SV40

P03070 SV40 large T antigen entry from InterPro

InterPro entry	Method accession	Graphical match	Method name
IPR001623	PF00226		DnaJ
IPR001623	PS00636	Match of status: N	DNAJ_1
IPR001623	PS50076		DNAJ_2
IPR001623	SM00271		DnaJ
IPR001623	SSF46565		DnaJ_N
IPR003133	PF02217		T_Ag_DNA_bind
NONE	d1gh6a_		d1gh6a_
NONE	d1tbd_		d1tbd_

What InterPro tells us

From the graphical match above, you can see that there are two InterPro entries associated with SV40 large-T antigen. These different entries give you information on the domain architecture of the large-T Ag. InterPro entry IPR001623 represents the N-terminal (J) domain of the heat shock protein DnaJ. This domain is represented by five signatures: PF00226 from PFAM, PS00636 pattern from PROSITE (recorded as (N) false negative), PS50076 profile from PROSITE, SM00271 from SMART, and SSF46565 from SUPERFAMILY. The J domain is found in many prokaryotic and eukaryotic proteins, including several yeast proteins (MAS5/YDJ1, MDJ1, CAJ1, SIS1), human proteins (HDJ1, HDJ2, HSJ1), plant DnaJ homologues, Escherichia coli proteins (cbpA, HSC20), and drosophila cysteine-string protein. Consequently, there are over 1500 proteins in this InterPro entry, all of which possess a J-like domain. The J domain is thought to function as a molecular chaperone. The J domain of the SV40 large-T Ag is important for viral replication, transcriptional regulation and viral assembly.

The other InterPro entry that describes the SV40 large-T antigen is IPR003133, which represents the ori-binding domain of the T antigen. This domain is represented by PF02217 from PFAM. This DNA-binding domain binds to the SV40 origin of DNA replication, and is sometimes referred to as the replication-binding domain. Several ori-binding domains share the same structural fold found in the SV40 large-T Ag, including the DNA-binding domain of the REP protein in geminivirus, the nuclease domain of the REP protein in adeno-associated virus, and the replication initiation protein E1 in bovine papillomavirus. This domain has two elements, A (aa 152-155) and B2 (aa 203-207) that form two loops, which define a continuous surface on the protein that directly contacts the DNA and are essential for origin-specific recognition.

The last two entries in the table are from the structural classification database SCOP, the names being derived from the PDB entries that they describe (for example, d1gh6a_ is from PDB entry 1gh6, chain a). These two entries lack an InterPro accession number, because they are structural links associated with specific proteins that have structures in PDB. The d1gh6a_ entry describes the J domain, and the d1tbd_ entry describes the ori DNA-binding domain of the SV40 large-T Ag. Following the links will take you to the SCOP pages describing the structural classification of these domains, and will provide you with links to the associated PDB entries.

The SV40 small-t Ag is described by IPR001623, since it shares a J domain in common with the large-T Ag, and by IPR003354 representing the small/middle-t Ag domain, which is conserved in small and middle-t antigen proteins.

Other SV40 proteins in InterPro

The remaining SV40 proteins are also represented in InterPro. The VP1 coat protein is represented by InterPro entries IPR000662 (Polyomavirus coat protein VP1 family), and IPR008975 (viral coat and capsid protein family). These two entries provide information on the family relationships of the SV40 VP1 protein. InterPro entry IPR008975 is a large family with over 8,000 protein matches. It describes structurally related viral coat proteins from animal viruses (SV40, poliovirus, parvovirus, rhinovirus, coxsackievirus, foot-and-mouth virus), insect viruses (nodavirus, cricket paralysis virus, galleria mellonella densovirus), plant viruses (SPMV, RYMV, TRSV, CMV), and bacteriophage (phi-X174, G4, alpha3). If you follow the links to IPR008975, you will find that there are several InterPro families listed under the section labelled ‘Children’, which represent the smaller, more closely related families that IPR008975 has been subdivided into. The SV40 VP1 coat protein is found within the subfamily IPR000662, which represents the Polyoma coat protein VP1 family.

The coat proteins VP2 and VP3 are represented by InterPro entry IPR001070 (Polyomavirus coat protein VP2 family). The SV40 agnoprotein is represented by InterPro entry IPR002643 (Polyomavirus agnoprotein family).

What the structure tells us

A description and visualisation of the structural features of the various SV40 proteins, including the large-T antigen and the capsid, can be found at the PDB database. Here you can see how the various proteins do their jobs.