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. The monomers assemble into a [http://www.pdb.org/pdb/explore/jmol.do?structureId=2FUF&bionumber=1 hexameric left-handed spiral], whose pitch complements the turn of DNA. Side-side interaction is necessary for hexamerization, in 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 the assembly of a double hexamer. A central pore 40 Angstroms wide is formed, large enough for dsDNA, carrying positive charge. A monomer is able to bind along a series of GAGGC pentanucleotides P1 through P4 at the origin, collectively known as Site II. <scene name='User:Udayan_Shevade/Sandbox1/Obd_residues/1'>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 fully assembled double hexamer is similarly conserved across a number of origin-binding proteins in different viruses, despite varying protein sequences, suggesting sequence-specificity. The Asn and Arg in the A1 motif primarily make up base-specific interactions with the 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. The monomers assemble into a [http://www.pdb.org/pdb/explore/jmol.do?structureId=2FUF&bionumber=1 hexameric left-handed spiral], whose pitch complements the turn of DNA. Side-side interaction is necessary for hexamerization, in 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 the assembly of a double hexamer. A central pore 40 Angstroms wide is formed, large enough for dsDNA, carrying positive charge. A monomer is able to bind along a series of GAGGC pentanucleotides P1 through P4 at the origin, collectively known as Site II. <scene name='User:Udayan_Shevade/Sandbox1/Obd_residues/1'>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 fully assembled double hexamer is similarly conserved across a number of origin-binding proteins in different viruses, despite varying protein sequences, suggesting sequence-specificity. The Asn and Arg in the A1 motif primarily make up base-specific interactions with the 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]] | [[Image:Tagobd_dna_interactions.jpg|200px|left|thumb]] | ||
Binding of large T antigen at the origin of replication allows replicative machinery to unwind and synthesize new DNA. Residues involved in DNA binding also bind ssDNA-binding protein human RPA<ref>PMID:2600586</ref>. T antigen also acts as a repressor of early gene transcription. When increased amounts of T antigen are present, it binds DNA and blocks the overlapping promoter sequence, thus behaving as its own regulator.</Structuresection> | Binding of large T antigen at the origin of replication allows replicative machinery to unwind and synthesize new DNA. Residues involved in DNA binding also bind ssDNA-binding protein human RPA<ref>PMID:2600586</ref>. T antigen also acts as a repressor of early gene transcription. When increased amounts of T antigen are present, it binds DNA and blocks the overlapping promoter sequence, thus behaving as its own regulator.</Structuresection> | ||
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{{STRUCTURE_1svm| PDB=1svm | SCENE= }} | {{STRUCTURE_1svm| PDB=1svm | SCENE= }} | ||
| - | + | ===== Helicase ===== | |
| - | ==== Helicase ==== | + | |
The helicase monomer consists of a AAA+ domain. Each monomer binds and hydrolyzes an ATP at this region in the presence of magnesium ion. Together, the monomers drive an overall conformational change in the hexamer. The helicase monomer can exist in one of three states: ATP-bound, ADP-bound and Nt-free. The transitions in conformation between these states enable the unwinding of viral dsDNA. There are both cis- and trans-monomer interactions involving ATP. ''Cis''-residues Lys 432, Thr 433 and Thr 434 of the P loop interact closely with the triphosphate groups, and Asp 474 and Asn 529 form H bonds with ATP on the same residue. Among these, Ilu 428, Thr 433 and Asp 474 adopt different conformations in the ADP-bound state. In the Nt-free state, Ilu 428 and Thr 434 are turned even further and sterically disallow the presence of ADP. A water molecule near the ATP is present for stability and nucleophilic attack during hydrolysis. Six ''trans''-residues, of which Lys 418 and Lys 419 stabilize ATP hydrolysis, interact