Proteopedia - User contributions [en]

https://proteopedia.org/api.php?action=feedcontributions&feedformat=atom&user=Udayan+Shevade Proteopedia - User contributions [en] 2026-09-20T13:30:34Z User contributions MediaWiki 1.43.8 https://proteopedia.org/index.php?title=Large_T_Antigen&diff=1393673 Large T Antigen 2012-05-20T17:43:20Z

<p>Udayan Shevade: /* Introduction */</p> <hr /> <div>=== Introduction ===<br /> <br /> The '''SV40 large tumor antigen''' is a multifunctional regulatory protein encoded by Simian Virus 40. It is classified under the AAA+ family of helicases <ref name="A">PMID:8946857</ref>. 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.<br /> <br /> === Structure and Function ===<br /> 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 <ref name="B">PMID:15454080</ref>.<br /> <br /> <Structuresection load='1tbd' side='right' caption='The origin binding domain of SV40 large T antigen, [[1tbd]]' size='345' scene='User:Udayan_Shevade/Sandbox1/Origin_binding_domain_0/4'><br /> ===== The Origin Binding Domain =====<br /> 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'>Phe183 and Ser185</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 is formed, large enough for dsDNA, carrying positive charge. A monomer along this pore 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, Arg154, Thr155 from the A1 motif</scene>; <scene name='User:Udayan_Shevade/Sandbox1/Obd_203_204/1'>His203, Arg204 from the B2 motif</scene>; as well as <scene name='User:Udayan_Shevade/Sandbox1/Obd_201_202/1'>His201 andArg 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>. <br /> [[Image:Tagobd_dna_interactions.jpg|200px|left|thumb]]<br /> 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><br /> <br /> <br /> <br /> {{STRUCTURE_1svm| PDB=1svm | SIZE=400| SCENE= |right|CAPTION=SV40 large tumor antigen complexed with ATP, Zn+2 and Mg+2 ions, [[1svm]] }}<br /> <br /> ===== Helicase =====<br /> The <scene name='User:Udayan_Shevade/Sandbox1/Taghelicase_aaa_monomer/1'>helicase monomer</scene> 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 [http://www.sciencedirect.com/cache/MiamiImageURL/1-s2.0-S0092867404008906-gr3_lrg.jpg/0?wchp=dGLbVlV-zSkWA transitions in conformation] between these states enable the unwinding of viral dsDNA. There are both cis- and trans-monomer interactions involving ATP. <br /> <br /> <scene name='User:Udayan_Shevade/Sandbox1/Helicase_cis_residues/2'>''Cis''-residues</scene> Lys432, Thr433 and Thr434 of the P loop interact closely with the triphosphate groups, and Asp474 and Asn529 form H bonds with ATP on the same residue. Among these, Ilu428, Thr433 and Asp474 adopt different conformations in the ADP-bound state. In the Nt-free state, Ilu428 and Thr434 are turned even further and sterically disallow the presence of ADP.<br /> <br /> <scene name='User:Udayan_Shevade/Sandbox1/Helicase_atp_water/1'>A water molecule</scene> near the ATP is present for stability and nucleophilic attack during hydrolysis. <br /> <br /> <scene name='User:Udayan_Shevade/Sandbox1/Helicase_trans_residues/1'>Six ''trans''-residues</scene>, of which Lys418 and Lys419 stabilize ATP hydrolysis, interact with ATP on adjacent monomers, important in producing conformational changes. <br /> <br /> These rearrangements affect the position of <scene name='User:Udayan_Shevade/Sandbox1/Taghelicase_betahairpin/1'>the "β hairpin,"</scene> a positively-charged structure that protrudes into the central channel. ''Trans''-residues Arg498, Asp499 and Asp502 are located at the base of the hairpin, lending a lever-like functionality. The [http://www.sciencedirect.com/cache/MiamiImageURL/1-s2.0-S0092867404008906-gr7_lrg.jpg/0?wchp=dGLbVlk-zSkWb motion of the β hairpin] unwinds the DNA through the central channel <ref name='D'>PMID:15454080</ref>.<br /> [[Image:1SVM_L_O.jpg|500px|left|thumb]]<br /> <br /> The helicase domain is also implicated in binding to p53, a transcription factor vital in tumor suppression. Binding of helicase inhibits the functional tetramerization of p53 on DNA<ref>PMID:1560412</ref>.<br /> <br /> <br /> <Structuresection load='1gh6' side='right' caption='Large T antigen complexed with retinoblastoma pocket, [[1gh6]]' size='345'><br /> <br /> ===== J domain and LxCxE motif =====<br /> In the transformation of the host cell, retinoblastoma, a tumor suppressor, is inactivated via both the N-terminal J domain and the LxCxE motif. The N-terminal region (residues 7-117), shown to the right in blue, consists of <scene name='User:Udayan_Shevade/Sandbox1/Tagnterminal_jdomain_helices/1'>four alpha helices</scene> and <scene name='User:Udayan_Shevade/Sandbox1/Tagnterminal_jdomain_loop/1'>an extended loop</scene>. These contain the J domain and the LxCxE motif respectively <ref name='E'>PMID:140208</ref>. The large T antigen J domain is a functional homolog of the molecular chaperone DnaJ protein, namely HDJ-1 of E. coli<ref>PMID:9364917</ref> and human Hsp40<ref>PMID:232328</ref>. The alpha helices α2 and α3 that form the core of the domain are stabilized by the dominant hydrophobicity of conserved residue sidechains, e.g. Leu17, Phe41, Trp95. Mutations in these residues cause disruptive perturbations. Additionally, <scene name='User:Udayan_Shevade/Sandbox1/Tagnterminal_jdomain_hbonds/1'>hydrogen bonds</scene> further stabilize the core. Residues <scene name='User:Udayan_Shevade/Sandbox1/Tagnterminal_jdomain_hpd/1'>His42, Pro43 and Asp44</scene> of Loop 2 are conserved across the J domain family<ref name='E'/> and are crucial in recognizing hsc70, a factor of Rb inactivation. However, though such similarity with homologs exists, there are structural differences. These include residues 68-78 of Loop 3, which form hydrogen bonds with the retinoblastoma pocket and stabilize the J domain internally; and 91-102 of helix α4, of which Asn96 and Glu100 form hydrogen bonds with Lys765 and Gln762 from the Rb pocket.<br /> <br /> The The LxCxE motif is accommodated by a groove in the Rb pocket and accounts for two-thirds of the total buried surface area in the interaction. A number of <scene name='User:Udayan_Shevade/Sandbox1/Tagnterminal_jdomain_loophbond/1'>hydrogen bonds</scene> occur along the loop. Furthermore, the end contains a <scene name='User:Udayan_Shevade/Sandbox1/Tagnterminal_loopacidicseq/1'>conserved acidic sequence</scene>. It is proposed that this region interacts with a cluster of lysine residues near the LxCxE binding site of Rb<ref>PMID:9495340</ref>. Kinase-mediated phosphorylation of Ser111 and Ser112 might then induce a conformational change in the loop which allows these interactions to occur more favorably.<br /> <br /> Both large T antigen and E2F are able to complex with the Rb pocket simultaneously, suggesting their respective sites are different. So binding is not competitive. Thus to resolve the question of how large T antigen mediates E2F release from Rb, its similarity to homologs is considered. DnaJ serves not only to aid in folding proteins, but also to disassemble complexes. As such, it is proposed [http://www.ncbi.nlm.nih.gov/core/lw/2.0/html/tileshop_pmc/tileshop_pmc_inline.html?title=An%20external%20file%20that%20holds%20a%20picture%2C%20illustration%2C%20etc.%0AObject%20name%20is%20cde030f5.jpg%20%5BObject%20name%20is%20cde030f5.jpg%5D&p=PMC3&id=140208_cde030f5.jpg the large T antigen J domain may recruit hsc70, which then dissociates the EF2-Rb complex]<ref name='E'/>. <scene name='User:Udayan_Shevade/Sandbox1/Tagnterminal_reload/1'>Reload molecule</scene>.<br /> <br /> <br /> </structuresection><br /> <br /> == 3D structures of large T antigen==<br /> <br /> [[1faf]] – LTA N terminal – murine polyomavirus – NMR<BR /><br /> [[1n25]], [[1svo]] – SVLTA helicase domain – SV40<br /><br /> [[2fuf]] - SVLTA DNA-binding domain<br /><br /> [[1tbd]] - SVLTA DNA-binding domain - NMR<BR /><br /> [[2ipr]], [[2itj]], [[2if9]], [[3qn2]] - SVLTA origin-binding domain<br /> <br /> ===Large T antigen complex with DNA===<br /> <br /> [[2itl]], [[2ntc]], [[3qk2]] - SVLTA origin-binding domain + DNA<br /><br /> [[3qfq]] - LTA origin-binding domain + DNA – Merkel cell polyomavirus<br /><br /> [[1svl]] - SVLTA helicase domain + ADP<br /><br /> [[1svm]] - SVLTA helicase domain + ATP<br /> <br /> ===Large T antigen complex with protein===<br /> <br /> [[1z1d]] – SVLTA origin-binding domain + replication protein A32 C terminal<br /><br /> [[2h1l]] - SVLTA helicase domain + p53 DNA-binding domain<br /><br /> [[1gh6]] – SVLTA + retinoblastoma protein <br /> <br /> <br /> ===Large T antigen peptide complex with protein===<br /> <br /> [[1bk6]], [[1ejl]], [[1q1s]], [[1q1t]] – SVLTA peptide + karyopherin α<br /> <br /> <br /> <br /> == References ==<br /> {{reflist}}<br /> [[Category:Topic Page]]</div>

Udayan Shevade https://proteopedia.org/index.php?title=User:Udayan_Shevade/Sandbox1&diff=1393672 User:Udayan Shevade/Sandbox1 2012-05-20T17:40:39Z

<p>Udayan Shevade: /* Introduction */</p> <hr /> <div>= SV40 Large T Antigen =<br /> <br /> === Introduction ===<br /> <br /> The '''SV40 large tumor antigen''' is a multifunctional regulatory protein encoded by Simian Virus 40. It is classified under the AAA+ family of helicases <ref name="A">PMID:8946857</ref>. 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.<br /> <br /> === Structure and Function ===<br /> 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 <ref name="B">PMID:15454080</ref>.<br /> <br /> <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'><br /> ===== The Origin Binding Domain =====<br /> 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'>Phe183 and Ser185</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 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, Arg154, Thr155 from the A1 motif</scene>; <scene name='User:Udayan_Shevade/Sandbox1/Obd_203_204/1'>His203, Arg204 from the B2 motif</scene>; as well as <scene name='User:Udayan_Shevade/Sandbox1/Obd_201_202/1'>His201 andArg 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>. <br /> [[Image:Tagobd_dna_interactions.jpg|200px|left|thumb]]<br /> 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><br /> <br /> {{STRUCTURE_1svm| PDB=1svm | SCENE= }}<br /> <br /> ===== Helicase =====<br /> The <scene name='User:Udayan_Shevade/Sandbox1/Taghelicase_aaa_monomer/1'>helicase monomer</scene> 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 [http://www.sciencedirect.com/cache/MiamiImageURL/1-s2.0-S0092867404008906-gr3_lrg.jpg/0?wchp=dGLbVlV-zSkWA transitions in conformation] between these states enable the unwinding of viral dsDNA. There are both cis- and trans-monomer interactions involving ATP. <br /> <br /> <scene name='User:Udayan_Shevade/Sandbox1/Helicase_cis_residues/2'>''Cis''-residues</scene> Lys432, Thr433 and Thr434 of the P loop interact closely with the triphosphate groups, and Asp474 and Asn529 form H bonds with ATP on the same residue. Among these, Ilu428, Thr433 and Asp474 adopt different conformations in the ADP-bound state. In the Nt-free state, Ilu428 and Thr434 are turned even further and sterically disallow the presence of ADP.<br /> <br /> <scene name='User:Udayan_Shevade/Sandbox1/Helicase_atp_water/1'>A water molecule</scene> near the ATP is present for stability and nucleophilic attack during hydrolysis. <br /> <br /> <scene name='User:Udayan_Shevade/Sandbox1/Helicase_trans_residues/1'>Six ''trans''-residues</scene>, of which Lys418 and Lys419 stabilize ATP hydrolysis, interact with ATP on adjacent monomers, important in producing conformational changes. <br /> <br /> These rearrangements affect the position of <scene name='User:Udayan_Shevade/Sandbox1/Taghelicase_betahairpin/1'>the "β hairpin,"</scene> a positively-charged structure that protrudes into the central channel. ''Trans''-residues Arg498, Asp499 and Asp502 are located at the base of the hairpin, lending a lever-like functionality. The [http://www.sciencedirect.com/cache/MiamiImageURL/1-s2.0-S0092867404008906-gr7_lrg.jpg/0?wchp=dGLbVlk-zSkWb motion of the β hairpin] unwinds the DNA through the central channel <ref name='D'>PMID:15454080</ref>.<br /> [[Image:1SVM_L_O.jpg|500px|left|thumb]]<br /> <br /> <br /> <Structuresection load='1gh6' side='right' caption='Large T antigen complexed with retinoblastoma pocket' size='345'><br /> <br /> ===== J domain and LxCxE motif =====<br /> In the transformation of the host cell, retinoblastoma, a tumor suppressor, is inactivated via both the N-terminal J domain and the LxCxE motif. The N-terminal region (residues 7-117), shown to the right in blue, consists of <scene name='User:Udayan_Shevade/Sandbox1/Tagnterminal_jdomain_helices/1'>four alpha helices</scene> and <scene name='User:Udayan_Shevade/Sandbox1/Tagnterminal_jdomain_loop/1'>an extended loop</scene>. These contain the J domain and the LxCxE motif respectively <ref name='E'>PMID:140208</ref>. The large T antigen J domain is a functional homolog of the molecular chaperone DnaJ protein, namely HDJ-1 of E. coli<ref>PMID:9364917</ref> and human Hsp40<ref>PMID:232328</ref>. The alpha helices α2 and α3 that form the core of the domain are stabilized by the dominant hydrophobicity of conserved residue sidechains, e.g. Leu17, Phe41, Trp95. Mutations in these residues cause disruptive perturbations. Additionally, <scene name='User:Udayan_Shevade/Sandbox1/Tagnterminal_jdomain_hbonds/1'>hydrogen bonds</scene> further stabilize the core. Residues <scene name='User:Udayan_Shevade/Sandbox1/Tagnterminal_jdomain_hpd/1'>His42, Pro43 and Asp44</scene> of Loop 2 are conserved across the J domain family<ref name='E'/> and are crucial in recognizing hsc70, a factor of Rb inactivation. However, though such similarity with homologs exists, there are structural differences. These include residues 68-78 of Loop 3, which form hydrogen bonds with the retinoblastoma pocket and stabilize the J domain internally; and 91-102 of helix α4, of which Asn96 and Glu100 form hydrogen bonds with Lys765 and Gln762 from the Rb pocket.<br /> <br /> The The LxCxE motif is accommodated by a groove in the Rb pocket and accounts for two-thirds of the total buried surface area in the interaction. A number of <scene name='User:Udayan_Shevade/Sandbox1/Tagnterminal_jdomain_loophbond/1'>hydrogen bonds</scene> occur along the loop. Furthermore, the end contains a <scene name='User:Udayan_Shevade/Sandbox1/Tagnterminal_loopacidicseq/1'>conserved acidic sequence</scene>. It is proposed that this region interacts with a cluster of lysine residues near the LxCxE binding site of Rb<ref>PMID:9495340</ref>. Kinase-mediated phosphorylation of Ser111 and Ser112 might then induce a conformational change in the loop which allows these interactions to occur more favorably.<br /> <br /> Both large T antigen and E2F are able to complex with the Rb pocket simultaneously, suggesting their respective sites are different. So binding is not competitive. Thus to resolve the question of how large T antigen mediates E2F release from Rb, its similarity to homologs is considered. DnaJ serves not only to aid in folding proteins, but also to disassemble complexes. As such, it is proposed [http://www.ncbi.nlm.nih.gov/core/lw/2.0/html/tileshop_pmc/tileshop_pmc_inline.html?title=An%20external%20file%20that%20holds%20a%20picture%2C%20illustration%2C%20etc.%0AObject%20name%20is%20cde030f5.jpg%20%5BObject%20name%20is%20cde030f5.jpg%5D&p=PMC3&id=140208_cde030f5.jpg the large T antigen J domain may recruit hsc70, which then dissociates the EF2-Rb complex]<ref name='E'/>. <scene name='User:Udayan_Shevade/Sandbox1/Tagnterminal_reload/1'>Reload molecule</scene>.<br /> <br /> <br /> </structuresection><br /> <br /> ==== References ====<br /> {{reflist}}</div>

