SEA-PHAGES | Phosphoesterase or metallophosphoesterase? A clarification question

Link to this post \| posted 10 Jun, 2023 05:47
fbaliraine	I am inclined to call a phosphoesterase function for subcluster M1 phages Glaske16_gp129 (66640-67299) & Dulcita gp 126 (66622-66181 bp), but will seek clarification given that the top 15 hits in phagesDB are to metallophosphoesterases. The sequence is 100% identical between the above phages: MSNVFFTSDLHIGHKKVVASRTTVDGEPAFPDLDNLPEWFGDFEIESYNRILADKWDTTVGKDDVVWVLGDISSGTKSGQEMALEWLSRRPGRKRLIKGNHDGVHPMYRDKAKWVKAYGEVFEDMDTAARIRVALSGGGHVDALLSHFPYMGDHTSVDRHTQWRLPNNGTILLHGHTHSSRRMSSCGGSLQVHVGVDAWNGYPVSMDEIRSYVEIWEDVZ According to the Official SEA-PHAGES Function List, a metallophosphoesterase, "Must contain a HEXXH motif to coordinate the metal ion." I can see the HEXXH motif in Luchodor_gp60, the sample gene for metallophosphoesterase in the Functions list. Whereas there are HHPred hits to metallophosphoesterase, my reasons for being weary about calling it a metallophosphoesterase rather than a phosphoesterase are two-fold: 1. I do not seem to see the HEXXH motif (except if the rule is flexible) 2. The top two HHPred hits are to phages D29 gp 66 & L5 gp 66, both of which are phosphoesterase. D29 is a well-studied, prototypic phage. According to Rudner, Fawcett & Losick (1999; https://www.pnas.org/doi/10.1073/pnas.96.26.14765), the conserved sequence HEXXH is a hallmark of metalloproteases. An HEXXH motif should have an "H" followed by an "E", then by any two amino acids followed by an "H" (see attached). I did a search for "HE" in each of the sequences. >phageD29_gp66 (phosphoesterase) HEXXH motif not seen MSNVWFTSDLHIGHAKVAEDRDWAGPDHDLHLAELWDEQVGKEDVVWILGDISSGGTRAQLDALGWLLNRPGRKRLILGNHDRPHPMYRDAPRLSRLYWNVLDYMSTAARLRVPLDGGGHTNVLLSHFPYVGDHTAEQRFTQWRLRDEGLILLHGHTHSRIIRSTMTNPRQIHVGLDAWHDLVPMDEVREMVNDIEEGL >Glaske16_gp129 (66640-67299) & Dulcita gp 126 (66622-66181 bp); HEXXH motif not seen MSNVFFTSDLHIGHKKVVASRTTVDGEPAFPDLDNLPEWFGDFEIESYNRILADKWDTTVGKDDVVWVLGDISSGTKSGQEMALEWLSRRPGRKRLIKGNHDGVHPMYRDKAKWVKAYGEVFEDMDTAARIRVALSGGGHVDALLSHFPYMGDHTSVDRHTQWRLPNNGTILLHGHTHSSRRMSSCGGSLQVHVGVDAWNGYPVSMDEIRSYVEIWEDVZ Luchodor_gp60 (metallophosphoesterase ref sequence) has the HEXXH motif (underlined) MSKRIVVVSDTQIPFDDRKALKAVVGFIGDTQPDEVVHIGDLMDYPSPSRWTKGTAEEFAQRIKPDSEQAKRRFLEPLRARYDGPVKVHEGNHDSRPFEYLHKFAPALVEYADQFRFQNLLDFDGFGVEVAPEFYKLAPGWVSTHGHRGGVRLTQKAGDTAYNAMMRFNTSVIIGHTHRQGLKPHTLGYGGHQKVLWSMEVGNLMNMHLAQYLKGATANWQTGFGLLTVDGHHVKPELVPVVGGSFSVDGHVWKV Based on the above, I would call the above Glaske16 & Dulcita genes phosphoesterases. Or could I be missing something? Thanks! Fred 365Kb