with ATP on adjacent monomers, important in producing conformational changes. These rearrangements affect the position of "the β hairpin," a positively-charged structure that protrudes into the central channel. ''Trans''-residues Arg 498, Asp 499 and Asp 502 are located at the base of the hairpin, lending a lever-like functionality. | The helicase monomer consists of a AAA+ domain. Each monomer binds and hydrolyzes an ATP at this region in the presence of magnesium ion. Together, the monomers drive an overall conformational change in the hexamer. The helicase monomer can exist in one of three states: ATP-bound, ADP-bound and Nt-free. The transitions in conformation between these states enable the unwinding of viral dsDNA. There are both cis- and trans-monomer interactions involving ATP. ''Cis''-residues Lys 432, Thr 433 and Thr 434 of the P loop interact closely with the triphosphate groups, and Asp 474 and Asn 529 form H bonds with ATP on the same residue. Among these, Ilu 428, Thr 433 and Asp 474 adopt different conformations in the ADP-bound state. In the Nt-free state, Ilu 428 and Thr 434 are turned even further and sterically disallow the presence of ADP. A water molecule near the ATP is present for stability and nucleophilic attack during hydrolysis. Six ''trans''-residues, of which Lys 418 and Lys 419 stabilize ATP hydrolysis, interact with ATP on adjacent monomers, important in producing conformational changes. These rearrangements affect the position of "the β hairpin," a positively-charged structure that protrudes into the central channel. ''Trans''-residues Arg 498, Asp 499 and Asp 502 are located at the base of the hairpin, lending a lever-like functionality. | ||
Revision as of 23:59, 13 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 consisting of three major domains: an N-terminal J domain, a central origin-binding domain, and a C-terminal helicase domain [2].
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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 helicase monomer consists of a AAA+ domain. Each monomer binds and hydrolyzes an ATP at this region in the presence of magnesium ion. Together, the monomers drive an overall conformational change in the hexamer. The helicase monomer can exist in one of three states: ATP-bound, ADP-bound and Nt-free. The transitions in conformation between these states enable the unwinding of viral dsDNA. There are both cis- and trans-monomer interactions involving ATP. Cis-residues Lys 432, Thr 433 and Thr 434 of the P loop interact closely with the triphosphate groups, and Asp 474 and Asn 529 form H bonds with ATP on the same residue. Among these, Ilu 428, Thr 433 and Asp 474 adopt different conformations in the ADP-bound state. In the Nt-free state, Ilu 428 and Thr 434 are turned even further and sterically disallow the presence of ADP. A water molecule near the ATP is present for stability and nucleophilic attack during hydrolysis. Six trans-residues, of which Lys 418 and Lys 419 stabilize ATP hydrolysis, interact with ATP on adjacent monomers, important in producing conformational changes. These rearrangements affect the position of "the β hairpin," a positively-charged structure that protrudes into the central channel. Trans-residues Arg 498, Asp 499 and Asp 502 are located at the base of the hairpin, lending a lever-like functionality.
References
- ↑ 1.0 1.1 Luo X, Sanford DG, Bullock PA, Bachovchin WW. Solution structure of the origin DNA-binding domain of SV40 T-antigen. Nat Struct Biol. 1996 Dec;3(12):1034-9. PMID:8946857
- ↑ Gai D, Zhao R, Li D, Finkielstein CV, Chen XS. Mechanisms of conformational change for a replicative hexameric helicase of SV40 large tumor antigen. Cell. 2004 Oct 1;119(1):47-60. PMID:15454080 doi:10.1016/j.cell.2004.09.017
- ↑ Falchuk KH, Czupryn M. Isolation of metallothioneins under metal-free conditions. Methods Enzymol. 1991;205:47-53. PMID:1779811
- ↑ Shafer WM, Onunka VC. Mechanism of staphylococcal resistance to non-oxidative antimicrobial action of neutrophils: importance of pH and ionic strength in determining the bactericidal action of cathepsin G. J Gen Microbiol. 1989 Apr;135(4):825-30. PMID:2600586