Udayan Shevade https://proteopedia.org/index.php?title=Large_T_Antigen&diff=1317837 Large T Antigen 2011-11-15T23:43:51Z

<p>Udayan Shevade: </p> <hr /> <div>=== Introduction ===<br /> <br /> The '''SV40 large tumor antigen''' is a multifunctional regulatory protein encoded by Simian Virus 40. It is classified under the AAA+ family of helicases <ref name="A">PMID:8946857</ref>. 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.<br /> <br /> <br /> === Structure and Function ===<br /> 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 <ref name="B">PMID:15454080</ref>.<br /> <br /> <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'><br /> ===== The Origin Binding Domain =====<br /> 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'>Phe183 and Ser185</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 is formed, large enough for dsDNA, carrying positive charge. A monomer along this pore 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, Arg154, Thr155 from the A1 motif</scene>; <scene name='User:Udayan_Shevade/Sandbox1/Obd_203_204/1'>His203, Arg204 from the B2 motif</scene>; as well as <scene name='User:Udayan_Shevade/Sandbox1/Obd_201_202/1'>His201 andArg 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>. <br /> [[Image:Tagobd_dna_interactions.jpg|200px|left|thumb]]<br /> 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><br /> <br /> {{STRUCTURE_1svm| PDB=1svm | SCENE= }}<br /> <br /> ===== Helicase =====<br /> The <scene name='User:Udayan_Shevade/Sandbox1/Taghelicase_aaa_monomer/1'>helicase monomer</scene> 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 [http://www.sciencedirect.com/cache/MiamiImageURL/1-s2.0-S0092867404008906-gr3_lrg.jpg/0?wchp=dGLbVlV-zSkWA transitions in conformation] between these states enable the unwinding of viral dsDNA. There are both cis- and trans-monomer interactions involving ATP. <br /> <br /> <scene name='User:Udayan_Shevade/Sandbox1/Helicase_cis_residues/2'>''Cis''-residues</scene> Lys432, Thr433 and Thr434 of the P loop interact closely with the triphosphate groups, and Asp474 and Asn529 form H bonds with ATP on the same residue. Among these, Ilu428, Thr433 and Asp474 adopt different conformations in the ADP-bound state. In the Nt-free state, Ilu428 and Thr434 are turned even further and sterically disallow the presence of ADP.<br /> <br /> <scene name='User:Udayan_Shevade/Sandbox1/Helicase_atp_water/1'>A water molecule</scene> near the ATP is present for stability and nucleophilic attack during hydrolysis. <br /> <br /> <scene name='User:Udayan_Shevade/Sandbox1/Helicase_trans_residues/1'>Six ''trans''-residues</scene>, of which Lys418 and Lys419 stabilize ATP hydrolysis, interact with ATP on adjacent monomers, important in producing conformational changes. <br /> <br /> These rearrangements affect the position of <scene name='User:Udayan_Shevade/Sandbox1/Taghelicase_betahairpin/1'>the "β hairpin,"</scene> a positively-charged structure that protrudes into the central channel. ''Trans''-residues Arg498, Asp499 and Asp502 are located at the base of the hairpin, lending a lever-like functionality. The [http://www.sciencedirect.com/cache/MiamiImageURL/1-s2.0-S0092867404008906-gr7_lrg.jpg/0?wchp=dGLbVlk-zSkWb motion of the β hairpin] unwinds the DNA through the central channel <ref name='D'>PMID:15454080</ref>.<br /> [[Image:1SVM_L_O.jpg|500px|left|thumb]]<br /> <br /> The helicase domain is also implicated in binding to p53, a transcription factor vital in tumor suppression. Binding of helicase inhibits the functional tetramerization of p53 on DNA<ref>PMID:1560412</ref>.<br /> <br /> <br /> <Structuresection load='1gh6' side='right' caption='Large T antigen complexed with retinoblastoma pocket' size='345'><br /> <br /> ===== J domain and LxCxE motif =====<br /> In the transformation of the host cell, retinoblastoma, a tumor suppressor, is inactivated via both the N-terminal J domain and the LxCxE motif. The N-terminal region (residues 7-117), shown to the right in blue, consists of <scene name='User:Udayan_Shevade/Sandbox1/Tagnterminal_jdomain_helices/1'>four alpha helices</scene> and <scene name='User:Udayan_Shevade/Sandbox1/Tagnterminal_jdomain_loop/1'>an extended loop</scene>. These contain the J domain and the LxCxE motif respectively <ref name='E'>PMID:140208</ref>. The large T antigen J domain is a functional homolog of the molecular chaperone DnaJ protein, namely HDJ-1 of E. coli<ref>PMID:9364917</ref> and human Hsp40<ref>PMID:232328</ref>. The alpha helices α2 and α3 that form the core of the domain are stabilized by the dominant hydrophobicity of conserved residue sidechains, e.g. Leu17, Phe41, Trp95. Mutations in these residues cause disruptive perturbations. Additionally, <scene name='User:Udayan_Shevade/Sandbox1/Tagnterminal_jdomain_hbonds/1'>hydrogen bonds</scene> further stabilize the core. Residues <scene name='User:Udayan_Shevade/Sandbox1/Tagnterminal_jdomain_hpd/1'>His42, Pro43 and Asp44</scene> of Loop 2 are conserved across the J domain family<ref name='E'/> and are crucial in recognizing hsc70, a factor of Rb inactivation. However, though such similarity with homologs exists, there are structural differences. These include residues 68-78 of Loop 3, which form hydrogen bonds with the retinoblastoma pocket and stabilize the J domain internally; and 91-102 of helix α4, of which Asn96 and Glu100 form hydrogen bonds with Lys765 and Gln762 from the Rb pocket.<br /> <br /> The The LxCxE motif is accommodated by a groove in the Rb pocket and accounts for two-thirds of the total buried surface area in the interaction. A number of <scene name='User:Udayan_Shevade/Sandbox1/Tagnterminal_jdomain_loophbond/1'>hydrogen bonds</scene> occur along the loop. Furthermore, the end contains a <scene name='User:Udayan_Shevade/Sandbox1/Tagnterminal_loopacidicseq/1'>conserved acidic sequence</scene>. It is proposed that this region interacts with a cluster of lysine residues near the LxCxE binding site of Rb<ref>PMID:9495340</ref>. Kinase-mediated phosphorylation of Ser111 and Ser112 might then induce a conformational change in the loop which allows these interactions to occur more favorably.<br /> <br /> Both large T antigen and E2F are able to complex with the Rb pocket simultaneously, suggesting their respective sites are different. So binding is not competitive. Thus to resolve the question of how large T antigen mediates E2F release from Rb, its similarity to homologs is considered. DnaJ serves not only to aid in folding proteins, but also to disassemble complexes. As such, it is proposed [http://www.ncbi.nlm.nih.gov/core/lw/2.0/html/tileshop_pmc/tileshop_pmc_inline.html?title=An%20external%20file%20that%20holds%20a%20picture%2C%20illustration%2C%20etc.%0AObject%20name%20is%20cde030f5.jpg%20%5BObject%20name%20is%20cde030f5.jpg%5D&p=PMC3&id=140208_cde030f5.jpg the large T antigen J domain may recruit hsc70, which then dissociates the EF2-Rb complex]<ref name='E'/>. <scene name='User:Udayan_Shevade/Sandbox1/Tagnterminal_reload/1'>Reload molecule</scene>.<br /> <br /> <br /> </structuresection><br /> <br /> === Structures ===<br /> <br /> [[2ntc]] - Co-crystal structure of origin binding domain and DNA <br /><br /> [[1z1d]] - Structural model for interaction between large T antigen obd and RPA32 <br /><br /> [[2nl8]] - Co-crystal structure of obd and nonspecific palindromic oligonucleotide<br /><br /> <br /> [[1svo]] - Unbound helicase domain <br /><br /> [[1svl]] - Co-crystal structure of helicase and ADP <br /><br /> <br /> [[2h1l]] - Complex of large T antigen and tumor suppressor p53 <br /><br /> <br /> === References ===<br /> {{reflist}}</div>

Udayan Shevade https://proteopedia.org/index.php?title=Large_T_Antigen&diff=1317836 Large T Antigen 2011-11-15T23:35:15Z

<p>Udayan Shevade: </p> <hr /> <div>=== Introduction ===<br /> <br /> The '''SV40 large tumor antigen''' is a multifunctional regulatory protein encoded by Simian Virus 40. It is classified under the AAA+ family of helicases <ref name="A">PMID:8946857</ref>. 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.<br /> <br /> <br /> === Structure and Function ===<br /> 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 <ref name="B">PMID:15454080</ref>.<br /> <br /> <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'><br /> ===== The Origin Binding Domain =====<br /> 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'>Phe183 and Ser185</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 is formed, large enough for dsDNA, carrying positive charge. A monomer along this pore 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, Arg154, Thr155 from the A1 motif</scene>; <scene name='User:Udayan_Shevade/Sandbox1/Obd_203_204/1'>His203, Arg204 from the B2 motif</scene>; as well as <scene name='User:Udayan_Shevade/Sandbox1/Obd_201_202/1'>His201 andArg 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>. <br /> [[Image:Tagobd_dna_interactions.jpg|200px|left|thumb]]<br /> 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><br /> <br /> {{STRUCTURE_1svm| PDB=1svm | SCENE= }}<br /> <br /> ===== Helicase =====<br /> The <scene name='User:Udayan_Shevade/Sandbox1/Taghelicase_aaa_monomer/1'>helicase monomer</scene> 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 [http://www.sciencedirect.com/cache/MiamiImageURL/1-s2.0-S0092867404008906-gr3_lrg.jpg/0?wchp=dGLbVlV-zSkWA transitions in conformation] between these states enable the unwinding of viral dsDNA. There are both cis- and trans-monomer interactions involving ATP. <br /> <br /> <scene name='User:Udayan_Shevade/Sandbox1/Helicase_cis_residues/2'>''Cis''-residues</scene> Lys432, Thr433 and Thr434 of the P loop interact closely with the triphosphate groups, and Asp474 and Asn529 form H bonds with ATP on the same residue. Among these, Ilu428, Thr433 and Asp474 adopt different conformations in the ADP-bound state. In the Nt-free state, Ilu428 and Thr434 are turned even further and sterically disallow the presence of ADP.<br /> <br /> <scene name='User:Udayan_Shevade/Sandbox1/Helicase_atp_water/1'>A water molecule</scene> near the ATP is present for stability and nucleophilic attack during hydrolysis. <br /> <br /> <scene name='User:Udayan_Shevade/Sandbox1/Helicase_trans_residues/1'>Six ''trans''-residues</scene>, of which Lys418 and Lys419 stabilize ATP hydrolysis, interact with ATP on adjacent monomers, important in producing conformational changes. <br /> <br /> These rearrangements affect the position of <scene name='User:Udayan_Shevade/Sandbox1/Taghelicase_betahairpin/1'>the "β hairpin,"</scene> a positively-charged structure that protrudes into the central channel. ''Trans''-residues Arg498, Asp499 and Asp502 are located at the base of the hairpin, lending a lever-like functionality. The [http://www.sciencedirect.com/cache/MiamiImageURL/1-s2.0-S0092867404008906-gr7_lrg.jpg/0?wchp=dGLbVlk-zSkWb motion of the β hairpin] unwinds the DNA through the central channel <ref name='D'>PMID:15454080</ref>.<br /> [[Image:1SVM_L_O.jpg|500px|left|thumb]]<br /> <br /> <br /> <Structuresection load='1gh6' side='right' caption='Large T antigen complexed with retinoblastoma pocket' size='345'><br /> <br /> ===== J domain and LxCxE motif =====<br /> In the transformation of the host cell, retinoblastoma, a tumor suppressor, is inactivated via both the N-terminal J domain and the LxCxE motif. The N-terminal region (residues 7-117), shown to the right in blue, consists of <scene name='User:Udayan_Shevade/Sandbox1/Tagnterminal_jdomain_helices/1'>four alpha helices</scene> and <scene name='User:Udayan_Shevade/Sandbox1/Tagnterminal_jdomain_loop/1'>an extended loop</scene>. These contain the J domain and the LxCxE motif respectively <ref name='E'>PMID:140208</ref>. The large T antigen J domain is a functional homolog of the molecular chaperone DnaJ protein, namely HDJ-1 of E. coli<ref>PMID:9364917</ref> and human Hsp40<ref>PMID:232328</ref>. The alpha helices α2 and α3 that form the core of the domain are stabilized by the dominant hydrophobicity of conserved residue sidechains, e.g. Leu17, Phe41, Trp95. Mutations in these residues cause disruptive perturbations. Additionally, <scene name='User:Udayan_Shevade/Sandbox1/Tagnterminal_jdomain_hbonds/1'>hydrogen bonds</scene> further stabilize the core. Residues <scene name='User:Udayan_Shevade/Sandbox1/Tagnterminal_jdomain_hpd/1'>His42, Pro43 and Asp44</scene> of Loop 2 are conserved across the J domain family<ref name='E'/> and are crucial in recognizing hsc70, a factor of Rb inactivation. However, though such similarity with homologs exists, there are structural differences. These include residues 68-78 of Loop 3, which form hydrogen bonds with the retinoblastoma pocket and stabilize the J domain internally; and 91-102 of helix α4, of which Asn96 and Glu100 form hydrogen bonds with Lys765 and Gln762 from the Rb pocket.<br /> <br /> The The LxCxE motif is accommodated by a groove in the Rb pocket and accounts for two-thirds of the total buried surface area in the interaction. A number of <scene name='User:Udayan_Shevade/Sandbox1/Tagnterminal_jdomain_loophbond/1'>hydrogen bonds</scene> occur along the loop. Furthermore, the end contains a <scene name='User:Udayan_Shevade/Sandbox1/Tagnterminal_loopacidicseq/1'>conserved acidic sequence</scene>. It is proposed that this region interacts with a cluster of lysine residues near the LxCxE binding site of Rb<ref>PMID:9495340</ref>. Kinase-mediated phosphorylation of Ser111 and Ser112 might then induce a conformational change in the loop which allows these interactions to occur more favorably.<br /> <br /> Both large T antigen and E2F are able to complex with the Rb pocket simultaneously, suggesting their respective sites are different. So binding is not competitive. Thus to resolve the question of how large T antigen mediates E2F release from Rb, its similarity to homologs is considered. DnaJ serves not only to aid in folding proteins, but also to disassemble complexes. As such, it is proposed [http://www.ncbi.nlm.nih.gov/core/lw/2.0/html/tileshop_pmc/tileshop_pmc_inline.html?title=An%20external%20file%20that%20holds%20a%20picture%2C%20illustration%2C%20etc.%0AObject%20name%20is%20cde030f5.jpg%20%5BObject%20name%20is%20cde030f5.jpg%5D&p=PMC3&id=140208_cde030f5.jpg the large T antigen J domain may recruit hsc70, which then dissociates the EF2-Rb complex]<ref name='E'/>. <scene name='User:Udayan_Shevade/Sandbox1/Tagnterminal_reload/1'>Reload molecule</scene>.<br /> <br /> <br /> </structuresection><br /> <br /> === Structures ===<br /> <br /> [[2ntc]] - Co-crystal structure of origin binding domain and DNA <br /><br /> [[1z1d]] - Structural model for interaction between large T antigen obd and RPA32 <br /><br /> [[2nl8]] - Co-crystal structure of obd and nonspecific palindromic oligonucleotide<br /><br /> <br /> [[1svo]] - Unbound helicase domain <br /><br /> [[1svl]] - Co-crystal structure of helicase and ADP <br /><br /> <br /> [[2h1l]] - Complex of large T antigen and tumor suppressor p53 <br /><br /> <br /> === References ===<br /> {{reflist}}</div>

