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, 30 (1), 281-3

CDD: A Database of Conserved Domain Alignments With Links to Domain Three-Dimensional Structure

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CDD: A Database of Conserved Domain Alignments With Links to Domain Three-Dimensional Structure

Aron Marchler-Bauer et al. Nucleic Acids Res.

Abstract

The Conserved Domain Database (CDD) is a compilation of multiple sequence alignments representing protein domains conserved in molecular evolution. It has been populated with alignment data from the public collections Pfam and SMART, as well as with contributions from colleagues at NCBI. The current version of CDD (v.1.54) contains 3693 such models. CDD alignments are linked to protein sequence and structure data in Entrez. The molecular structure viewer Cn3D serves as a tool to interactively visualize alignments and three-dimensional structure, and to link three-dimensional residue coordinates to descriptions of evolutionary conservation. CDD can be accessed on the World Wide Web at http://www.ncbi.nlm.nih.gov/Structure/cdd/cdd.shtml. Protein query sequences may be compared against databases of position-specific score matrices derived from alignments in CDD, using a service named CD-Search, which can be found at http://www.ncbi.nlm.nih.gov/Structure/cdd/wrpsb.cgi. CD-Search runs reverse-position-specific BLAST (RPS-BLAST), a variant of the widely used PSI-BLAST algorithm. CD-Search is run by default for protein-protein queries submitted to NCBI's BLAST service at http://www.ncbi.nlm.nih.gov/BLAST.

Figures

Figure 1
Figure 1
Cn3D 3.0 view showing a subset of aligned sequences from the CD sm (ATPase domain of DNA mismatch repair MUTS family). Residues corresponding to the P-loop motif around the ADP/Mg2+ binding site have been annotated in Cn3D and are highlighted in green: GLY614-x(4)-GLY619-LYS620-SER621 in 1E3M chain A (12). The ADP/Mg2+ complex is colored magenta. In the related human MSH2 protein, a somatic GLY→SER mutation in the position corresponding to GLY619 (highlighted in yellow) has been associated with type 1 familial non-polyposis colon cancer. From analyzing the image one may understand how a substitution of the side chain at this position interferes with ADP/Mg2+ binding and may therefore impede the DNA mismatch repair system.

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