Link to this post | posted 10 Jun, 2023 05:47

I am inclined to call a phosphoesterase function for subcluster M1 phages Glaske16_gp129 (66640-67299) & Dulcita gp 126 (66622-66181 bp), but will seek clarification given that the top 15 hits in phagesDB are to metallophosphoesterases. The sequence is 100% identical between the above phages:

MSNVFFTSDLHIGHKKVVASRTTVDGEPAFPDLDNLPEWFGDFEIESYNRILADKWDTTVGKDDVVWVLGDISSGTKSGQEMALEWLSRRPGRKRLIKGNHDGVHPMYRDKAKWVKAYGEVFEDMDTAARIRVALSGGGHVDALLSHFPYMGDHTSVDRHTQWRLPNNGTILLHGHTHSSRRMSSCGGSLQVHVGVDAWNGYPVSMDEIRSYVEIWEDVZ

According to the Official SEA-PHAGES Function List, a metallophosphoesterase, "Must contain a HEXXH motif to coordinate the metal ion." I can see the HEXXH motif in Luchodor_gp60, the sample gene for metallophosphoesterase in the Functions list.

Whereas there are HHPred hits to metallophosphoesterase, my reasons for being weary about calling it a metallophosphoesterase rather than a phosphoesterase are two-fold:

1. I do not seem to see the HEXXH motif (except if the rule is flexible)
2. The top two HHPred hits are to phages D29 gp 66 & L5 gp 66, both of which are phosphoesterase. D29 is a well-studied, prototypic phage.

According to Rudner, Fawcett & Losick (1999; https://www.pnas.org/doi/10.1073/pnas.96.26.14765), the conserved sequence HEXXH is a hallmark of metalloproteases. An HEXXH motif should have an "H" followed by an "E", then by any two amino acids followed by an "H" (see attached). I did a search for "HE" in each of the sequences.

>phageD29_gp66 (phosphoesterase) HEXXH motif not seen
MSNVWFTSDLHIGHAKVAEDRDWAGPDHDLHLAELWDEQVGKEDVVWILGDISSGGTRAQLDALGWLLNRPGRKRLILGNHDRPHPMYRDAPRLSRLYWNVLDYMSTAARLRVPLDGGGHTNVLLSHFPYVGDHTAEQRFTQWRLRDEGLILLHGHTHSRIIRSTMTNPRQIHVGLDAWHDLVPMDEVREMVNDIEEGL

>Glaske16_gp129 (66640-67299) & Dulcita gp 126 (66622-66181 bp); HEXXH motif not seen
MSNVFFTSDLHIGHKKVVASRTTVDGEPAFPDLDNLPEWFGDFEIESYNRILADKWDTTVGKDDVVWVLGDISSGTKSGQEMALEWLSRRPGRKRLIKGNHDGVHPMYRDKAKWVKAYGEVFEDMDTAARIRVALSGGGHVDALLSHFPYMGDHTSVDRHTQWRLPNNGTILLHGHTHSSRRMSSCGGSLQVHVGVDAWNGYPVSMDEIRSYVEIWEDVZ

Luchodor_gp60 (metallophosphoesterase ref sequence) has the HEXXH motif (underlined)
MSKRIVVVSDTQIPFDDRKALKAVVGFIGDTQPDEVVHIGDLMDYPSPSRWTKGTAEEFAQRIKPDSEQAKRRFLEPLRARYDGPVKVHEGNHDSRPFEYLHKFAPALVEYADQFRFQNLLDFDGFGVEVAPEFYKLAPGWVSTHGHRGGVRLTQKAGDTAYNAMMRFNTSVIIGHTHRQGLKPHTLGYGGHQKVLWSMEVGNLMNMHLAQYLKGATANWQTGFGLLTVDGHHVKPELVPVVGGSFSVDGHVWKV

Based on the above, I would call the above Glaske16 & Dulcita genes phosphoesterases. Or could I be missing something?
Thanks!
Fred

Link to this post \| posted 15 Jun, 2023 00:33
debbie	I would call this a phosphoesterase too. debbie

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Phosphoesterase or metallophosphoesterase? A clarification question