Link to this post | posted 21 Feb, 2024 15:31

brueschhoff

Greetings, We are investigating the function of a protein with sequence: MEYMPADLARTLSAMARGTHNEICGFILDDWTLISVRNVAKLPTISFEMSMNAILGAVEMAAASGREILGTYHSHPGGSTEPSETDLHGWPRFIDGSYARYWVVTGDTVREFERTGEGSEIGFQLIHSIGIGVVVKRPEEGMDQSVPEDZ It belongs to a pham that indicates it is a metalloprotease. BLAST Hits indicate either a tail protein or a metalloprotease. If we look at HHPRED, many hits come as a metalloprotease, but without the HEXXH motif. Rather it has a JAMM/MPN Zinc Binding domain. Should we annotate this as a metalloprotease, even without the HEXXH motif? Thank you for your assistance! Beth Rueschhoff Indiana University Southeast Edited 21 Feb, 2024 15:32

Link to this post | posted 21 Feb, 2024 18:20
debbie	Hi Beth, What phage are you annotating? Could you provide the phamerator gene number and its stop codon. Thanks, debbie

Link to this post | posted 22 Feb, 2024 15:59
brueschhoff	Sure, Sorry about that! We are annotating DoobyDoo and the phamerator feature number is 10. The stop codon is 8910.

Link to this post | posted 22 Feb, 2024 21:31

cdshaffer

When I use that sequence in an HHPRED search I get an alignment to roughly the 1st half of crystal 5LD9 the JAMM/MPN(+) Protease ( amino acids 10 - 90). On the PDB page for the crystal it looks like the crystal has the same amino acid coordinates as does the native protein, so I can use those ~10 - 90 coordinates where I look at the literature on this protein. According to this paper the active site residues of the JAMM protease motif are (ExnH xHx7Sx2D ). This motif has a nice match in the phage protein, (the HxH are at 73 and 75, the S and D are also there at the correct distance ) so I think this phage protein is also, like JAMM/MPN(+), a metalloprotease. So now the question is more of an issue of nomenclature/semantics. Should there be two terms in the approved list (something like "metalloprotease HEXXH type" and "metalloprotease EHHSD type" ) or should we lump together the HEXXH and EHHSD types under the same "metalloprotease" term and update the approved terms list to maybe say "Typically has HEXXH motif but other metalloprotease motifs (e.g. "ExnHxHx7Sx2D" ) have been described and can be used to support this function if present" or words to that effect. Edited 22 Feb, 2024 21:40

Link to this post | posted 22 Feb, 2024 21:48
debbie	I changed the approve function to say: "Typically has HEXXH motif but other metalloprotease motifs (e.g. "ExnHxHx7Sx2D)" debbie

Link to this post | posted 23 Feb, 2024 16:36
brueschhoff	Thank you so much to both of you for your help. Very interesting!