Summary: Origin of replication binding protein
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Origin of replication binding protein Provide feedback
This domain of large T antigen binds to the SV40 origin of DNA replication .
External database links
This tab holds annotation information from the InterPro database.
InterPro entry IPR003133
The group of polyomaviruses is formed by the homonymous murine virus (Py) as well as other representative members such as the simian virus 40 (SV40) and the human BK and JC viruses [PUBMED:8824775]. Their large T antigen (T-ag) protein binds to and activates DNA replication from the origin of DNA replication (ori). Insofar as is known, the T-ag binds to the origin first as a monomer to its pentanucleotide recognition element. The monomers are then thought to assemble into hexamers and double hexamers, which constitute the form that is active in initiation of DNA replication. When bound to the ori, T-ag double hexamers encircle DNA [PUBMED:17139255]. T-ag is a multidomain protein that contains an N-terminal J domain, which mediates protein interactions (see PROSITEDOC, INTERPRO), a central origin-binding domain (OBD), and a C-terminal superfamily 3 helicase domain (see PROSITEDOC, INTERPRO) [PUBMED:16611889].
This entry represents the central origin-binding domain (OBD). The overall fold of the ~130-residue T-ag OBD can be described as a central five-stranded antiparallel beta-sheet flanked by two alpha-helices on one side and one alpha-helix and one 3(10)-helix on the other. Both faces of the central beta-sheet are largely hydrophobic and are protected from solvent by the helices, thus forming two hydrophobic cores [PUBMED:8946857]. The T-ag OBD molecules are arranged as a spiral with a left-handed twist having six T-ag OBD's per turn. The spiral surrounds a central channel, the inner wall of which consists of alpha helices [PUBMED:8946857].
The mapping between Pfam and Gene Ontology is provided by InterPro. If you use this data please cite InterPro.
|Molecular function||DNA replication origin binding (GO:0003688)|
|Biological process||DNA replication (GO:0006260)|
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This clan includes replication proteins for viruses and plasmids. This domain is known to bind DNA. The members of this clan have three motifs. The central HXH is conserved in most families in the clan.
The clan contains the following 10 members:DUF1424 Gemini_AL1 Mob_Pre MobA_MobL Phage_GPA Relaxase Rep_1 Rep_N T_Ag_DNA_bind Viral_Rep
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Curation and family details
|Seed source:||Pfam-B_827 (release 5.2)|
|Number in seed:||11|
|Number in full:||509|
|Average length of the domain:||90.10 aa|
|Average identity of full alignment:||68 %|
|Average coverage of the sequence by the domain:||14.46 %|
|HMM build commands:||
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 80369284 -E 1000 --cpu 4 HMM pfamseq
|Family (HMM) version:||12|
|Download:||download the raw HMM for this family|
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There are 2 interactions for this family. More...
We determine these interactions using iPfam, which considers the interactions between residues in three-dimensional protein structures and maps those interactions back to Pfam families. You can find more information about the iPfam algorithm in the journal article that accompanies the website.
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 T_Ag_DNA_bind domain has been found. There are 33 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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