reductases and sirohaem sulfite reductases in sulfate-reducing and sulfur-oxidizing prokaryotes

Towards the phylogeny of APS reductases and sirohaem sulfite reductases in sulfate-reducing and sulfur-oxidizing prokaryotes

The cAMP binding domain: An ancient signaling module

Mining Molecular Structure Data for the Patterns of Interactions Between Protein and RNA

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