Udayan Shevade https://proteopedia.org/index.php?title=Large_T_Antigen&diff=1317834 Large T Antigen 2011-11-15T23:28:51Z

<p>Udayan Shevade: </p> <hr /> <div>=== Introduction ===<br /> <br /> The '''SV40 large tumor antigen''' is a multifunctional regulatory protein encoded by Simian Virus 40. It is classified under the AAA+ family of helicases <ref name="A">PMID:8946857</ref>. 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.<br /> <br /> <br /> === Structure and Function ===<br /> 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 <ref name="B">PMID:15454080</ref>.<br /> <br /> <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'><br /> ===== The Origin Binding Domain =====<br /> 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'>Phe183 and Ser185</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 is formed, large enough for dsDNA, carrying positive charge. A monomer along this pore 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, Arg154, Thr155 from the A1 motif</scene>; <scene name='User:Udayan_Shevade/Sandbox1/Obd_203_204/1'>His203, Arg204 from the B2 motif</scene>; as well as <scene name='User:Udayan_Shevade/Sandbox1/Obd_201_202/1'>His201 andArg 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>. <br /> [[Image:Tagobd_dna_interactions.jpg|200px|left|thumb]]<br /> 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><br /> <br /> {{STRUCTURE_1svm| PDB=1svm | SCENE= }}<br /> <br /> ===== Helicase =====<br /> The <scene name='User:Udayan_Shevade/Sandbox1/Taghelicase_aaa_monomer/1'>helicase monomer</scene> 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 [http://www.sciencedirect.com/cache/MiamiImageURL/1-s2.0-S0092867404008906-gr3_lrg.jpg/0?wchp=dGLbVlV-zSkWA transitions in conformation] between these states enable the unwinding of viral dsDNA. There are both cis- and trans-monomer interactions involving ATP. <br /> <br /> <scene name='User:Udayan_Shevade/Sandbox1/Helicase_cis_residues/2'>''Cis''-residues</scene> Lys432, Thr433 and Thr434 of the P loop interact closely with the triphosphate groups, and Asp474 and Asn529 form H bonds with ATP on the same residue. Among these, Ilu428, Thr433 and Asp474 adopt different conformations in the ADP-bound state. In the Nt-free state, Ilu428 and Thr434 are turned even further and sterically disallow the presence of ADP.<br /> <br /> <scene name='User:Udayan_Shevade/Sandbox1/Helicase_atp_water/1'>A water molecule</scene> near the ATP is present for stability and nucleophilic attack during hydrolysis. <br /> <br /> <scene name='User:Udayan_Shevade/Sandbox1/Helicase_trans_residues/1'>Six ''trans''-residues</scene>, of which Lys418 and Lys419 stabilize ATP hydrolysis, interact with ATP on adjacent monomers, important in producing conformational changes. <br /> <br /> These rearrangements affect the position of <scene name='User:Udayan_Shevade/Sandbox1/Taghelicase_betahairpin/1'>the "β hairpin,"</scene> a positively-charged structure that protrudes into the central channel. ''Trans''-residues Arg498, Asp499 and Asp502 are located at the base of the hairpin, lending a lever-like functionality. The [http://www.sciencedirect.com/cache/MiamiImageURL/1-s2.0-S0092867404008906-gr7_lrg.jpg/0?wchp=dGLbVlk-zSkWb motion of the β hairpin] unwinds the DNA through the central channel <ref name='D'>PMID:15454080</ref>.<br /> [[Image:1SVM_L_O.jpg|500px|left|thumb]]<br /> <br /> <br /> <Structuresection load='1gh6' side='right' caption='Large T antigen complexed with retinoblastoma pocket' size='345'><br /> <br /> ===== J domain and LxCxE motif =====<br /> In the transformation of the host cell, retinoblastoma, a tumor suppressor, is inactivated via both the N-terminal J domain and the LxCxE motif. The N-terminal region (residues 7-117), shown to the right in blue, consists of <scene name='User:Udayan_Shevade/Sandbox1/Tagnterminal_jdomain_helices/1'>four alpha helices</scene> and <scene name='User:Udayan_Shevade/Sandbox1/Tagnterminal_jdomain_loop/1'>an extended loop</scene>. These contain the J domain and the LxCxE motif respectively <ref name='E'>PMID:140208</ref>. The large T antigen J domain is a functional homolog of the molecular chaperone DnaJ protein, namely HDJ-1 of E. coli<ref>PMID:9364917</ref> and human Hsp40<ref>PMID:232328</ref>. The alpha helices α2 and α3 that form the core of the domain are stabilized by the dominant hydrophobicity of conserved residue sidechains, e.g. Leu17, Phe41, Trp95. Mutations in these residues cause disruptive perturbations. Additionally, <scene name='User:Udayan_Shevade/Sandbox1/Tagnterminal_jdomain_hbonds/1'>hydrogen bonds</scene> further stabilize the core. Residues <scene name='User:Udayan_Shevade/Sandbox1/Tagnterminal_jdomain_hpd/1'>His42, Pro43 and Asp44</scene> of Loop 2 are conserved across the J domain family<ref name='E'/> and are crucial in recognizing hsc70, a factor of Rb inactivation. However, though such similarity with homologs exists, there are structural differences. These include residues 68-78 of Loop 3, which form hydrogen bonds with the retinoblastoma pocket and stabilize the J domain internally; and 91-102 of helix α4, of which Asn96 and Glu100 form hydrogen bonds with Lys765 and Gln762 from the Rb pocket.<br /> <br /> The The LxCxE motif is accommodated by a groove in the Rb pocket and accounts for two-thirds of the total buried surface area in the interaction. A number of <scene name='User:Udayan_Shevade/Sandbox1/Tagnterminal_jdomain_loophbond/1'>hydrogen bonds</scene> occur along the loop. Furthermore, the end contains a <scene name='User:Udayan_Shevade/Sandbox1/Tagnterminal_loopacidicseq/1'>conserved acidic sequence</scene>. It is proposed that this region interacts with a cluster of lysine residues near the LxCxE binding site of Rb<ref>PMID:9495340</ref>. Kinase-mediated phosphorylation of Ser111 and Ser112 might then induce a conformational change in the loop which allows these interactions to occur more favorably.<br /> <br /> Both large T antigen and E2F are able to complex with the Rb pocket simultaneously, suggesting their respective sites are different. So binding is not competitive. Thus to resolve the question of how large T antigen mediates E2F release from Rb, its similarity to homologs is considered. DnaJ serves not only to aid in folding proteins, but also to disassemble complexes. As such, it is proposed [http://www.ncbi.nlm.nih.gov/core/lw/2.0/html/tileshop_pmc/tileshop_pmc_inline.html?title=An%20external%20file%20that%20holds%20a%20picture%2C%20illustration%2C%20etc.%0AObject%20name%20is%20cde030f5.jpg%20%5BObject%20name%20is%20cde030f5.jpg%5D&p=PMC3&id=140208_cde030f5.jpg the large T antigen J domain may recruit hsc70, which then dissociates the EF2-Rb complex]<ref name='E'/>. <scene name='User:Udayan_Shevade/Sandbox1/Tagnterminal_reload/1'>Reload molecule</scene>.<br /> <br /> <br /> </structuresection><br /> <br /> === Structures ===<br /> <br /> [[2NTC]] - Co-crystal structure of origin binding domain and DNA <br /><br /> [[1Z1D]] - Structural model for interaction between large T antigen obd and RPA32 <br /><br /> [[2NL8]] - Co-crystal structure of obd and nonspecific palindromic oligonucleotide<br /><br /> <br /> [[1SVO]] - Unbound helicase domain <br /><br /> [[1SVL]] - Co-crystal structure of helicase and ADP <br /><br /> <br /> [[2H1L]] - Complex of large T antigen and tumor suppressor p53 <br /><br /> <br /> === References ===<br /> {{reflist}}</div>

Udayan Shevade https://proteopedia.org/index.php?title=Large_T_Antigen&diff=1317784 Large T Antigen 2011-11-15T19:22:27Z

<p>Udayan Shevade: </p> <hr /> <div>=== Introduction ===<br /> <br /> The '''SV40 large tumor antigen''' is a multifunctional regulatory protein encoded by Simian Virus 40. It is classified under the AAA+ family of helicases <ref name="A">PMID:8946857</ref>. 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.<br /> <br /> <br /> === Structure and Function ===<br /> 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 <ref name="B">PMID:15454080</ref>.<br /> <br /> <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'><br /> ===== The Origin Binding Domain =====<br /> 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'>Phe183 and Ser185</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 is formed, large enough for dsDNA, carrying positive charge. A monomer along this pore 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, Arg154, Thr155 from the A1 motif</scene>; <scene name='User:Udayan_Shevade/Sandbox1/Obd_203_204/1'>His203, Arg204 from the B2 motif</scene>; as well as <scene name='User:Udayan_Shevade/Sandbox1/Obd_201_202/1'>His201 andArg 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>. <br /> [[Image:Tagobd_dna_interactions.jpg|200px|left|thumb]]<br /> 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><br /> <br /> {{STRUCTURE_1svm| PDB=1svm | SCENE= }}<br /> <br /> ===== Helicase =====<br /> The <scene name='User:Udayan_Shevade/Sandbox1/Taghelicase_aaa_monomer/1'>helicase monomer</scene> 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 [http://www.sciencedirect.com/cache/MiamiImageURL/1-s2.0-S0092867404008906-gr3_lrg.jpg/0?wchp=dGLbVlV-zSkWA transitions in conformation] between these states enable the unwinding of viral dsDNA. There are both cis- and trans-monomer interactions involving ATP. <br /> <br /> <scene name='User:Udayan_Shevade/Sandbox1/Helicase_cis_residues/2'>''Cis''-residues</scene> Lys432, Thr433 and Thr434 of the P loop interact closely with the triphosphate groups, and Asp474 and Asn529 form H bonds with ATP on the same residue. Among these, Ilu428, Thr433 and Asp474 adopt different conformations in the ADP-bound state. In the Nt-free state, Ilu428 and Thr434 are turned even further and sterically disallow the presence of ADP.<br /> <br /> <scene name='User:Udayan_Shevade/Sandbox1/Helicase_atp_water/1'>A water molecule</scene> near the ATP is present for stability and nucleophilic attack during hydrolysis. <br /> <br /> <scene name='User:Udayan_Shevade/Sandbox1/Helicase_trans_residues/1'>Six ''trans''-residues</scene>, of which Lys418 and Lys419 stabilize ATP hydrolysis, interact with ATP on adjacent monomers, important in producing conformational changes. <br /> <br /> These rearrangements affect the position of <scene name='User:Udayan_Shevade/Sandbox1/Taghelicase_betahairpin/1'>the "β hairpin,"</scene> a positively-charged structure that protrudes into the central channel. ''Trans''-residues Arg498, Asp499 and Asp502 are located at the base of the hairpin, lending a lever-like functionality. The [http://www.sciencedirect.com/cache/MiamiImageURL/1-s2.0-S0092867404008906-gr7_lrg.jpg/0?wchp=dGLbVlk-zSkWb motion of the β hairpin] unwinds the DNA through the central channel <ref name='D'>PMID:15454080</ref>.<br /> [[Image:1SVM_L_O.jpg|500px|left|thumb]]<br /> <br /> <br /> <Structuresection load='1gh6' side='right' caption='Large T antigen complexed with retinoblastoma pocket' size='345'><br /> <br /> ===== J domain and LxCxE motif =====<br /> In the transformation of the host cell, retinoblastoma, a tumor suppressor, is inactivated via both the N-terminal J domain and the LxCxE motif. The N-terminal region (residues 7-117), shown to the right in blue, consists of <scene name='User:Udayan_Shevade/Sandbox1/Tagnterminal_jdomain_helices/1'>four alpha helices</scene> and <scene name='User:Udayan_Shevade/Sandbox1/Tagnterminal_jdomain_loop/1'>an extended loop</scene>. These contain the J domain and the LxCxE motif respectively <ref name='E'>PMID:140208</ref>. The large T antigen J domain is a functional homolog of the molecular chaperone DnaJ protein, namely HDJ-1 of E. coli<ref>PMID:9364917</ref> and human Hsp40<ref>PMID:232328</ref>. The alpha helices α2 and α3 that form the core of the domain are stabilized by the dominant hydrophobicity of conserved residue sidechains, e.g. Leu17, Phe41, Trp95. Mutations in these residues cause disruptive perturbations. Additionally, <scene name='User:Udayan_Shevade/Sandbox1/Tagnterminal_jdomain_hbonds/1'>hydrogen bonds</scene> further stabilize the core. Residues <scene name='User:Udayan_Shevade/Sandbox1/Tagnterminal_jdomain_hpd/1'>His42, Pro43 and Asp44</scene> of Loop 2 are conserved across the J domain family<ref name='E'/> and are crucial in recognizing hsc70, a factor of Rb inactivation. However, though such similarity with homologs exists, there are structural differences. These include residues 68-78 of Loop 3, which form hydrogen bonds with the retinoblastoma pocket and stabilize the J domain internally; and 91-102 of helix α4, of which Asn96 and Glu100 form hydrogen bonds with Lys765 and Gln762 from the Rb pocket.<br /> <br /> The The LxCxE motif is accommodated by a groove in the Rb pocket and accounts for two-thirds of the total buried surface area in the interaction. A number of <scene name='User:Udayan_Shevade/Sandbox1/Tagnterminal_jdomain_loophbond/1'>hydrogen bonds</scene> occur along the loop. Furthermore, the end contains a <scene name='User:Udayan_Shevade/Sandbox1/Tagnterminal_loopacidicseq/1'>conserved acidic sequence</scene>. It is proposed that this region interacts with a cluster of lysine residues near the LxCxE binding site of Rb<ref>PMID:9495340</ref>. Kinase-mediated phosphorylation of Ser111 and Ser112 might then induce a conformational change in the loop which allows these interactions to occur more favorably.<br /> <br /> Both large T antigen and E2F are able to complex with the Rb pocket simultaneously, suggesting their respective sites are different. So binding is not competitive. Thus to resolve the question of how large T antigen mediates E2F release from Rb, its similarity to homologs is considered. DnaJ serves not only to aid in folding proteins, but also to disassemble complexes. As such, it is proposed [http://www.ncbi.nlm.nih.gov/core/lw/2.0/html/tileshop_pmc/tileshop_pmc_inline.html?title=An%20external%20file%20that%20holds%20a%20picture%2C%20illustration%2C%20etc.%0AObject%20name%20is%20cde030f5.jpg%20%5BObject%20name%20is%20cde030f5.jpg%5D&p=PMC3&id=140208_cde030f5.jpg the large T antigen J domain may recruit hsc70, which then dissociates the EF2-Rb complex]<ref name='E'/>. <scene name='User:Udayan_Shevade/Sandbox1/Tagnterminal_reload/1'>Reload molecule</scene>.<br /> <br /> <br /> </structuresection><br /> <br /> === 3D Structures ===<br /> <br /> [[1SVO]] - Crystal structure of unbound SV40 large T antigen<br /> [[1SVL]] - Co-crystal structure of unbound SV40 large T antigen and ADP<br /> [[1Z1D]] - Structural model for interaction between large T antigen obd and RPA32<br /> [[2H1L]] - Large T antigen complexed with tumor suppressor p53<br /> [[2ITL]]<br /> [[2NL8]]<br /> <br /> === References ===<br /> {{reflist}}</div>

