User:Udayan Shevade/Sandbox1
From Proteopedia
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<Structuresection load='1tbd' side='right' caption='The origin binding domain of SV40 large T antigen' size='345' scene='User:Udayan_Shevade/Sandbox1/Origin_binding_domain_0/4'> | <Structuresection load='1tbd' side='right' caption='The origin binding domain of SV40 large T antigen' size='345' scene='User:Udayan_Shevade/Sandbox1/Origin_binding_domain_0/4'> | ||
==== The Origin Binding Domain ==== | ==== The Origin Binding Domain ==== | ||
| - | The origin binding domain monomer consists of five anti-parallel beta sheets flanked on either side by a pair of alpha helices. These monomers assemble tightly into a [http://www.pdb.org/pdb/explore/jmol.do?structureId=2FUF&bionumber=1 hexameric left-handed spiral], whose pitch complements that of DNA. Side-side interaction of the monomers is necessary in hexamer assembly, for which residues <scene name='User:Udayan_Shevade/Sandbox1/Obd_183_185/1'>Phe 183 and Ser 185</scene> are crucial. Residues along the B3 motif are necessary in assembly of a double hexamer. The complex forms a central pore 40 Angstroms wide, large enough for double stranded DNA, and carries a positive charge. The monomers are each capable of binding along a series of GAGGC pentanucleotides P1 through P4, collectively known as Site II. <scene name='User:Udayan_Shevade/Sandbox1/Obd_residues/1'>The residues</scene> implicated in DNA binding are <scene name='User:Udayan_Shevade/Sandbox1/Obd_153_154_155/5'>Asn 153, Arg 154, Thr 155 from the A1 motif</scene>; <scene name='User:Udayan_Shevade/Sandbox1/Obd_203_204/1'>His 203, Arg 204 from the B2 motif</scene>; as well as <scene name='User:Udayan_Shevade/Sandbox1/Obd_201_202/1'>His 201 and Arg 202</scene><ref name="A"/>. The structural fold adopted by the double hexamer is a similarly conserved feature across a number of origin-binding proteins in different viruses, despite varying protein sequences, suggesting sequence-specificity. The Asn and Arg within the A1 motif make the base-specific interactions with DNA, whereas residues from the B2 loop interact mainly with the phosphate backbone. These specific interactions bury a large surface area of the protein and give rise to a 60nM K<sub>d</sub>.<ref name="C">PMID:1779811</ref>. | + | The origin binding domain monomer consists of five anti-parallel beta sheets flanked on either side by a pair of alpha helices. These monomers assemble tightly into a [http://www.pdb.org/pdb/explore/jmol.do?structureId=2FUF&bionumber=1 hexameric left-handed spiral], whose pitch complements that of DNA. Side-side interaction of the monomers is necessary in hexamer assembly, for which residues <scene name='User:Udayan_Shevade/Sandbox1/Obd_183_185/1'>Phe 183 and Ser 185</scene> are crucial. Residues along the <scene name='User:Udayan_Shevade/Sandbox1/Obd_double_hexamer_residues/1'>B3 motif</scene> are necessary in assembly of a double hexamer. The complex forms a central pore 40 Angstroms wide, large enough for double stranded DNA, and carries a positive charge. The monomers are each capable of binding along a series of GAGGC pentanucleotides P1 through P4, collectively known as Site II. <scene name='User:Udayan_Shevade/Sandbox1/Obd_residues/1'>The residues</scene> implicated in DNA binding are <scene name='User:Udayan_Shevade/Sandbox1/Obd_153_154_155/5'>Asn 153, Arg 154, Thr 155 from the A1 motif</scene>; <scene name='User:Udayan_Shevade/Sandbox1/Obd_203_204/1'>His 203, Arg 204 from the B2 motif</scene>; as well as <scene name='User:Udayan_Shevade/Sandbox1/Obd_201_202/1'>His 201 and Arg 202</scene><ref name="A"/>. The structural fold adopted by the double hexamer is a similarly conserved feature across a number of origin-binding proteins in different viruses, despite varying protein sequences, suggesting sequence-specificity. The Asn and Arg within the A1 motif make the base-specific interactions with DNA, whereas residues from the B2 loop interact mainly with the phosphate backbone. These specific interactions bury a large surface area of the protein and give rise to a 60nM K<sub>d</sub>.<ref name="C">PMID:1779811</ref>. |
[[Image:Tagobd_dna_interactions.jpg|200px|left|thumb]]</Structuresection> | [[Image:Tagobd_dna_interactions.jpg|200px|left|thumb]]</Structuresection> | ||
Revision as of 22:20, 12 November 2011
Contents |
SV40 Large T Antigen
Introduction
The SV40 large tumor antigen is a multifunctional regulatory protein encoded by Simian Virus 40. It is classified under the AAA+ family of helicases [1]. Noteworthy for its versatility, the protein is responsible for initiation of viral DNA replication, regulation of viral transcription and transformation of the host cell to promote viral infectivity. Large T-antigen is an early gene product of SV40 and is produced via differential mRNA splicing.
Structure
T antigen is a 708-amino acid protein with three major domains: an N-terminal J domain, a central origin-binding domain, and a C-terminal helicase domain [2]. The activities of each are covered briefly below.
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| 1svm, resolution 1.94Å () | |||||||||
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| Ligands: | , , | ||||||||
| Related: | 1svl, 1svo | ||||||||
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| Resources: | FirstGlance, OCA, RCSB, PDBsum | ||||||||
| Coordinates: | save as pdb, mmCIF, xml | ||||||||
Helicase
The monomer of the hexameric helicase contains a AAA+ domain. Each monomer binds and hydrolyzes an ATP in the presence of magnesium ion and drives an overall conformational change in the hexamer.
