Please note: this site relies heavily on the use of javascript. Without a javascript-enabled browser, this site will not function correctly. Please enable javascript and reload the page, or switch to a different browser.
2  structures 108  species 0  interactions 204  sequences 2  architectures

Family: Viral_DNA_bp (PF00747)

Summary: ssDNA binding protein

Pfam includes annotations and additional family information from a range of different sources. These sources can be accessed via the tabs below.

This is the Wikipedia entry entitled "Single-strand binding protein". More...

Single-strand binding protein Edit Wikipedia article

Single-stranded DNA-binding protein, or SSB, binds to single-stranded regions of DNA to prevent premature annealing, to protect the single-stranded DNA from being digested by nucleases, and to remove secondary structure from the DNA to allow other enzymes to function effectively upon it. Single-stranded DNA is produced during all aspects of DNA metabolism: replication, recombination and repair. As well as stabilizing this single-stranded DNA, SSB proteins bind to and modulate the function of numerous proteins involved in all of these processes.

SSB proteins have been identified in both viruses and organisms from bacteria to humans. The only organisms known to lack them are Thermoproteales, a group of extremophile archaea, where they have been displaced by the protein ThermoDBP. While many phage and viral SSBs function as monomers and eukaryotes encode heterotrimeric RPA (Replication Protein A), the best characterized SSB is that from the bacteria E. coli which, like most bacterial SSBs exists as a tetramer. Active E. coli SSB is composed of four identical 19 kDa subunits. Binding of single-stranded DNA to the tetramer can occur in different "modes", with SSB occupying different numbers of DNA bases depending on a number of factors, including salt concentration. For example, the (SSB)65 binding mode, in which approximately 65 nucleotides of DNA wrap around the SSB tetramer and contact all four of its subunits, is favoured at high salt concentrations in vitro. At lower salt concentrations, the (SSB)35 binding mode, in which about 35 nucleotides bind to only two of the SSB subunits, tends to form. Further work is required to elucidate the functions of the various binding modes in vivo.

Viral SSB

Viral_DNA_bp
PDB 1urj EBI.jpg
Single Stranded DNA-binding protein(icp8) from Herpes simplex virus-1
Identifiers
Symbol Viral_DNA_bp
Pfam PF00747
InterPro IPR000635

Function

Herpes simplex virus (HSV-1) single stranded DNA (ssDNA)-binding protein (SSB), ICP8, is a nuclear protein that, along other replication proteins is required for viral DNA replication during lytic infection.[1]

Structure

The head consists of the eight alpha helices. The front side of the neck region consists of a five-stranded beta-sheet and two alpha helices whereas the back side is a three-stranded beta-sheet The shoulder part of the N-terminal domain contains an alpha-helical and beta-sheet region.[1]

Mechanism

Although the overall picture of Human cytomegalovirus (HHV-5) DNA synthesis appears typical of the Herpesviruses, some novel features are emerging. Six herpes virus-group-common genes encode proteins that likely constitute the replication fork machinery, including a two-subunit DNA polymerase, a helicas-primase complex and a single-stranded DNA-binding protein.[2] The Human herpesvirus 1 (HHV-1) single-strand DNA-binding protein ICP8 is a 128kDa zinc metalloprotein. Photoaffinity labeling has shown that the region encompassing residues 368-902 contains the single-strand DNA-binding site of ICP8.[3] The HHHV-1 UL5, UL8, and UL52 genes encode an essential heterotrimeric DNA helicase-primase that is responsible for concomitant DNA unwinding and primer synthesis at the viral DNA replication fork. ICP8 may stimulate DNA unwinding and enable bypass of cisplatin damaged DNA by recruiting the helicase-primase to the DNA.[4]

Bacterial SSB

SSB
PDB 1v1q EBI.jpg
Crystal structure of PriB- a primosomal DNA replication protein of Escherichia coli
Identifiers
Symbol SSB
Pfam PF00436
Pfam clan CL0021
InterPro IPR000424
PROSITE PDOC00602
SCOP 1kaw
SUPERFAMILY 1kaw
TCDB 3.A.7

In molecular biology, SSB protein domain in bacteria are important in its function of maintaining DNA metabolism, more specifically DNA replication, repair and recombination.[5] It has a structure of three beta-strands to a single six-stranded beta-sheet to form a dimer.[6]

