Primary Citation PubMed: 8841119
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AlignHUSH: alignment of HMMs using structure and hydrophobicity information.
(2011) BMC Bioinformatics 12
PubMed: 21729312 | PubMedCentral: PMC3228556 | DOI: 10.1186/1471-2105-12-275
The nucleotide binding residues in 1miv (Asp40 and Asp42) are seen to be aligned with the nucleotide binding residues of 7icq (Asp190 and Asp192).
For example, two proteins with PDB codes 1miv (tRNA CCA-adding enzyme, head domain) and 7icq (DNA polymerase beta-like), are both classified into the nucleotidyltransferase superfamily but their active sites are not exactly superposable (see Figure 4a ).
The Aspartate residues that bind to Mg 2+ ion are conserved in the two proteins shown in Figure 4a , but the catalytic Arginine residue in 1miv is not conserved in the 7icq protein.
a) The structural alignment between two proteins in the SCOP superfamily of Nucleotidyltransferase, 1miv (shown in blue) and 7icq (shown in green).
The active site residues in 1miv are shown in red, and the active site residues of 7icq are shown in blue, both in the stick format.
Publication Year: 2011
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