The ConSurf Server identifies regions of a protein conserved over a wide phylogenetic range very quickly and easily. However, it allows limited control over the selection of sequences used in the alignment.
Protein Explorer's MSA3D requires that you bring an alignment to it, from which it will color the protein to show regions of conservation. Selecting the sequences to be aligned for MSA3D requires more effort, but has the advantage that you have full control over the sequences used in the alignment and for coloring the protein. Thus, with MSA3D you could limit the phylogenetic range represented, or visualize the locations of mutations in a protein from a single species.
To generate the images below in rotatable form (and to see the alignments), simply go to ConSurf and enter the PDB ID code, or go to Protein Explorer's MSA3D and use the built-in demonstrations.
Translational repressors of the PUF family bind to the 3' untranslated region of mRNA. 1IB2 is a crystal structure for a human pumilio-homology domain, a member of the PUF family. It is shaped like a half donut, and the concave face is believed to bind to mRNA. David S. Bernstein (Univ. Wisconsin), whose graduate work concerns PUF proteins, manually selected seven sequences to represent phylogenetic diversity, including human, Xenopus, Drosophila, C. elegans, yeast (2), and Dictyostelium. The resulting alignment was installed as a ready-made demonstration in the MSA3D component of Protein Explorer (PE). MSA3D uses the alignment to color the PUF protein to show regions of conservation (dark green in left image).
In the image at right, conserved regions (dark purple) were identified automatically by the ConSurf Server. Only the human PDB ID code (1IB2) had to be specified. Using its default settings, ConSurf aligned ten sequences, including human (2), Drosophila (2), C. elegans, and yeast (6),
Yeast enolase (4ENL) was aligned with 4 other enolases from Drosophila, human, eubacteria (2) and archebacteria (2) by Garry Duncan (Nebraska Wesleyan College). This, too, is installed as a built-in demonstration in PE's MSA3D, which produced the image at left (dark green residues are conserved, and cluster in the catalytic site).
ConSurf's result for 4ENL is at right (dark purple residues are conserved, and cluster in the catalytic site). At default settings, ConSurf aligned 84 sequences with 4ENL.