Udayan Shevade https://proteopedia.org/index.php?title=Large_T_Antigen&diff=1317782 Large T Antigen 2011-11-15T19:14:11Z

<p>Udayan Shevade: </p> <hr /> <div>=== Introduction ===<br /> <br /> The '''SV40 large tumor antigen''' is a multifunctional regulatory protein encoded by Simian Virus 40. It is classified under the AAA+ family of helicases <ref name="A">PMID:8946857</ref>. 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.<br /> <br /> <br /> === Structure and Function ===<br /> 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 <ref name="B">PMID:15454080</ref>.<br /> <br /> <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'><br /> ===== The Origin Binding Domain =====<br /> 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'>Phe183 and Ser185</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 is formed, large enough for dsDNA, carrying positive charge. A monomer along this pore 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, Arg154, Thr155 from the A1 motif</scene>; <scene name='User:Udayan_Shevade/Sandbox1/Obd_203_204/1'>His203, Arg204 from the B2 motif</scene>; as well as <scene name='User:Udayan_Shevade/Sandbox1/Obd_201_202/1'>His201 andArg 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>. <br /> [[Image:Tagobd_dna_interactions.jpg|200px|left|thumb]]<br /> 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><br /> <br /> {{STRUCTURE_1svm| PDB=1svm | SCENE= }}<br /> <br /> ===== Helicase =====<br /> The <scene name='User:Udayan_Shevade/Sandbox1/Taghelicase_aaa_monomer/1'>helicase monomer</scene> 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 [http://www.sciencedirect.com/cache/MiamiImageURL/1-s2.0-S0092867404008906-gr3_lrg.jpg/0?wchp=dGLbVlV-zSkWA transitions in conformation] between these states enable the unwinding of viral dsDNA. There are both cis- and trans-monomer interactions involving ATP. <br /> <br /> <scene name='User:Udayan_Shevade/Sandbox1/Helicase_cis_residues/2'>''Cis''-residues</scene> Lys432, Thr433 and Thr434 of the P loop interact closely with the triphosphate groups, and Asp474 and Asn529 form H bonds with ATP on the same residue. Among these, Ilu428, Thr433 and Asp474 adopt different conformations in the ADP-bound state. In the Nt-free state, Ilu428 and Thr434 are turned even further and sterically disallow the presence of ADP.<br /> <br /> <scene name='User:Udayan_Shevade/Sandbox1/Helicase_atp_water/1'>A water molecule</scene> near the ATP is present for stability and nucleophilic attack during hydrolysis. <br /> <br /> <scene name='User:Udayan_Shevade/Sandbox1/Helicase_trans_residues/1'>Six ''trans''-residues</scene>, of which Lys418 and Lys419 stabilize ATP hydrolysis, interact with ATP on adjacent monomers, important in producing conformational changes. <br /> <br /> These rearrangements affect the position of <scene name='User:Udayan_Shevade/Sandbox1/Taghelicase_betahairpin/1'>the "β hairpin,"</scene> a positively-charged structure that protrudes into the central channel. ''Trans''-residues Arg498, Asp499 and Asp502 are located at the base of the hairpin, lending a lever-like functionality. The [http://www.sciencedirect.com/cache/MiamiImageURL/1-s2.0-S0092867404008906-gr7_lrg.jpg/0?wchp=dGLbVlk-zSkWb motion of the β hairpin] unwinds the DNA through the central channel <ref name='D'>PMID:15454080</ref>.<br /> [[Image:1SVM_L_O.jpg|500px|left|thumb]]<br /> <br /> <br /> <Structuresection load='1gh6' side='right' caption='Large T antigen complexed with retinoblastoma pocket' size='345'><br /> <br /> ===== J domain and LxCxE motif =====<br /> In the transformation of the host cell, retinoblastoma, a tumor suppressor, is inactivated via both the N-terminal J domain and the LxCxE motif. The N-terminal region (residues 7-117), shown to the right in blue, consists of <scene name='User:Udayan_Shevade/Sandbox1/Tagnterminal_jdomain_helices/1'>four alpha helices</scene> and <scene name='User:Udayan_Shevade/Sandbox1/Tagnterminal_jdomain_loop/1'>an extended loop</scene>. These contain the J domain and the LxCxE motif respectively <ref name='E'>PMID:140208</ref>. The large T antigen J domain is a functional homolog of the molecular chaperone DnaJ protein, namely HDJ-1 of E. coli<ref>PMID:9364917</ref> and human Hsp40<ref>PMID:232328</ref>. The alpha helices α2 and α3 that form the core of the domain are stabilized by the dominant hydrophobicity of conserved residue sidechains, e.g. Leu17, Phe41, Trp95. Mutations in these residues cause disruptive perturbations. Additionally, <scene name='User:Udayan_Shevade/Sandbox1/Tagnterminal_jdomain_hbonds/1'>hydrogen bonds</scene> further stabilize the core. Residues <scene name='User:Udayan_Shevade/Sandbox1/Tagnterminal_jdomain_hpd/1'>His42, Pro43 and Asp44</scene> of Loop 2 are conserved across the J domain family<ref name='E'/> and are crucial in recognizing hsc70, a factor of Rb inactivation. However, though such similarity with homologs exists, there are structural differences. These include residues 68-78 of Loop 3, which form hydrogen bonds with the retinoblastoma pocket and stabilize the J domain internally; and 91-102 of helix α4, of which Asn96 and Glu100 form hydrogen bonds with Lys765 and Gln762 from the Rb pocket.<br /> <br /> The The LxCxE motif is accommodated by a groove in the Rb pocket and accounts for two-thirds of the total buried surface area in the interaction. A number of <scene name='User:Udayan_Shevade/Sandbox1/Tagnterminal_jdomain_loophbond/1'>hydrogen bonds</scene> occur along the loop. Furthermore, the end contains a <scene name='User:Udayan_Shevade/Sandbox1/Tagnterminal_loopacidicseq/1'>conserved acidic sequence</scene>. It is proposed that this region interacts with a cluster of lysine residues near the LxCxE binding site of Rb<ref>PMID:9495340</ref>. Kinase-mediated phosphorylation of Ser111 and Ser112 might then induce a conformational change in the loop which allows these interactions to occur more favorably.<br /> <br /> Both large T antigen and E2F are able to complex with the Rb pocket simultaneously, suggesting their respective sites are different. So binding is not competitive. Thus to resolve the question of how large T antigen mediates E2F release from Rb, its similarity to homologs is considered. DnaJ serves not only to aid in folding proteins, but also to disassemble complexes. As such, it is proposed [http://www.ncbi.nlm.nih.gov/core/lw/2.0/html/tileshop_pmc/tileshop_pmc_inline.html?title=An%20external%20file%20that%20holds%20a%20picture%2C%20illustration%2C%20etc.%0AObject%20name%20is%20cde030f5.jpg%20%5BObject%20name%20is%20cde030f5.jpg%5D&p=PMC3&id=140208_cde030f5.jpg the large T antigen J domain may recruit hsc70, which then dissociates the EF2-Rb complex]<ref name='E'/>. <scene name='User:Udayan_Shevade/Sandbox1/Tagnterminal_reload/1'>Reload molecule</scene>.<br /> <br /> <br /> </structuresection><br /> <br /> === References ===<br /> {{reflist}}</div>

Udayan Shevade https://proteopedia.org/index.php?title=Large_T_Antigen&diff=1317767 Large T Antigen 2011-11-15T12:13:48Z

<p>Udayan Shevade: New page: === 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 <ref name="...</p> <hr /> <div>=== Introduction ===<br /> <br /> The '''SV40 large tumor antigen''' is a multifunctional regulatory protein encoded by Simian Virus 40. It is classified under the AAA+ family of helicases <ref name="A">PMID:8946857</ref>. 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.<br /> <br /> <br /> === Structure and Function ===<br /> 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 <ref name="B">PMID:15454080</ref>.<br /> <br /> <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'><br /> ===== The Origin Binding Domain =====<br /> 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'>Phe183 and Ser185</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 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, Arg154, Thr155 from the A1 motif</scene>; <scene name='User:Udayan_Shevade/Sandbox1/Obd_203_204/1'>His203, Arg204 from the B2 motif</scene>; as well as <scene name='User:Udayan_Shevade/Sandbox1/Obd_201_202/1'>His201 andArg 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>. <br /> [[Image:Tagobd_dna_interactions.jpg|200px|left|thumb]]<br /> 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><br /> <br /> {{STRUCTURE_1svm| PDB=1svm | SCENE= }}<br /> <br /> ===== Helicase =====<br /> The <scene name='User:Udayan_Shevade/Sandbox1/Taghelicase_aaa_monomer/1'>helicase monomer</scene> 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 [http://www.sciencedirect.com/cache/MiamiImageURL/1-s2.0-S0092867404008906-gr3_lrg.jpg/0?wchp=dGLbVlV-zSkWA transitions in conformation] between these states enable the unwinding of viral dsDNA. There are both cis- and trans-monomer interactions involving ATP. <br /> <br /> <scene name='User:Udayan_Shevade/Sandbox1/Helicase_cis_residues/2'>''Cis''-residues</scene> Lys432, Thr433 and Thr434 of the P loop interact closely with the triphosphate groups, and Asp474 and Asn529 form H bonds with ATP on the same residue. Among these, Ilu428, Thr433 and Asp474 adopt different conformations in the ADP-bound state. In the Nt-free state, Ilu428 and Thr434 are turned even further and sterically disallow the presence of ADP.<br /> <br /> <scene name='User:Udayan_Shevade/Sandbox1/Helicase_atp_water/1'>A water molecule</scene> near the ATP is present for stability and nucleophilic attack during hydrolysis. <br /> <br /> <scene name='User:Udayan_Shevade/Sandbox1/Helicase_trans_residues/1'>Six ''trans''-residues</scene>, of which Lys418 and Lys419 stabilize ATP hydrolysis, interact with ATP on adjacent monomers, important in producing conformational changes. <br /> <br /> These rearrangements affect the position of <scene name='User:Udayan_Shevade/Sandbox1/Taghelicase_betahairpin/1'>the "β hairpin,"</scene> a positively-charged structure that protrudes into the central channel. ''Trans''-residues Arg498, Asp499 and Asp502 are located at the base of the hairpin, lending a lever-like functionality. The [http://www.sciencedirect.com/cache/MiamiImageURL/1-s2.0-S0092867404008906-gr7_lrg.jpg/0?wchp=dGLbVlk-zSkWb motion of the β hairpin] unwinds the DNA through the central channel <ref name='D'>PMID:15454080</ref>.<br /> [[Image:1SVM_L_O.jpg|500px|left|thumb]]<br /> <br /> <br /> <Structuresection load='1gh6' side='right' caption='Large T antigen complexed with retinoblastoma pocket' size='345'><br /> <br /> ===== J domain and LxCxE motif =====<br /> In the transformation of the host cell, retinoblastoma, a tumor suppressor, is inactivated via both the N-terminal J domain and the LxCxE motif. The N-terminal region (residues 7-117), shown to the right in blue, consists of <scene name='User:Udayan_Shevade/Sandbox1/Tagnterminal_jdomain_helices/1'>four alpha helices</scene> and <scene name='User:Udayan_Shevade/Sandbox1/Tagnterminal_jdomain_loop/1'>an extended loop</scene>. These contain the J domain and the LxCxE motif respectively <ref name='E'>PMID:140208</ref>. The large T antigen J domain is a functional homolog of the molecular chaperone DnaJ protein, namely HDJ-1 of E. coli<ref>PMID:9364917</ref> and human Hsp40<ref>PMID:232328</ref>. The alpha helices α2 and α3 that form the core of the domain are stabilized by the dominant hydrophobicity of conserved residue sidechains, e.g. Leu17, Phe41, Trp95. Mutations in these residues cause disruptive perturbations. Additionally, <scene name='User:Udayan_Shevade/Sandbox1/Tagnterminal_jdomain_hbonds/1'>hydrogen bonds</scene> further stabilize the core. Residues <scene name='User:Udayan_Shevade/Sandbox1/Tagnterminal_jdomain_hpd/1'>His42, Pro43 and Asp44</scene> of Loop 2 are conserved across the J domain family<ref name='E'/> and are crucial in recognizing hsc70, a factor of Rb inactivation. However, though such similarity with homologs exists, there are structural differences. These include residues 68-78 of Loop 3, which form hydrogen bonds with the retinoblastoma pocket and stabilize the J domain internally; and 91-102 of helix α4, of which Asn96 and Glu100 form hydrogen bonds with Lys765 and Gln762 from the Rb pocket.<br /> <br /> The The LxCxE motif is accommodated by a groove in the Rb pocket and accounts for two-thirds of the total buried surface area in the interaction. A number of <scene name='User:Udayan_Shevade/Sandbox1/Tagnterminal_jdomain_loophbond/1'>hydrogen bonds</scene> occur along the loop. Furthermore, the end contains a <scene name='User:Udayan_Shevade/Sandbox1/Tagnterminal_loopacidicseq/1'>conserved acidic sequence</scene>. It is proposed that this region interacts with a cluster of lysine residues near the LxCxE binding site of Rb<ref>PMID:9495340</ref>. Kinase-mediated phosphorylation of Ser111 and Ser112 might then induce a conformational change in the loop which allows these interactions to occur more favorably.<br /> <br /> Both large T antigen and E2F are able to complex with the Rb pocket simultaneously, suggesting their respective sites are different. So binding is not competitive. Thus to resolve the question of how large T antigen mediates E2F release from Rb, its similarity to homologs is considered. DnaJ serves not only to aid in folding proteins, but also to disassemble complexes. As such, it is proposed [http://www.ncbi.nlm.nih.gov/core/lw/2.0/html/tileshop_pmc/tileshop_pmc_inline.html?title=An%20external%20file%20that%20holds%20a%20picture%2C%20illustration%2C%20etc.%0AObject%20name%20is%20cde030f5.jpg%20%5BObject%20name%20is%20cde030f5.jpg%5D&p=PMC3&id=140208_cde030f5.jpg the large T antigen J domain may recruit hsc70, which then dissociates the EF2-Rb complex]<ref name='E'/>. <scene name='User:Udayan_Shevade/Sandbox1/Tagnterminal_reload/1'>Reload molecule</scene>.<br /> <br /> <br /> </structuresection><br /> <br /> === References ===<br /> {{reflist}}</div>

