SEA-PHAGES | FUNCTION: Tail Terminator - Current Official Function List Confirmatory Question

Link to this post \| posted 11 Apr, 2019 15:31
GregFrederick@letu.edu	Welkin and or Debbie. We are looking at this closely since we are annotating seven phages all in the same subcluster. We are trying to avoid setting incorrect precedent. So thanks in advance for help with this call. The gene in questions is gp13 in Megiddo. The amino acid sequence is here in case you wish to rerun the analysis: Megiddo gp13>> MIELLDREAPPDIRFLRAWLLPVGGGVGAKRETGDPFPFTLIQKFDGWENSHTQYGFYQFDHLAVAADGKSAYTACEDYARTIKRRMLYLRDRPWTEVTVPGWGVATADVVRCTASPRHDPYNNTDVERFIARYSVHLRLVSVASZ The HHPred analysis will be here for another week or so: https://toolkit.tuebingen.mpg.de/#/jobs/4365093 A top HHPred hit includes: https://www.rcsb.org/structure/3FZ2 RCSB PDB - 3FZ2: Crystal structure of the tail terminator protein from phage lambda (gpU-D74A) www.rcsb.org The X-ray crystal structure of the phage lambda tail terminator protein reveals the biologically relevant hexameric ring structure and demonstrates a conserved mechanism of tail termination among diverse long-tailed phages. The Official Function List states that the Tail terminator “must have an HHPRED alignment to one of the following: SPP1 17 (5A21 chain G in the macromolecular complex) or Lambda U (3FZ2_F)” PROBLEM: When we look closely at this identified protein it is actually 3FZ2_B not 3FZ2_F. That protein lists this way: 3FZ2_B Minor tail protein U; Mixed Alpha-Beta fold, VIRAL PROTEIN; HET: MSE, SO4; 2.7A {Enterobacteria phage lambda} SCOP: d.323.1.1, l.1.1.1 However, once the link is clicked, the loaded page reads: 3FZ2 Crystal structure of the tail terminator protein from phage lambda (gpU-D74A) • DOI: 10.2210/pdb3FZ2/pdb QUESTION: We feel that HHPred supports a functional call of “Tail Terminator”. However, we would be breaking guidelines in the Official Functional List by calling the function. What should we do with this info? Thanks. Edited 11 Apr, 2019 15:35

Link to this post | posted 11 Apr, 2019 15:31

Welkin and or Debbie.

We are looking at this closely since we are annotating seven phages all in the same subcluster. We are trying to avoid setting incorrect precedent. So thanks in advance for help with this call.

The gene in questions is gp13 in Megiddo. The amino acid sequence is here in case you wish to rerun the analysis:

Megiddo gp13>>
MIELLDREAPPDIRFLRAWLLPVGGGVGAKRETGDPFPFTLIQKFDGWENSHTQYGFYQFDHLAVAADGKSAYTACEDYARTIKRRMLYLRDRPWTEVTVPGWGVATADVVRCTASPRHDPYNNTDVERFIARYSVHLRLVSVASZ

The HHPred analysis will be here for another week or so: https://toolkit.tuebingen.mpg.de/#/jobs/4365093

A top HHPred hit includes:

https://www.rcsb.org/structure/3FZ2
RCSB PDB - 3FZ2: Crystal structure of the tail terminator protein from phage lambda (gpU-D74A)
www.rcsb.org

The X-ray crystal structure of the phage lambda tail terminator protein reveals the biologically relevant hexameric ring structure and demonstrates a conserved mechanism of tail termination among diverse long-tailed phages.

The Official Function List states that the Tail terminator “must have an HHPRED alignment to one of the following: SPP1 17 (5A21 chain G in the macromolecular complex) or Lambda U (3FZ2_F)”

PROBLEM: When we look closely at this identified protein it is actually 3FZ2_B not 3FZ2_F.

That protein lists this way:

3FZ2_B Minor tail protein U; Mixed Alpha-Beta fold, VIRAL PROTEIN; HET: MSE, SO4; 2.7A {Enterobacteria phage lambda} SCOP: d.323.1.1, l.1.1.1

However, once the link is clicked, the loaded page reads:

3FZ2
Crystal structure of the tail terminator protein from phage lambda (gpU-D74A)
• DOI: 10.2210/pdb3FZ2/pdb

QUESTION: We feel that HHPred supports a functional call of “Tail Terminator”. However, we would be breaking guidelines in the Official Functional List by calling the function. What should we do with this info? Thanks.

Edited 11 Apr, 2019 15:35

Link to this post \| posted 11 Apr, 2019 15:39
welkin	Hi Greg, Thanks for your question. yes, this is the tail terminator. The Lambda U crystal structure 3FZ2 is of a homohexamer complex— all six chains are from the same polypeptide. so 3FZ2_B is valid, as are chains _A through _F. I will update the official function notes. Best, Welkin

Link to this post \| posted 11 Apr, 2019 17:53
GregFrederick@letu.edu	Super! This makes perfect sense now. I saw the "homohexamer" in the description. I had not stopped to ponder that one monomer would be designated "A" and another "B" and so on…. Thanks for your help on this! Greg Edited 11 Apr, 2019 17:57

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FUNCTION: Tail Terminator - Current Official Function List Confirmatory Question