SEA-PHAGES | NifU-like protein

Link to this post \| posted 01 Mar, 2017 16:03
mpedulla	Do we annotate a function for “NifU-like proteins?” It has 100% amino acid match with other phages that coined NifU-like protein in Genbank. (Barriga gp95)

Link to this post \| posted 01 Mar, 2017 17:30
welkin	Hi Marisa, This is a great question. The NifU annotation came from our collaborators in Brazil, so Debbie and I weren't directly involved with the functional assignment in phage Barriga. I had to spend some time digging into "NifU" and what it does. NifU is a scaffold protein for Fe-S cluster complexes (not to be confused with the phage capsid scaffolding protein). It is frequently (but not always) involved in nitrogen fixation, as it is also found in species that do not fix nitrogen. The Barriga gene appears to align well with the NifU N , that is the N-terminal domain of NifU, but it is too short to contain both the N and C terminal domains of the protein. The N-terminal domain alone coordinates the binding of a single Fe while the C-terminal domain facilitates the binding to the rest of the Fe-S cluster. There are three Cys residues required for N-terminal Fe binding: Cys35, Cys62, and Cys106. A Smith-Waterman alignment places Barriga's cysteines in exactly the right place. So I think it is appropriate to add NifU-like protein (N-terminal domain) to our annotation list, and we should probably correct the others on phagesdb.org It would be interesting to see your phage has the C-terminal portion somewhere in a different gene. Here is the pubmed abstract on NifU, if you and your students are interested in further reading. https://www.ncbi.nlm.nih.gov/pubmed/10819462 Best, Welkin Edited 01 Mar, 2017 18:45

Link to this post | posted 01 Mar, 2017 17:30

welkin

Hi Marisa,
This is a great question. The NifU annotation came from our collaborators in Brazil, so Debbie and I weren't directly involved with the functional assignment in phage Barriga. I had to spend some time digging into "NifU" and what it does.
NifU is a scaffold protein for Fe-S cluster complexes (not to be confused with the phage capsid scaffolding protein). It is frequently (but not always) involved in nitrogen fixation, as it is also found in species that do not fix nitrogen. The Barriga gene appears to align well with the NifU N , that is the N-terminal domain of NifU, but it is too short to contain both the N and C terminal domains of the protein. The N-terminal domain alone coordinates the binding of a single Fe while the C-terminal domain facilitates the binding to the rest of the Fe-S cluster. There are three Cys residues required for N-terminal Fe binding: Cys35, Cys62, and Cys106. A Smith-Waterman alignment places Barriga's cysteines in exactly the right place.

So I think it is appropriate to add NifU-like protein (N-terminal domain) to our annotation list, and we should probably correct the others on phagesdb.org

It would be interesting to see your phage has the C-terminal portion somewhere in a different gene.

Here is the pubmed abstract on NifU, if you and your students are interested in further reading.
https://www.ncbi.nlm.nih.gov/pubmed/10819462

Best,
Welkin

Edited 01 Mar, 2017 18:45

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NifU-like protein