Udayan Shevade https://proteopedia.org/index.php?title=User:Udayan_Shevade/Sandbox1&diff=1317766 User:Udayan Shevade/Sandbox1 2011-11-15T12:07:59Z

<p>Udayan Shevade: </p> <hr /> <div>= SV40 Large T Antigen =<br /> <br /> === Introduction ===<br /> <br /> The '''SV40 large tumor antigen''' is a multifunctional regulatory protein encoded by Simian Virus 40. It is classified under the AAA+ family of helicases <ref name="A">PMID:8946857</ref>. 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.<br /> <br /> <br /> === Structure and Function ===<br /> 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 <ref name="B">PMID:15454080</ref>.<br /> <br /> <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'><br /> ===== The Origin Binding Domain =====<br /> 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'>Phe183 and Ser185</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 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, Arg154, Thr155 from the A1 motif</scene>; <scene name='User:Udayan_Shevade/Sandbox1/Obd_203_204/1'>His203, Arg204 from the B2 motif</scene>; as well as <scene name='User:Udayan_Shevade/Sandbox1/Obd_201_202/1'>His201 andArg 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>. <br /> [[Image:Tagobd_dna_interactions.jpg|200px|left|thumb]]<br /> 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><br /> <br /> {{STRUCTURE_1svm| PDB=1svm | SCENE= }}<br /> <br /> ===== Helicase =====<br /> The <scene name='User:Udayan_Shevade/Sandbox1/Taghelicase_aaa_monomer/1'>helicase monomer</scene> 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 [http://www.sciencedirect.com/cache/MiamiImageURL/1-s2.0-S0092867404008906-gr3_lrg.jpg/0?wchp=dGLbVlV-zSkWA transitions in conformation] between these states enable the unwinding of viral dsDNA. There are both cis- and trans-monomer interactions involving ATP. <br /> <br /> <scene name='User:Udayan_Shevade/Sandbox1/Helicase_cis_residues/2'>''Cis''-residues</scene> Lys432, Thr433 and Thr434 of the P loop interact closely with the triphosphate groups, and Asp474 and Asn529 form H bonds with ATP on the same residue. Among these, Ilu428, Thr433 and Asp474 adopt different conformations in the ADP-bound state. In the Nt-free state, Ilu428 and Thr434 are turned even further and sterically disallow the presence of ADP.<br /> <br /> <scene name='User:Udayan_Shevade/Sandbox1/Helicase_atp_water/1'>A water molecule</scene> near the ATP is present for stability and nucleophilic attack during hydrolysis. <br /> <br /> <scene name='User:Udayan_Shevade/Sandbox1/Helicase_trans_residues/1'>Six ''trans''-residues</scene>, of which Lys418 and Lys419 stabilize ATP hydrolysis, interact with ATP on adjacent monomers, important in producing conformational changes. <br /> <br /> These rearrangements affect the position of <scene name='User:Udayan_Shevade/Sandbox1/Taghelicase_betahairpin/1'>the "β hairpin,"</scene> a positively-charged structure that protrudes into the central channel. ''Trans''-residues Arg498, Asp499 and Asp502 are located at the base of the hairpin, lending a lever-like functionality. The [http://www.sciencedirect.com/cache/MiamiImageURL/1-s2.0-S0092867404008906-gr7_lrg.jpg/0?wchp=dGLbVlk-zSkWb motion of the β hairpin] unwinds the DNA through the central channel <ref name='D'>PMID:15454080</ref>.<br /> [[Image:1SVM_L_O.jpg|500px|left|thumb]]<br /> <br /> <br /> <Structuresection load='1gh6' side='right' caption='Large T antigen complexed with retinoblastoma pocket' size='345'><br /> <br /> ===== J domain and LxCxE motif =====<br /> In the transformation of the host cell, retinoblastoma, a tumor suppressor, is inactivated via both the N-terminal J domain and the LxCxE motif. The N-terminal region (residues 7-117), shown to the right in blue, consists of <scene name='User:Udayan_Shevade/Sandbox1/Tagnterminal_jdomain_helices/1'>four alpha helices</scene> and <scene name='User:Udayan_Shevade/Sandbox1/Tagnterminal_jdomain_loop/1'>an extended loop</scene>. These contain the J domain and the LxCxE motif respectively <ref name='E'>PMID:140208</ref>. The large T antigen J domain is a functional homolog of the molecular chaperone DnaJ protein, namely HDJ-1 of E. coli<ref>PMID:9364917</ref> and human Hsp40<ref>PMID:232328</ref>. The alpha helices α2 and α3 that form the core of the domain are stabilized by the dominant hydrophobicity of conserved residue sidechains, e.g. Leu17, Phe41, Trp95. Mutations in these residues cause disruptive perturbations. Additionally, <scene name='User:Udayan_Shevade/Sandbox1/Tagnterminal_jdomain_hbonds/1'>hydrogen bonds</scene> further stabilize the core. Residues <scene name='User:Udayan_Shevade/Sandbox1/Tagnterminal_jdomain_hpd/1'>His42, Pro43 and Asp44</scene> of Loop 2 are conserved across the J domain family<ref name='E'/> and are crucial in recognizing hsc70, a factor of Rb inactivation. However, though such similarity with homologs exists, there are structural differences. These include residues 68-78 of Loop 3, which form hydrogen bonds with the retinoblastoma pocket and stabilize the J domain internally; and 91-102 of helix α4, of which Asn96 and Glu100 form hydrogen bonds with Lys765 and Gln762 from the Rb pocket.<br /> <br /> The The LxCxE motif is accommodated by a groove in the Rb pocket and accounts for two-thirds of the total buried surface area in the interaction. A number of <scene name='User:Udayan_Shevade/Sandbox1/Tagnterminal_jdomain_loophbond/1'>hydrogen bonds</scene> occur along the loop. Furthermore, the end contains a <scene name='User:Udayan_Shevade/Sandbox1/Tagnterminal_loopacidicseq/1'>conserved acidic sequence</scene>. It is proposed that this region interacts with a cluster of lysine residues near the LxCxE binding site of Rb<ref>PMID:9495340</ref>. Kinase-mediated phosphorylation of Ser111 and Ser112 might then induce a conformational change in the loop which allows these interactions to occur more favorably.<br /> <br /> Both large T antigen and E2F are able to complex with the Rb pocket simultaneously, suggesting their respective sites are different. So binding is not competitive. Thus to resolve the question of how large T antigen mediates E2F release from Rb, its similarity to homologs is considered. DnaJ serves not only to aid in folding proteins, but also to disassemble complexes. As such, it is proposed [http://www.ncbi.nlm.nih.gov/core/lw/2.0/html/tileshop_pmc/tileshop_pmc_inline.html?title=An%20external%20file%20that%20holds%20a%20picture%2C%20illustration%2C%20etc.%0AObject%20name%20is%20cde030f5.jpg%20%5BObject%20name%20is%20cde030f5.jpg%5D&p=PMC3&id=140208_cde030f5.jpg the large T antigen J domain may recruit hsc70, which then dissociates the EF2-Rb complex]<ref name='E'/>. <scene name='User:Udayan_Shevade/Sandbox1/Tagnterminal_reload/1'>Reload molecule</scene>.<br /> <br /> <br /> </structuresection><br /> <br /> ==== References ====<br /> {{reflist}}</div>

Udayan Shevade https://proteopedia.org/index.php?title=File:1SVM_L_O.jpg&diff=1317765 File:1SVM L O.jpg 2011-11-15T12:04:07Z

<p>Udayan Shevade: Three comparative images of ATP-bound 1SVM, ADP-bound 1SVL, and Nt-free 1SVO, showing a widening of the central pore.</p> <hr /> <div>Three comparative images of ATP-bound 1SVM, ADP-bound 1SVL, and Nt-free 1SVO, showing a widening of the central pore.</div>

Udayan Shevade https://proteopedia.org/index.php?title=User:Udayan_Shevade/Sandbox1&diff=1317764 User:Udayan Shevade/Sandbox1 2011-11-15T11:52:58Z

<p>Udayan Shevade: </p> <hr /> <div>= SV40 Large T Antigen =<br /> <br /> === Introduction ===<br /> <br /> The '''SV40 large tumor antigen''' is a multifunctional regulatory protein encoded by Simian Virus 40. It is classified under the AAA+ family of helicases <ref name="A">PMID:8946857</ref>. 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.<br /> <br /> <br /> === Structure and Function ===<br /> 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 <ref name="B">PMID:15454080</ref>.<br /> <br /> <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'><br /> ===== The Origin Binding Domain =====<br /> 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'>Phe183 and Ser185</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 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, Arg154, Thr155 from the A1 motif</scene>; <scene name='User:Udayan_Shevade/Sandbox1/Obd_203_204/1'>His203, Arg204 from the B2 motif</scene>; as well as <scene name='User:Udayan_Shevade/Sandbox1/Obd_201_202/1'>His201 andArg 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>. <br /> [[Image:Tagobd_dna_interactions.jpg|200px|left|thumb]]<br /> 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><br /> <br /> {{STRUCTURE_1svm| PDB=1svm | SCENE= }}<br /> <br /> ===== Helicase =====<br /> The <scene name='User:Udayan_Shevade/Sandbox1/Taghelicase_aaa_monomer/1'>helicase monomer</scene> 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 [http://www.sciencedirect.com/cache/MiamiImageURL/1-s2.0-S0092867404008906-gr3_lrg.jpg/0?wchp=dGLbVlV-zSkWA transitions in conformation] between these states enable the unwinding of viral dsDNA. There are both cis- and trans-monomer interactions involving ATP. <br /> <br /> <scene name='User:Udayan_Shevade/Sandbox1/Helicase_cis_residues/2'>''Cis''-residues</scene> Lys432, Thr433 and Thr434 of the P loop interact closely with the triphosphate groups, and Asp474 and Asn529 form H bonds with ATP on the same residue. Among these, Ilu428, Thr433 and Asp474 adopt different conformations in the ADP-bound state. In the Nt-free state, Ilu428 and Thr434 are turned even further and sterically disallow the presence of ADP.<br /> <br /> <scene name='User:Udayan_Shevade/Sandbox1/Helicase_atp_water/1'>A water molecule</scene> near the ATP is present for stability and nucleophilic attack during hydrolysis. <br /> <br /> <scene name='User:Udayan_Shevade/Sandbox1/Helicase_trans_residues/1'>Six ''trans''-residues</scene>, of which Lys418 and Lys419 stabilize ATP hydrolysis, interact with ATP on adjacent monomers, important in producing conformational changes. <br /> <br /> These rearrangements affect the position of <scene name='User:Udayan_Shevade/Sandbox1/Taghelicase_betahairpin/1'>the "β hairpin,"</scene> a positively-charged structure that protrudes into the central channel. ''Trans''-residues Arg498, Asp499 and Asp502 are located at the base of the hairpin, lending a lever-like functionality. The [http://www.sciencedirect.com/cache/MiamiImageURL/1-s2.0-S0092867404008906-gr7_lrg.jpg/0?wchp=dGLbVlk-zSkWb motion of the β hairpin] unwinds the DNA through the central channel <ref name='D'>PMID:15454080</ref>.<br /> <br /> <br /> <Structuresection load='1gh6' side='right' caption='Large T antigen complexed with retinoblastoma pocket' size='345'><br /> <br /> ===== J domain and LxCxE motif =====<br /> In the transformation of the host cell, retinoblastoma, a tumor suppressor, is inactivated via both the N-terminal J domain and the LxCxE motif. The N-terminal region (residues 7-117), shown to the right in blue, consists of <scene name='User:Udayan_Shevade/Sandbox1/Tagnterminal_jdomain_helices/1'>four alpha helices</scene> and <scene name='User:Udayan_Shevade/Sandbox1/Tagnterminal_jdomain_loop/1'>an extended loop</scene>. These contain the J domain and the LxCxE motif respectively <ref name='E'>PMID:140208</ref>. The large T antigen J domain is a functional homolog of the molecular chaperone DnaJ protein, namely HDJ-1 of E. coli<ref>PMID:9364917</ref> and human Hsp40<ref>PMID:232328</ref>. The alpha helices α2 and α3 that form the core of the domain are stabilized by the dominant hydrophobicity of conserved residue sidechains, e.g. Leu17, Phe41, Trp95. Mutations in these residues cause disruptive perturbations. Additionally, <scene name='User:Udayan_Shevade/Sandbox1/Tagnterminal_jdomain_hbonds/1'>hydrogen bonds</scene> further stabilize the core. Residues <scene name='User:Udayan_Shevade/Sandbox1/Tagnterminal_jdomain_hpd/1'>His42, Pro43 and Asp44</scene> of Loop 2 are conserved across the J domain family<ref name='E'/> and are crucial in recognizing hsc70, a factor of Rb inactivation. However, though such similarity with homologs exists, there are structural differences. These include residues 68-78 of Loop 3, which form hydrogen bonds with the retinoblastoma pocket and stabilize the J domain internally; and 91-102 of helix α4, of which Asn96 and Glu100 form hydrogen bonds with Lys765 and Gln762 from the Rb pocket.<br /> <br /> The The LxCxE motif is accommodated by a groove in the Rb pocket and accounts for two-thirds of the total buried surface area in the interaction. A number of <scene name='User:Udayan_Shevade/Sandbox1/Tagnterminal_jdomain_loophbond/1'>hydrogen bonds</scene> occur along the loop. Furthermore, the end contains a <scene name='User:Udayan_Shevade/Sandbox1/Tagnterminal_loopacidicseq/1'>conserved acidic sequence</scene>. It is proposed that this region interacts with a cluster of lysine residues near the LxCxE binding site of Rb<ref>PMID:9495340</ref>. Kinase-mediated phosphorylation of Ser111 and Ser112 might then induce a conformational change in the loop which allows these interactions to occur more favorably.<br /> <br /> Both large T antigen and E2F are able to complex with the Rb pocket simultaneously, suggesting their respective sites are different. So binding is not competitive. Thus to resolve the question of how large T antigen mediates E2F release from Rb, its similarity to homologs is considered. DnaJ serves not only to aid in folding proteins, but also to disassemble complexes. As such, it is proposed [http://www.ncbi.nlm.nih.gov/core/lw/2.0/html/tileshop_pmc/tileshop_pmc_inline.html?title=An%20external%20file%20that%20holds%20a%20picture%2C%20illustration%2C%20etc.%0AObject%20name%20is%20cde030f5.jpg%20%5BObject%20name%20is%20cde030f5.jpg%5D&p=PMC3&id=140208_cde030f5.jpg the large T antigen J domain may recruit hsc70, which then dissociates the EF2-Rb complex]<ref name='E'/>. <scene name='User:Udayan_Shevade/Sandbox1/Tagnterminal_reload/1'>Reload molecule</scene>.<br /> <br /> <br /> </structuresection><br /> <br /> ==== References ====<br /> {{reflist}}</div>

