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1  structure 56  species 1  interaction 58  sequences 2  architectures

Family: T4_Gp59_C (PF08994)

Summary: T4 gene Gp59 loader of gp41 DNA helicase C-term

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T4 gene Gp59 loader of gp41 DNA helicase C-term Provide feedback

Bacteriophage T4 gene-59 helicase assembly protein is required for recombination-dependent DNA replication, which is the predominant mode of DNA replication in the late stage of T4 infection. T4 gene-59 helicase assembly protein accelerates the loading of the T4 gene-41 helicase during DNA synthesis by the T4 replication system in vitro. T4 gene-59 helicase assembly protein binds to both T4 gene-41 helicase and T4 gene-32 single-stranded DNA binding protein, and to single and double-stranded DNA. The structure of T4 gene-59 helicase assembly protein reveals a novel alpha-helical bundle fold with two domains of similar size, this being the C-terminal domain that consists of seven alpha-helices with short intervening loops and turns. The surface of the domain contains large regions of exposed hydrophobic residues and clusters of acidic and basic residues. The hydrophobic region on the 'bottom' surface of the domain near the C-terminal helix binds the leading strand DNA, whilst the hydrophobic region on the 'top' surface of the domain lies between the two arms of the fork DNA, allowing for T4 gene 41 helicase binding and assembly into a hexameric complex around the lagging strand [1].

Literature references

  1. Mueser TC, Jones CE, Nossal NG, Hyde CC; , J Mol Biol. 2000;296:597-612.: Bacteriophage T4 gene 59 helicase assembly protein binds replication fork DNA. The 1.45 A resolution crystal structure reveals a novel alpha-helical two-domain fold. PUBMED:10669611 EPMC:10669611


External database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR015086

The Bacteriophage T4 gene 59 helicase assembly protein is required for recombination-dependent DNA replication, which is the predominant mode of DNA replication in the late stage of T4 infection. T4 gene 59 helicase assembly protein accelerates the loading of the T4 gene 41 helicase during DNA synthesis by the T4 replication system in vitro. T4 gene 59 helicase assembly protein binds to both T4 gene 41 helicase and T4 gene 32 single-stranded DNA binding protein, and to single and double-stranded DNA.

The C-terminal domain of the T4 gene 59 helicase assembly protein consists of seven alpha-helices with short intervening loops and turns; the surface of the domain contains large regions of exposed hydrophobic residues and clusters of acidic and basic residues. The hydrophobic region on the 'bottom' surface of the domain near the C-terminal helix binds the leading strand DNA, whilst the hydrophobic region on the, top, surface of the domain lies between the two arms of the fork DNA, allowing for T4 gene 41 helicase binding and assembly into a hexameric complex around the lagging strand [PUBMED:10669611].

Domain organisation

Below is a listing of the unique domain organisations or architectures in which this domain is found. More...

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Alignments

We store a range of different sequence alignments for families. As well as the seed alignment from which the family is built, we provide the full alignment, generated by searching the sequence database using the family HMM. We also generate alignments using four representative proteomes (RP) sets, the NCBI sequence database, and our metagenomics sequence database. More...

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We make a range of alignments for each Pfam-A family. You can see a description of each above. You can view these alignments in various ways but please note that some types of alignment are never generated while others may not be available for all families, most commonly because the alignments are too large to handle.

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(10)
Full
(58)
Representative proteomes NCBI
(50)
Meta
(390)
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(0)
RP35
(0)
RP55
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RP75
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Format an alignment

  Seed
(10)
Full
(58)
Representative proteomes NCBI
(50)
Meta
(390)
RP15
(0)
RP35
(0)
RP55
(0)
RP75
(0)
Alignment:
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We make all of our alignments available in Stockholm format. You can download them here as raw, plain text files or as gzip-compressed files.

  Seed
(10)
Full
(58)
Representative proteomes NCBI
(50)
Meta
(390)
RP15
(0)
RP35
(0)
RP55
(0)
RP75
(0)
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You can also download a FASTA format file containing the full-length sequences for all sequences in the full alignment.

External links

MyHits provides a collection of tools to handle multiple sequence alignments. For example, one can refine a seed alignment (sequence addition or removal, re-alignment or manual edition) and then search databases for remote homologs using HMMER3.

HMM logo

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Trees

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Curation and family details

This section shows the detailed information about the Pfam family. You can see the definitions of many of the terms in this section in the glossary and a fuller explanation of the scoring system that we use in the scores section of the help pages.

Curation View help on the curation process

Seed source: pdb_1c1k
Previous IDs: T4-helicase_C;
Type: Domain
Author: Mistry J, Sammut SJ
Number in seed: 10
Number in full: 58
Average length of the domain: 101.80 aa
Average identity of full alignment: 38 %
Average coverage of the sequence by the domain: 50.40 %

HMM information View help on HMM parameters

HMM build commands:
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 23193494 -E 1000 --cpu 4 HMM pfamseq
Model details:
Parameter Sequence Domain
Gathering cut-off 25.0 25.0
Trusted cut-off 64.7 63.9
Noise cut-off 21.7 21.0
Model length: 103
Family (HMM) version: 5
Download: download the raw HMM for this family

Species distribution

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Interactions

There is 1 interaction for this family. More...

T4_Gp59_N

Structures

For those sequences which have a structure in the Protein DataBank, we use the mapping between UniProt, PDB and Pfam coordinate systems from the PDBe group, to allow us to map Pfam domains onto UniProt sequences and three-dimensional protein structures. The table below shows the structures on which the T4_Gp59_C domain has been found. There are 1 instances of this domain found in the PDB. Note that there may be multiple copies of the domain in a single PDB structure, since many structures contain multiple copies of the same protein seqence.

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