See also

References

  1. ^ a b Mapelli M, Panjikar S, Tucker PA (2005). "The crystal structure of the herpes simplex virus 1 ssDNA-binding protein suggests the structural basis for flexible, cooperative single-stranded DNA binding.". J Biol Chem 280 (4): 2990–7. doi:10.1074/jbc.M406780200. PMID 15507432. 
  2. ^ Anders DG, McCue LA (1996). "The human cytomegalovirus genes and proteins required for DNA synthesis". Intervirology 39 (5-6): 378–88. PMID 9130047. 
  3. ^ White EJ, Boehmer PE (October 1999). "Photoaffinity labeling of the herpes simplex virus type-1 single-strand DNA-binding protein (ICP8) with oligodeoxyribonucleotides". Biochem. Biophys. Res. Commun. 264 (2): 493–7. doi:10.1006/bbrc.1999.1566. PMID 10529391. 
  4. ^ Tanguy Le Gac N, Villani G, Boehmer PE (May 1998). "Herpes simplex virus type-1 single-strand DNA-binding protein (ICP8) enhances the ability of the viral DNA helicase-primase to unwind cisplatin-modified DNA". J. Biol. Chem. 273 (22): 13801–7. doi:10.1074/jbc.273.22.13801. PMID 9593724. 
  5. ^ Meyer RR, Laine PS (December 1990). "The single-stranded DNA-binding protein of Escherichia coli". Microbiol. Rev. 54 (4): 342–80. PMC 372786. PMID 2087220. 
  6. ^ Raghunathan S, Ricard CS, Lohman TM, Waksman G (June 1997). "Crystal structure of the homo-tetrameric DNA binding domain of Escherichia coli single-stranded DNA-binding protein determined by multiwavelength x-ray diffraction on the selenomethionyl protein at 2.9-A resolution". Proc. Natl. Acad. Sci. U.S.A. 94 (13): 6652–7. doi:10.1073/pnas.94.13.6652. PMC 21213. PMID 9192620. 

This article incorporates text from the public domain Pfam and InterPro IPR000635

External links

This page is based on a Wikipedia article. The text is available under the Creative Commons Attribution/Share-Alike License.

This tab holds the annotation information that is stored in the Pfam database. As we move to using Wikipedia as our main source of annotation, the contents of this tab will be gradually replaced by the Wikipedia tab.

ssDNA binding protein Provide feedback

This protein is found in herpesviruses and is needed for replication.

External database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR000635

Although the overall picture of Human cytomegalovirus (HHV-5) DNA synthesis appears typical of the Herpesviruses, some novel features are emerging. Six herpesvirus-group-common genes encode proteins that likely constitute the replication fork machinery, including a two-subunit DNA polymerase, a helicas-primase complex and a single-stranded DNA-binding protein [PUBMED:9130047].

The Human herpesvirus 1 (HHV-1) single-strand DNA-binding protein ICP8 is a 128kDa zinc metalloprotein. Photoaffinity labeling has shown that the region encompassing residues 368-902 contains the single-strand DNA-binding site of ICP8 [PUBMED:10529391]. The HHHV-1 UL5, UL8, and UL52 genes encode an essential heterotrimeric DNA helicase-primase that is responsible for concomitant DNA unwinding and primer synthesis at the viral DNA replication fork. ICP8 may stimulate DNA unwinding and enable bypass of cisplatin damaged DNA by recruiting the helicase-primase to the DNA [PUBMED:9593724].

Gene Ontology

The mapping between Pfam and Gene Ontology is provided by InterPro. If you use this data please cite InterPro.

Domain organisation

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

Loading domain graphics...

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...

View options

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.

  Seed
(11)
Full
(204)
Representative proteomes NCBI
(187)
Meta
(0)
RP15
(0)
RP35
(0)
RP55
(0)
RP75
(0)
Jalview View  View          View   
HTML View  View             
PP/heatmap 1 View             
Pfam viewer View  View             

1Cannot generate PP/Heatmap alignments for seeds; no PP data available

Key: ✓ available, x not generated, not available.

Format an alignment

  Seed
(11)
Full
(204)
Representative proteomes NCBI
(187)
Meta
(0)
RP15
(0)
RP35
(0)
RP55
(0)
RP75
(0)
Alignment:
Format:
Order:
Sequence:
Gaps:
Download/view:

Download options

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
(11)
Full
(204)
Representative proteomes NCBI
(187)
Meta
(0)
RP15
(0)
RP35
(0)
RP55
(0)
RP75
(0)
Raw Stockholm Download   Download           Download    
Gzipped Download   Download           Download    

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

HMM logos is one way of visualising profile HMMs. Logos provide a quick overview of the properties of an HMM in a graphical form. You can see a more detailed description of HMM logos and find out how you can interpret them here. More...

Trees

This page displays the phylogenetic tree for this family's seed alignment. We use FastTree to calculate neighbour join trees with a local bootstrap based on 100 resamples (shown next to the tree nodes). FastTree calculates approximately-maximum-likelihood phylogenetic trees from our seed alignment.

Note: You can also download the data file for the tree.

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: Pfam-B_490 (release 2.1)
Previous IDs: viral_DNA_bp;
Type: Family
Author: Bateman A
Number in seed: 11
Number in full: 204
Average length of the domain: 910.50 aa
Average identity of full alignment: 32 %
Average coverage of the sequence by the domain: 95.55 %

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 40.9 40.8
Noise cut-off 19.7 19.4
Model length: 1122
Family (HMM) version: 12
Download: download the raw HMM for this family

Species distribution

Sunburst controls

Show

This visualisation provides a simple graphical representation of the distribution of this family across species. You can find the original interactive tree in the adjacent tab. More...

Loading sunburst data...

Tree controls

Hide

The tree shows the occurrence of this domain across different species. More...

Loading...

Please note: for large trees this can take some time. While the tree is loading, you can safely switch away from this tab but if you browse away from the family page entirely, the tree will not be loaded.

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 Viral_DNA_bp domain has been found. There are 2 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.

Loading structure mapping...