Udayan Shevade https://proteopedia.org/index.php?title=User:Udayan_Shevade/Sandbox1&diff=1317761 User:Udayan Shevade/Sandbox1 2011-11-15T11:37:28Z

<p>Udayan Shevade: </p> <hr /> <div>= SV40 Large T Antigen =<br /> <br /> === Introduction ===<br /> <br /> The '''SV40 large tumor antigen''' is a multifunctional regulatory protein encoded by Simian Virus 40. It is classified under the AAA+ family of helicases <ref name="A">PMID:8946857</ref>. 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.<br /> <br /> <br /> === Structure and Function ===<br /> 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 <ref name="B">PMID:15454080</ref>.<br /> <br /> <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'><br /> ===== The Origin Binding Domain =====<br /> 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'>Phe183 and Ser185</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 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, Arg154, Thr155 from the A1 motif</scene>; <scene name='User:Udayan_Shevade/Sandbox1/Obd_203_204/1'>His203, Arg204 from the B2 motif</scene>; as well as <scene name='User:Udayan_Shevade/Sandbox1/Obd_201_202/1'>His201 andArg 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>. <br /> [[Image:Tagobd_dna_interactions.jpg|200px|left|thumb]]<br /> 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><br /> <br /> {{STRUCTURE_1svm| PDB=1svm | SCENE= }}<br /> <br /> ===== Helicase =====<br /> The <scene name='User:Udayan_Shevade/Sandbox1/Taghelicase_aaa_monomer/1'>helicase monomer</scene> 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 [http://www.sciencedirect.com/cache/MiamiImageURL/1-s2.0-S0092867404008906-gr3_lrg.jpg/0?wchp=dGLbVlV-zSkWA transitions in conformation] between these states enable the unwinding of viral dsDNA. There are both cis- and trans-monomer interactions involving ATP. <br /> <br /> <scene name='User:Udayan_Shevade/Sandbox1/Helicase_cis_residues/2'>''Cis''-residues</scene> Lys432, Thr433 and Thr434 of the P loop interact closely with the triphosphate groups, and Asp474 and Asn529 form H bonds with ATP on the same residue. Among these, Ilu428, Thr433 and Asp474 adopt different conformations in the ADP-bound state. In the Nt-free state, Ilu428 and Thr434 are turned even further and sterically disallow the presence of ADP.<br /> <br /> <scene name='User:Udayan_Shevade/Sandbox1/Helicase_atp_water/1'>A water molecule</scene> near the ATP is present for stability and nucleophilic attack during hydrolysis. <br /> <br /> <scene name='User:Udayan_Shevade/Sandbox1/Helicase_trans_residues/1'>Six ''trans''-residues</scene>, of which Lys418 and Lys419 stabilize ATP hydrolysis, interact with ATP on adjacent monomers, important in producing conformational changes. <br /> <br /> These rearrangements affect the position of <scene name='User:Udayan_Shevade/Sandbox1/Taghelicase_betahairpin/1'>the "β hairpin,"</scene> a positively-charged structure that protrudes into the central channel. ''Trans''-residues Arg498, Asp499 and Asp502 are located at the base of the hairpin, lending a lever-like functionality. The [http://www.sciencedirect.com/cache/MiamiImageURL/1-s2.0-S0092867404008906-gr7_lrg.jpg/0?wchp=dGLbVlk-zSkWb motion of the β hairpin] unwinds the DNA through the central channel <ref name='D'>PMID:15454080</ref>.<br /> <br /> <br /> <Structuresection load='1gh6' side='right' caption='Large T antigen complexed with retinoblastoma pocket' size='345'><br /> <br /> ===== J domain and LxCxE motif =====<br /> In the transformation of the host cell, retinoblastoma, a tumor suppressor, is inactivated via both the N-terminal J domain and the LxCxE motif. The N-terminal region (residues 7-117), shown to the right in blue, consists of <scene name='User:Udayan_Shevade/Sandbox1/Tagnterminal_jdomain_helices/1'>four alpha helices</scene> and <scene name='User:Udayan_Shevade/Sandbox1/Tagnterminal_jdomain_loop/1'>an extended loop</scene>. These contain the J domain and the LxCxE motif respectively <ref name='E'>PMID:140208</ref>. The large T antigen J domain is a functional homolog of the molecular chaperone DnaJ protein, namely HDJ-1 of E. coli<ref>PMID:9364917</ref> and human Hsp40<ref>PMID:232328</ref>. The alpha helices α2 and α3 that form the core of the domain are stabilized by the dominant hydrophobicity of conserved residue sidechains, e.g. Leu17, Phe41, Trp95. Mutations in these residues cause disruptive perturbations. Additionally, <scene name='User:Udayan_Shevade/Sandbox1/Tagnterminal_jdomain_hbonds/1'>hydrogen bonds</scene> further stabilize the core. Residues <scene name='User:Udayan_Shevade/Sandbox1/Tagnterminal_jdomain_hpd/1'>His42, Pro43 and Asp44</scene> of Loop 2 are conserved across the J domain family<ref name='E'/> and are crucial in recognizing hsc70, a factor of Rb inactivation. However, though such similarity with homologs exists, there are structural differences. These include residues 68-78 of Loop 3, which form hydrogen bonds with the retinoblastoma pocket and stabilize the J domain internally; and 91-102 of helix α4, of which Asn96 and Glu100 form hydrogen bonds with Lys765 and Gln762 from the Rb pocket.<br /> <br /> The The LxCxE motif is accommodated by a groove in the Rb pocket and accounts for two-thirds of the total buried surface area in the interaction. A number of <scene name='User:Udayan_Shevade/Sandbox1/Tagnterminal_jdomain_loophbond/1'>hydrogen bonds</scene> occur along the loop. Furthermore, the end contains a conserved acidic sequence. It is proposed that this region interacts with a cluster of lysine residues near the LxCxE binding site of Rb<ref>PMID:9495340</ref>. Kinase-mediated phosphorylation of Ser111 and Ser112 might then induce a conformational change in the loop which allows these interactions to occur more favorably.<br /> <br /> Both large T antigen and E2F are able to complex with the Rb pocket simultaneously, suggesting their respective sites are different. So binding is not competitive. Thus to resolve the question of how large T antigen mediates E2F release from Rb, its similarity to homologs is considered. DnaJ serves not only to aid in folding proteins, but also to disassemble complexes. As such, it is proposed [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC140208/figure/cde030f5/ the large T antigen J domain may recruit hsc70, which then dissociates the EF2-Rb complex]<ref name='E'/>. <scene name='User:Udayan_Shevade/Sandbox1/Tagnterminal_reload/1'>Reload</scene>.<br /> <br /> <br /> </structuresection><br /> <br /> ==== References ====<br /> {{reflist}}</div>

Udayan Shevade https://proteopedia.org/index.php?title=User:Udayan_Shevade/Sandbox1&diff=1317760 User:Udayan Shevade/Sandbox1 2011-11-15T11:35:26Z

<p>Udayan Shevade: </p> <hr /> <div>= SV40 Large T Antigen =<br /> <br /> === Introduction ===<br /> <br /> The '''SV40 large tumor antigen''' is a multifunctional regulatory protein encoded by Simian Virus 40. It is classified under the AAA+ family of helicases <ref name="A">PMID:8946857</ref>. 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.<br /> <br /> <br /> === Structure and Function ===<br /> 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 <ref name="B">PMID:15454080</ref>.<br /> <br /> <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'><br /> ===== The Origin Binding Domain =====<br /> 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'>Phe183 and Ser185</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 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, Arg154, Thr155 from the A1 motif</scene>; <scene name='User:Udayan_Shevade/Sandbox1/Obd_203_204/1'>His203, Arg204 from the B2 motif</scene>; as well as <scene name='User:Udayan_Shevade/Sandbox1/Obd_201_202/1'>His201 andArg 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>. <br /> [[Image:Tagobd_dna_interactions.jpg|200px|left|thumb]]<br /> 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><br /> <br /> {{STRUCTURE_1svm| PDB=1svm | SCENE= }}<br /> <br /> ===== Helicase =====<br /> The <scene name='User:Udayan_Shevade/Sandbox1/Taghelicase_aaa_monomer/1'>helicase monomer</scene> 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 [http://www.sciencedirect.com/cache/MiamiImageURL/1-s2.0-S0092867404008906-gr3_lrg.jpg/0?wchp=dGLbVlV-zSkWA transitions in conformation] between these states enable the unwinding of viral dsDNA. There are both cis- and trans-monomer interactions involving ATP. <br /> <br /> <scene name='User:Udayan_Shevade/Sandbox1/Helicase_cis_residues/2'>''Cis''-residues</scene> Lys432, Thr433 and Thr434 of the P loop interact closely with the triphosphate groups, and Asp474 and Asn529 form H bonds with ATP on the same residue. Among these, Ilu428, Thr433 and Asp474 adopt different conformations in the ADP-bound state. In the Nt-free state, Ilu428 and Thr434 are turned even further and sterically disallow the presence of ADP.<br /> <br /> <scene name='User:Udayan_Shevade/Sandbox1/Helicase_atp_water/1'>A water molecule</scene> near the ATP is present for stability and nucleophilic attack during hydrolysis. <br /> <br /> <scene name='User:Udayan_Shevade/Sandbox1/Helicase_trans_residues/1'>Six ''trans''-residues</scene>, of which Lys418 and Lys419 stabilize ATP hydrolysis, interact with ATP on adjacent monomers, important in producing conformational changes. <br /> <br /> These rearrangements affect the position of <scene name='User:Udayan_Shevade/Sandbox1/Taghelicase_betahairpin/1'>the "β hairpin,"</scene> a positively-charged structure that protrudes into the central channel. ''Trans''-residues Arg498, Asp499 and Asp502 are located at the base of the hairpin, lending a lever-like functionality. The [http://www.sciencedirect.com/cache/MiamiImageURL/1-s2.0-S0092867404008906-gr7_lrg.jpg/0?wchp=dGLbVlk-zSkWb motion of the β hairpin] unwinds the DNA through the central channel <ref name='D'>PMID:15454080</ref>.<br /> <br /> <br /> <Structuresection load='1gh6' side='right' caption='Large T antigen complexed with retinoblastoma pocket. <scene name='User:Udayan_Shevade/Sandbox1/Tagnterminal_reload/1'>Reload.</scene>' size='345'><br /> <br /> ===== J domain and LxCxE motif =====<br /> In the transformation of the host cell, retinoblastoma, a tumor suppressor, is inactivated via both the N-terminal J domain and the LxCxE motif. The N-terminal region (residues 7-117), shown to the right in blue, consists of <scene name='User:Udayan_Shevade/Sandbox1/Tagnterminal_jdomain_helices/1'>four alpha helices</scene> and <scene name='User:Udayan_Shevade/Sandbox1/Tagnterminal_jdomain_loop/1'>an extended loop</scene>. These contain the J domain and the LxCxE motif respectively <ref name='E'>PMID:140208</ref>. The large T antigen J domain is a functional homolog of the molecular chaperone DnaJ protein, namely HDJ-1 of E. coli<ref>PMID:9364917</ref> and human Hsp40<ref>PMID:232328</ref>. The alpha helices α2 and α3 that form the core of the domain are stabilized by the dominant hydrophobicity of conserved residue sidechains, e.g. Leu17, Phe41, Trp95. Mutations in these residues cause disruptive perturbations. Additionally, <scene name='User:Udayan_Shevade/Sandbox1/Tagnterminal_jdomain_hbonds/1'>hydrogen bonds</scene> further stabilize the core. Residues <scene name='User:Udayan_Shevade/Sandbox1/Tagnterminal_jdomain_hpd/1'>His42, Pro43 and Asp44</scene> of Loop 2 are conserved across the J domain family<ref name='E'/> and are crucial in recognizing hsc70, a factor of Rb inactivation. However, though such similarity with homologs exists, there are structural differences. These include residues 68-78 of Loop 3, which form hydrogen bonds with the retinoblastoma pocket and stabilize the J domain internally; and 91-102 of helix α4, of which Asn96 and Glu100 form hydrogen bonds with Lys765 and Gln762 from the Rb pocket.<br /> <br /> The The LxCxE motif is accommodated by a groove in the Rb pocket and accounts for two-thirds of the total buried surface area in the interaction. A number of <scene name='User:Udayan_Shevade/Sandbox1/Tagnterminal_jdomain_loophbond/1'>hydrogen bonds</scene> occur along the loop. Furthermore, the end contains a conserved acidic sequence. It is proposed that this region interacts with a cluster of lysine residues near the LxCxE binding site of Rb<ref>PMID:9495340</ref>. Kinase-mediated phosphorylation of Ser111 and Ser112 might then induce a conformational change in the loop which allows these interactions to occur more favorably.<br /> <br /> Both large T antigen and E2F are able to complex with the Rb pocket simultaneously, suggesting their respective sites are different. So binding is not competitive. Thus to resolve the question of how large T antigen mediates E2F release from Rb, its similarity to homologs is considered. DnaJ serves not only to aid in folding proteins, but also to disassemble complexes. As such, it is proposed [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC140208/figure/cde030f5/ the large T antigen J domain may recruit hsc70, which then dissociates the EF2-Rb complex]<ref name='E'/>.<br /> <br /> <br /> </structuresection><br /> <br /> ==== References ====<br /> {{reflist}}</div>

