Biomaterial Database

Sequence comparison of single-stranded DNA binding proteins and its structural implications. 1987

B V Prasad, and W Chiu

The primary sequences were compared among several proteins: gene product 5 protein (GP5) from phage M13; PIKE from phage Ike; gene product 32 protein (GP32) from phage T4; RecA, SSB and SSF from Escherichia coli. These proteins bind strongly and cooperatively to single-stranded DNA with no sequence specificity. GP5 is the smallest in this group and its three-dimensional structure is well-characterized. Using the entire sequence of GP5 as a template we searched for the regions in other single-stranded DNA binding proteins yielding the best alignment of aromatic and basic residues. The identified domains show alignment of five aromatic and four charged residues in these proteins. The domains in PIKE, GP32 and RecA exhibit statistically significant sequence homology with GP5. These observations strongly favor the hypothesis that the protein-single-stranded DNA complex in this class of proteins is stabilized by the stacking interaction of the aromatic residues with the bases of the DNA, and by the electrostatic interaction of the basic residues with the phosphate groups of the DNA. We also find that the DNA binding domains of these proteins have similar secondary structural preferences, mainly beta structures. The triple-stranded beta-sheet may be a common motif in the DNA binding domains of these proteins.

UI	MeSH Term	Description	Entries
D004268	DNA-Binding Proteins	Proteins which bind to DNA. The family includes proteins which bind to both double- and single-stranded DNA and also includes specific DNA binding proteins in serum which can be used as markers for malignant diseases.	DNA Helix Destabilizing Proteins,DNA-Binding Protein,Single-Stranded DNA Binding Proteins,DNA Binding Protein,DNA Single-Stranded Binding Protein,SS DNA BP,Single-Stranded DNA-Binding Protein,Binding Protein, DNA,DNA Binding Proteins,DNA Single Stranded Binding Protein,DNA-Binding Protein, Single-Stranded,Protein, DNA-Binding,Single Stranded DNA Binding Protein,Single Stranded DNA Binding Proteins
D004926	Escherichia coli	A species of gram-negative, facultatively anaerobic, rod-shaped bacteria (GRAM-NEGATIVE FACULTATIVELY ANAEROBIC RODS) commonly found in the lower part of the intestine of warm-blooded animals. It is usually nonpathogenic, but some strains are known to produce DIARRHEA and pyogenic infections. Pathogenic strains (virotypes) are classified by their specific pathogenic mechanisms such as toxins (ENTEROTOXIGENIC ESCHERICHIA COLI), etc.	Alkalescens-Dispar Group,Bacillus coli,Bacterium coli,Bacterium coli commune,Diffusely Adherent Escherichia coli,E coli,EAggEC,Enteroaggregative Escherichia coli,Enterococcus coli,Diffusely Adherent E. coli,Enteroaggregative E. coli,Enteroinvasive E. coli,Enteroinvasive Escherichia coli
D000595	Amino Acid Sequence	The order of amino acids as they occur in a polypeptide chain. This is referred to as the primary structure of proteins. It is of fundamental importance in determining PROTEIN CONFORMATION.	Protein Structure, Primary,Amino Acid Sequences,Sequence, Amino Acid,Sequences, Amino Acid,Primary Protein Structure,Primary Protein Structures,Protein Structures, Primary,Structure, Primary Protein,Structures, Primary Protein
D012984	Software	Sequential operating programs and data which instruct the functioning of a digital computer.	Computer Programs,Computer Software,Open Source Software,Software Engineering,Software Tools,Computer Applications Software,Computer Programs and Programming,Computer Software Applications,Application, Computer Software,Applications Software, Computer,Applications Softwares, Computer,Applications, Computer Software,Computer Applications Softwares,Computer Program,Computer Software Application,Engineering, Software,Open Source Softwares,Program, Computer,Programs, Computer,Software Application, Computer,Software Applications, Computer,Software Tool,Software, Computer,Software, Computer Applications,Software, Open Source,Softwares, Computer Applications,Softwares, Open Source,Source Software, Open,Source Softwares, Open,Tool, Software,Tools, Software