Udayan Shevade https://proteopedia.org/index.php?title=User:Udayan_Shevade/Sandbox1&diff=1317751 User:Udayan Shevade/Sandbox1 2011-11-15T11:24:46Z

<p>Udayan Shevade: </p> <hr /> <div>= SV40 Large T Antigen =<br /> <br /> === Introduction ===<br /> <br /> The '''SV40 large tumor antigen''' is a multifunctional regulatory protein encoded by Simian Virus 40. It is classified under the AAA+ family of helicases <ref name="A">PMID:8946857</ref>. 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.<br /> <br /> <br /> === Structure and Function ===<br /> 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 <ref name="B">PMID:15454080</ref>.<br /> <br /> <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'><br /> ===== The Origin Binding Domain =====<br /> 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'>Phe183 and Ser185</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 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, Arg154, Thr155 from the A1 motif</scene>; <scene name='User:Udayan_Shevade/Sandbox1/Obd_203_204/1'>His203, Arg204 from the B2 motif</scene>; as well as <scene name='User:Udayan_Shevade/Sandbox1/Obd_201_202/1'>His201 andArg 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>. <br /> [[Image:Tagobd_dna_interactions.jpg|200px|left|thumb]]<br /> 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><br /> <br /> {{STRUCTURE_1svm| PDB=1svm | SCENE= }}<br /> <br /> ===== Helicase =====<br /> The <scene name='User:Udayan_Shevade/Sandbox1/Taghelicase_aaa_monomer/1'>helicase monomer</scene> 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 [http://www.sciencedirect.com/cache/MiamiImageURL/1-s2.0-S0092867404008906-gr3_lrg.jpg/0?wchp=dGLbVlV-zSkWA transitions in conformation] between these states enable the unwinding of viral dsDNA. There are both cis- and trans-monomer interactions involving ATP. <br /> <br /> <scene name='User:Udayan_Shevade/Sandbox1/Helicase_cis_residues/2'>''Cis''-residues</scene> Lys432, Thr433 and Thr434 of the P loop interact closely with the triphosphate groups, and Asp474 and Asn529 form H bonds with ATP on the same residue. Among these, Ilu428, Thr433 and Asp474 adopt different conformations in the ADP-bound state. In the Nt-free state, Ilu428 and Thr434 are turned even further and sterically disallow the presence of ADP.<br /> <br /> <scene name='User:Udayan_Shevade/Sandbox1/Helicase_atp_water/1'>A water molecule</scene> near the ATP is present for stability and nucleophilic attack during hydrolysis. <br /> <br /> <scene name='User:Udayan_Shevade/Sandbox1/Helicase_trans_residues/1'>Six ''trans''-residues</scene>, of which Lys418 and Lys419 stabilize ATP hydrolysis, interact with ATP on adjacent monomers, important in producing conformational changes. <br /> <br /> These rearrangements affect the position of <scene name='User:Udayan_Shevade/Sandbox1/Taghelicase_betahairpin/1'>the "β hairpin,"</scene> a positively-charged structure that protrudes into the central channel. ''Trans''-residues Arg498, Asp499 and Asp502 are located at the base of the hairpin, lending a lever-like functionality. The [http://www.sciencedirect.com/cache/MiamiImageURL/1-s2.0-S0092867404008906-gr7_lrg.jpg/0?wchp=dGLbVlk-zSkWb motion of the β hairpin] unwinds the DNA through the central channel <ref name='D'>PMID:15454080</ref>.<br /> <br /> <br /> <Structuresection load='1gh6' side='right' caption='Large T antigen complexed with retinoblastoma pocket' size='345'><br /> <br /> ===== J domain and LxCxE motif =====<br /> In the transformation of the host cell, retinoblastoma, a tumor suppressor, is inactivated via both the N-terminal J domain and the LxCxE motif. The N-terminal region (residues 7-117), shown to the right in blue, consists of <scene name='User:Udayan_Shevade/Sandbox1/Tagnterminal_jdomain_helices/1'>four alpha helices</scene> and <scene name='User:Udayan_Shevade/Sandbox1/Tagnterminal_jdomain_loop/1'>an extended loop</scene>. These contain the J domain and the LxCxE motif respectively <ref name='E'>PMID:140208</ref>. The large T antigen J domain is a functional homolog of the molecular chaperone DnaJ protein, namely HDJ-1 of E. coli<ref>PMID:9364917</ref> and human Hsp40<ref>PMID:232328</ref>. The alpha helices α2 and α3 that form the core of the domain are stabilized by the dominant hydrophobicity of conserved residue sidechains, e.g. Leu17, Phe41, Trp95. Mutations in these residues cause disruptive perturbations. Additionally, <scene name='User:Udayan_Shevade/Sandbox1/Tagnterminal_jdomain_hbonds/1'>hydrogen bonds</scene> further stabilize the core. Residues <scene name='User:Udayan_Shevade/Sandbox1/Tagnterminal_jdomain_hpd/1'>His42, Pro43 and Asp44</scene> of Loop 2 are conserved across the J domain family<ref name='E'/> and are crucial in recognizing hsc70, a factor of Rb inactivation. However, though such similarity with homologs exists, there are structural differences. These include residues 68-78 of Loop 3, which form hydrogen bonds with the retinoblastoma pocket and stabilize the J domain internally; and 91-102 of helix α4, of which Asn96 and Glu100 form hydrogen bonds with Lys765 and Gln762 from the Rb pocket.<br /> <br /> The The LxCxE motif is accommodated by a groove in the Rb pocket and accounts for two-thirds of the total buried surface area in the interaction. A number of <scene name='User:Udayan_Shevade/Sandbox1/Tagnterminal_jdomain_loophbond/1'>hydrogen bonds</scene> occur along the loop. Furthermore, the end contains a conserved acidic sequence. It is proposed that this region interacts with a cluster of lysine residues near the LxCxE binding site of Rb<ref>PMID:9495340</ref>. Kinase-mediated phosphorylation of Ser111 and Ser112 might then induce a conformational change in the loop which allows these interactions to occur more favorably.<br /> <br /> Both large T antigen and E2F are able to complex with the Rb pocket simultaneously, suggesting their respective sites are different. So binding is not competitive. Thus to resolve the question of how large T antigen mediates E2F release from Rb, its similarity to homologs is considered. DnaJ serves not only to aid in folding proteins, but also to disassemble complexes. As such, it is proposed [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC140208/figure/cde030f5/ the large T antigen J domain may recruit hsc70, which then dissociates the EF2-Rb complex]<ref name='E'/>.<br /> <br /> <br /> </structuresection><br /> <br /> ==== References ====<br /> {{reflist}}</div>

Udayan Shevade https://proteopedia.org/index.php?title=User:Udayan_Shevade/Sandbox1&diff=1317740 User:Udayan Shevade/Sandbox1 2011-11-15T09:58:50Z

<p>Udayan Shevade: </p> <hr /> <div>= SV40 Large T Antigen =<br /> <br /> === Introduction ===<br /> <br /> The '''SV40 large tumor antigen''' is a multifunctional regulatory protein encoded by Simian Virus 40. It is classified under the AAA+ family of helicases <ref name="A">PMID:8946857</ref>. 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.<br /> <br /> <br /> === Structure and Function ===<br /> 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 <ref name="B">PMID:15454080</ref>.<br /> <br /> <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'><br /> ===== The Origin Binding Domain =====<br /> 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'>Phe183 and Ser185</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 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, Arg154, Thr155 from the A1 motif</scene>; <scene name='User:Udayan_Shevade/Sandbox1/Obd_203_204/1'>His203, Arg204 from the B2 motif</scene>; as well as <scene name='User:Udayan_Shevade/Sandbox1/Obd_201_202/1'>His201 andArg 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>. <br /> [[Image:Tagobd_dna_interactions.jpg|200px|left|thumb]]<br /> 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><br /> <br /> {{STRUCTURE_1svm| PDB=1svm | SCENE= }}<br /> <br /> ===== Helicase =====<br /> The <scene name='User:Udayan_Shevade/Sandbox1/Taghelicase_aaa_monomer/1'>helicase monomer</scene> 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 [http://www.sciencedirect.com/cache/MiamiImageURL/1-s2.0-S0092867404008906-gr3_lrg.jpg/0?wchp=dGLbVlV-zSkWA transitions in conformation] between these states enable the unwinding of viral dsDNA. There are both cis- and trans-monomer interactions involving ATP. <br /> <br /> <scene name='User:Udayan_Shevade/Sandbox1/Helicase_cis_residues/2'>''Cis''-residues</scene> Lys432, Thr433 and Thr434 of the P loop interact closely with the triphosphate groups, and Asp474 and Asn529 form H bonds with ATP on the same residue. Among these, Ilu428, Thr433 and Asp474 adopt different conformations in the ADP-bound state. In the Nt-free state, Ilu428 and Thr434 are turned even further and sterically disallow the presence of ADP.<br /> <br /> <scene name='User:Udayan_Shevade/Sandbox1/Helicase_atp_water/1'>A water molecule</scene> near the ATP is present for stability and nucleophilic attack during hydrolysis. <br /> <br /> <scene name='User:Udayan_Shevade/Sandbox1/Helicase_trans_residues/1'>Six ''trans''-residues</scene>, of which Lys418 and Lys419 stabilize ATP hydrolysis, interact with ATP on adjacent monomers, important in producing conformational changes. <br /> <br /> These rearrangements affect the position of <scene name='User:Udayan_Shevade/Sandbox1/Taghelicase_betahairpin/1'>the "β hairpin,"</scene> a positively-charged structure that protrudes into the central channel. ''Trans''-residues Arg498, Asp499 and Asp502 are located at the base of the hairpin, lending a lever-like functionality. The [http://www.sciencedirect.com/cache/MiamiImageURL/1-s2.0-S0092867404008906-gr7_lrg.jpg/0?wchp=dGLbVlk-zSkWb motion of the β hairpin] unwinds the DNA through the central channel <ref name='D'>PMID:15454080</ref>.<br /> <br /> <br /> <Structuresection load='1gh6' side='right' caption='Large T antigen complexed with retinoblastoma pocket' size='345'><br /> <br /> ===== J domain and LxCxE motif =====<br /> In the transformation of the host cell, retinoblastoma, a tumor suppressor, is inactivated via both the N-terminal J domain and the LxCxE motif. The N-terminal region (residues 7-117), shown to the right in blue, consists of <scene name='User:Udayan_Shevade/Sandbox1/Tagnterminal_jdomain_helices/1'>four alpha helices</scene> and <scene name='User:Udayan_Shevade/Sandbox1/Tagnterminal_jdomain_loop/1'>an extended loop</scene>. These contain the J domain and the LxCxE motif respectively <ref name='E'>PMID:140208</ref>. The J domain is a functional homolog of the molecular chaperone DnaJ, HDJ-1 of E. coli<ref>PMID:9364917</ref> and human Hsp40<ref>PMID:232328</ref>. The alpha helices α2 and α3 that form the core of the domain are stabilized by the dominant hydrophobicity of conserved residue sidechains, e.g. Leu17, Phe41, Trp95. Mutations in these residues cause disruptive perturbations. Additionally, <scene name='User:Udayan_Shevade/Sandbox1/Tagnterminal_jdomain_hbonds/1'>hydrogen bonds</scene> further stabilize the core. Residues <scene name='User:Udayan_Shevade/Sandbox1/Tagnterminal_jdomain_hpd/1'>His 42, Pro 43 and Asp 44</scene> of Loop 2 are conserved across the J domain family<ref name='E'/>. However, though such similarity with homologs exists, there are structural differences. These include residues 68-78 of Loop 3, which form hydrogen bonds with the retinoblastoma pocket and stabilize the J domain internally; and 91-102 of helix α4. <br /> <br /> The The LxCxE motif is accommodated by a groove in the Rb pocket and accounts for two-thirds of the total buried surface area in the interaction. <br /> <br /> <br /> </structuresection><br /> <br /> ==== References ====<br /> {{reflist}}</div>

Udayan Shevade https://proteopedia.org/index.php?title=User:Udayan_Shevade/Sandbox1&diff=1317739 User:Udayan Shevade/Sandbox1 2011-11-15T09:57:59Z

<p>Udayan Shevade: </p> <hr /> <div>= SV40 Large T Antigen =<br /> <br /> === Introduction ===<br /> <br /> The '''SV40 large tumor antigen''' is a multifunctional regulatory protein encoded by Simian Virus 40. It is classified under the AAA+ family of helicases <ref name="A">PMID:8946857</ref>. 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.<br /> <br /> <br /> === Structure and Function ===<br /> 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 <ref name="B">PMID:15454080</ref>.<br /> <br /> <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'><br /> ===== The Origin Binding Domain =====<br /> 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'>Phe183 and Ser185</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 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, Arg154, Thr155 from the A1 motif</scene>; <scene name='User:Udayan_Shevade/Sandbox1/Obd_203_204/1'>His203, Arg204 from the B2 motif</scene>; as well as <scene name='User:Udayan_Shevade/Sandbox1/Obd_201_202/1'>His201 andArg 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>. <br /> [[Image:Tagobd_dna_interactions.jpg|200px|left|thumb]]<br /> 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><br /> <br /> {{STRUCTURE_1svm| PDB=1svm | SCENE= }}<br /> <br /> ===== Helicase =====<br /> The <scene name='User:Udayan_Shevade/Sandbox1/Taghelicase_aaa_monomer/1'>helicase monomer</scene> 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 [http://www.sciencedirect.com/cache/MiamiImageURL/1-s2.0-S0092867404008906-gr3_lrg.jpg/0?wchp=dGLbVlV-zSkWA transitions in conformation] between these states enable the unwinding of viral dsDNA. There are both cis- and trans-monomer interactions involving ATP. <br /> <br /> <scene name='User:Udayan_Shevade/Sandbox1/Helicase_cis_residues/2'>''Cis''-residues</scene> Lys432, Thr433 and Thr434 of the P loop interact closely with the triphosphate groups, and Asp474 and Asn529 form H bonds with ATP on the same residue. Among these, Ilu428, Thr433 and Asp474 adopt different conformations in the ADP-bound state. In the Nt-free state, Ilu428 and Thr434 are turned even further and sterically disallow the presence of ADP.<br /> <br /> <scene name='User:Udayan_Shevade/Sandbox1/Helicase_atp_water/1'>A water molecule</scene> near the ATP is present for stability and nucleophilic attack during hydrolysis. <br /> <br /> <scene name='User:Udayan_Shevade/Sandbox1/Helicase_trans_residues/1'>Six ''trans''-residues</scene>, of which Lys418 and Lys419 stabilize ATP hydrolysis, interact with ATP on adjacent monomers, important in producing conformational changes. <br /> <br /> These rearrangements affect the position of <scene name='User:Udayan_Shevade/Sandbox1/Taghelicase_betahairpin/1'>the "β hairpin,"</scene> a positively-charged structure that protrudes into the central channel. ''Trans''-residues Arg498, Asp499 and Asp502 are located at the base of the hairpin, lending a lever-like functionality. The [http://www.sciencedirect.com/cache/MiamiImageURL/1-s2.0-S0092867404008906-gr7_lrg.jpg/0?wchp=dGLbVlk-zSkWb motion of the β hairpin] unwinds the DNA through the central channel <ref name='D'>PMID:15454080</ref>.<br /> <br /> <br /> <Structuresection load='1gh6' side='right' caption='Large T antigen complexed with retinoblastoma pocket' size='345'><br /> <br /> ===== J domain and LxCxE motif =====<br /> In the transformation of the host cell, retinoblastoma, a tumor suppressor, is inactivated via both the N-terminal J domain and the LxCxE motif. The N-terminal region (residues 7-117), shown to the right, consists of <scene name='User:Udayan_Shevade/Sandbox1/Tagnterminal_jdomain_helices/1'>four alpha helices</scene> and <scene name='User:Udayan_Shevade/Sandbox1/Tagnterminal_jdomain_loop/1'>an extended loop</scene>. These contain the J domain and the LxCxE motif respectively <ref name='E'>PMID:140208</ref>. The J domain is a functional homolog of the molecular chaperone DnaJ, HDJ-1 of E. coli<ref>PMID:9364917</ref> and human Hsp40<ref>PMID:232328</ref>. The alpha helices α2 and α3 that form the core of the domain are stabilized by the dominant hydrophobicity of conserved residue sidechains, e.g. Leu17, Phe41, Trp95. Mutations in these residues cause disruptive perturbations. Additionally, <scene name='User:Udayan_Shevade/Sandbox1/Tagnterminal_jdomain_hbonds/1'>hydrogen bonds</scene> further stabilize the core. Residues <scene name='User:Udayan_Shevade/Sandbox1/Tagnterminal_jdomain_hpd/1'>His 42, Pro 43 and Asp 44</scene> of Loop 2 are conserved across the J domain family<ref name='E'/>. However, though such similarity with homologs exists, there are structural differences. These include residues 68-78 of Loop 3, which form hydrogen bonds with the retinoblastoma pocket and stabilize the J domain internally; and 91-102 of helix α4. <br /> <br /> The The LxCxE motif is accommodated by a groove in the Rb pocket and accounts for two-thirds of the total buried surface area in the interaction. <br /> <br /> <br /> </structuresection><br /> <br /> ==== References ====<br /> {{reflist}}</div>

Udayan Shevade https://proteopedia.org/index.php?title=User:Udayan_Shevade/Sandbox1&diff=1317736 User:Udayan Shevade/Sandbox1 2011-11-15T09:55:24Z

<p>Udayan Shevade: </p> <hr /> <div>= SV40 Large T Antigen =<br /> <br /> === Introduction ===<br /> <br /> The '''SV40 large tumor antigen''' is a multifunctional regulatory protein encoded by Simian Virus 40. It is classified under the AAA+ family of helicases <ref name="A">PMID:8946857</ref>. 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.<br /> <br /> <br /> === Structure and Function ===<br /> 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 <ref name="B">PMID:15454080</ref>.<br /> <br /> <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'><br /> ===== The Origin Binding Domain =====<br /> 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'>Phe183 and Ser185</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 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, Arg154, Thr155 from the A1 motif</scene>; <scene name='User:Udayan_Shevade/Sandbox1/Obd_203_204/1'>His203, Arg204 from the B2 motif</scene>; as well as <scene name='User:Udayan_Shevade/Sandbox1/Obd_201_202/1'>His201 andArg 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>. <br /> [[Image:Tagobd_dna_interactions.jpg|200px|left|thumb]]<br /> 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><br /> <br /> {{STRUCTURE_1svm| PDB=1svm | SCENE= }}<br /> <br /> ===== Helicase =====<br /> The <scene name='User:Udayan_Shevade/Sandbox1/Taghelicase_aaa_monomer/1'>helicase monomer</scene> 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 [http://www.sciencedirect.com/cache/MiamiImageURL/1-s2.0-S0092867404008906-gr3_lrg.jpg/0?wchp=dGLbVlV-zSkWA transitions in conformation] between these states enable the unwinding of viral dsDNA. There are both cis- and trans-monomer interactions involving ATP. <br /> <br /> <scene name='User:Udayan_Shevade/Sandbox1/Helicase_cis_residues/2'>''Cis''-residues</scene> Lys432, Thr433 and Thr434 of the P loop interact closely with the triphosphate groups, and Asp474 and Asn529 form H bonds with ATP on the same residue. Among these, Ilu428, Thr433 and Asp474 adopt different conformations in the ADP-bound state. In the Nt-free state, Ilu428 and Thr434 are turned even further and sterically disallow the presence of ADP.<br /> <br /> <scene name='User:Udayan_Shevade/Sandbox1/Helicase_atp_water/1'>A water molecule</scene> near the ATP is present for stability and nucleophilic attack during hydrolysis. <br /> <br /> <scene name='User:Udayan_Shevade/Sandbox1/Helicase_trans_residues/1'>Six ''trans''-residues</scene>, of which Lys418 and Lys419 stabilize ATP hydrolysis, interact with ATP on adjacent monomers, important in producing conformational changes. <br /> <br /> These rearrangements affect the position of <scene name='User:Udayan_Shevade/Sandbox1/Taghelicase_betahairpin/1'>the "β hairpin,"</scene> a positively-charged structure that protrudes into the central channel. ''Trans''-residues Arg498, Asp499 and Asp502 are located at the base of the hairpin, lending a lever-like functionality. The [http://www.sciencedirect.com/cache/MiamiImageURL/1-s2.0-S0092867404008906-gr7_lrg.jpg/0?wchp=dGLbVlk-zSkWb motion of the β hairpin] unwinds the DNA through the central channel <ref name='D'>PMID:15454080</ref>.<br /> <br /> <br /> <Structuresection load='1gh6' side='right' caption='Large T antigen complexed with retinoblastoma pocket' size='345'><br /> <br /> ===== J domain and LxCxE motif =====<br /> In the transformation of the host cell, retinoblastoma, a tumor suppressor, is inactivated via both the N-terminal J domain and the LxCxE motif. The N-terminal region (residues 7-117), shown to the right, consists of <scene name='User:Udayan_Shevade/Sandbox1/Tagnterminal_jdomain_helices/1'>four alpha helices</scene> and <scene name='User:Udayan_Shevade/Sandbox1/Tagnterminal_jdomain_loop/1'>an extended loop</scene>. These contain the J domain and the LxCxE motif respectively <ref name='E'>PMID:140208</ref>. The J domain is a functional homolog of the molecular chaperone DnaJ, HDJ-1 of E. coli<ref>PMID:9364917</ref> and human Hsp40<ref>PMID:232328</ref>. The alpha helices α2 and α3 that form the core of the domain are stabilized by the dominant hydrophobicity of conserved residue sidechains, e.g. Leu17, Phe41, Trp95. Mutations in these residues cause disruptive perturbations. Additionally, <scene name='User:Udayan_Shevade/Sandbox1/Tagnterminal_jdomain_hbonds/1'>hydrogen bonds</scene> further stabilize the core. Residues <scene name='User:Udayan_Shevade/Sandbox1/Tagnterminal_jdomain_hpd/1'>His 42, Pro 43 and Asp 44</scene> of Loop 2 are conserved across the J domain family</ref name='E'>. However, though such similarity with homologs exists, there are structural differences. These include residues 68-78 of Loop 3, which form hydrogen bonds with the retinoblastoma pocket and stabilize the J domain internally; and 91-102 of helix α4. <br /> <br /> The The LxCxE motif is accommodated by a groove in the Rb pocket and accounts for two-thirds of the total buried surface area in the interaction. <br /> <br /> <br /> </structuresection><br /> <br /> ==== References ====<br /> {{reflist}}</div>

Udayan Shevade https://proteopedia.org/index.php?title=User:Udayan_Shevade/Sandbox1&diff=1317728 User:Udayan Shevade/Sandbox1 2011-11-15T08:34:59Z

<p>Udayan Shevade: </p> <hr /> <div>= SV40 Large T Antigen =<br /> <br /> === Introduction ===<br /> <br /> The '''SV40 large tumor antigen''' is a multifunctional regulatory protein encoded by Simian Virus 40. It is classified under the AAA+ family of helicases <ref name="A">PMID:8946857</ref>. 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.<br /> <br /> <br /> === Structure and Function ===<br /> 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 <ref name="B">PMID:15454080</ref>.<br /> <br /> <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'><br /> ===== The Origin Binding Domain =====<br /> 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>. <br /> [[Image:Tagobd_dna_interactions.jpg|200px|left|thumb]]<br /> 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><br /> <br /> {{STRUCTURE_1svm| PDB=1svm | SCENE= }}<br /> <br /> ===== Helicase =====<br /> The <scene name='User:Udayan_Shevade/Sandbox1/Taghelicase_aaa_monomer/1'>helicase monomer</scene> 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 [http://www.sciencedirect.com/cache/MiamiImageURL/1-s2.0-S0092867404008906-gr3_lrg.jpg/0?wchp=dGLbVlV-zSkWA transitions in conformation] between these states enable the unwinding of viral dsDNA. There are both cis- and trans-monomer interactions involving ATP. <br /> <br /> <scene name='User:Udayan_Shevade/Sandbox1/Helicase_cis_residues/2'>''Cis''-residues</scene> 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. <br /> <br /> <scene name='User:Udayan_Shevade/Sandbox1/Helicase_atp_water/1'>A water molecule</scene> near the ATP is present for stability and nucleophilic attack during hydrolysis. <br /> <br /> <scene name='User:Udayan_Shevade/Sandbox1/Helicase_trans_residues/1'>Six ''trans''-residues</scene>, 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 <scene name='User:Udayan_Shevade/Sandbox1/Taghelicase_betahairpin/1'>the "β hairpin,"</scene> 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 [http://www.sciencedirect.com/cache/MiamiImageURL/1-s2.0-S0092867404008906-gr7_lrg.jpg/0?wchp=dGLbVlk-zSkWb motion of the β hairpin] unwinds the DNA through the central channel <ref name='D'>PMID:15454080</ref>.<br /> <br /> <br /> <Structuresection load='1gh6' side='right' caption='Large T antigen complexed with retinoblastoma pocket' size='345'><br /> <br /> ===== J domain and LxCxE motif =====<br /> In the transformation of the host cell, retinoblastoma, a tumor suppressor, is inactivated via both the N-terminal J domain and the LxCxE motif <ref name='E'>PMID:140208</ref>. The J domain is a molecular chaperone domain <ref>PMID:9364917</ref>. The N-terminal region (residues 7-117), shown to the right, consists of four alpha helices and an extended loop.<br /> <br /> <br /> </structuresection><br /> <br /> ==== References ====<br /> {{reflist}}</div>

Udayan Shevade https://proteopedia.org/index.php?title=User:Udayan_Shevade/Sandbox1&diff=1317727 User:Udayan Shevade/Sandbox1 2011-11-15T08:27:00Z

<p>Udayan Shevade: </p> <hr /> <div>= SV40 Large T Antigen =<br /> <br /> === Introduction ===<br /> <br /> The '''SV40 large tumor antigen''' is a multifunctional regulatory protein encoded by Simian Virus 40. It is classified under the AAA+ family of helicases <ref name="A">PMID:8946857</ref>. 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.<br /> <br /> <br /> === Structure and Function ===<br /> 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 <ref name="B">PMID:15454080</ref>.<br /> <br /> <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'><br /> ===== The Origin Binding Domain =====<br /> 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>. <br /> [[Image:Tagobd_dna_interactions.jpg|200px|left|thumb]]<br /> 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><br /> <br /> {{STRUCTURE_1svm| PDB=1svm | SCENE= }}<br /> <br /> ===== Helicase =====<br /> The <scene name='User:Udayan_Shevade/Sandbox1/Taghelicase_aaa_monomer/1'>helicase monomer</scene> 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 [http://www.sciencedirect.com/cache/MiamiImageURL/1-s2.0-S0092867404008906-gr3_lrg.jpg/0?wchp=dGLbVlV-zSkWA transitions in conformation] between these states enable the unwinding of viral dsDNA. There are both cis- and trans-monomer interactions involving ATP. <scene name='User:Udayan_Shevade/Sandbox1/Helicase_cis_residues/2'>''Cis''-residues</scene> 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. <scene name='User:Udayan_Shevade/Sandbox1/Helicase_atp_water/1'>A water molecule</scene> near the ATP is present for stability and nucleophilic attack during hydrolysis. <scene name='User:Udayan_Shevade/Sandbox1/Helicase_trans_residues/1'>Six ''trans''-residues</scene>, 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 <scene name='User:Udayan_Shevade/Sandbox1/Taghelicase_betahairpin/1'>the "β hairpin,"</scene> 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 [http://www.sciencedirect.com/cache/MiamiImageURL/1-s2.0-S0092867404008906-gr7_lrg.jpg/0?wchp=dGLbVlk-zSkWb motion of the β hairpin] unwinds the DNA through the central channel <ref name='D'>PMID:15454080</ref>.<br /> <br /> <br /> <Structuresection load='1gh6' side='right' caption='Large T antigen complexed with retinoblastoma pocket' size='345'><br /> <br /> ===== J domain and LxCxE motif =====<br /> In the transformation of the host cell, retinoblastoma, a tumor suppressor, is inactivated via both the N-terminal J domain and the LxCxE motif <ref name='E'>PMID:140208</ref>. The J domain is a molecular chaperone domain <ref>PMID:9364917</ref>. The N-terminal region (residues 7-117), shown to the right, consists of four alpha helices and an extended loop.<br /> <br /> <br /> ==== References ====<br /> {{reflist}}</div>

Udayan Shevade https://proteopedia.org/index.php?title=User:Udayan_Shevade/Sandbox1&diff=1317696 User:Udayan Shevade/Sandbox1 2011-11-15T04:15:13Z

<p>Udayan Shevade: </p> <hr /> <div>= SV40 Large T Antigen =<br /> <br /> === Introduction ===<br /> <br /> The '''SV40 large tumor antigen''' is a multifunctional regulatory protein encoded by Simian Virus 40. It is classified under the AAA+ family of helicases <ref name="A">PMID:8946857</ref>. 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.<br /> <br /> <br /> === Structure ===<br /> 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 <ref name="B">PMID:15454080</ref>.<br /> <br /> <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'><br /> ===== The Origin Binding Domain =====<br /> 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>. <br /> [[Image:Tagobd_dna_interactions.jpg|200px|left|thumb]]<br /> 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><br /> <br /> {{STRUCTURE_1svm| PDB=1svm | SCENE= }}<br /> <br /> ===== Helicase =====<br /> The <scene name='User:Udayan_Shevade/Sandbox1/Taghelicase_aaa_monomer/1'>helicase monomer</scene> 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 [http://www.sciencedirect.com/cache/MiamiImageURL/1-s2.0-S0092867404008906-gr3_lrg.jpg/0?wchp=dGLbVlV-zSkWA transitions in conformation] between these states enable the unwinding of viral dsDNA. There are both cis- and trans-monomer interactions involving ATP. <scene name='User:Udayan_Shevade/Sandbox1/Helicase_cis_residues/1'>''Cis''-residues</scene> 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. <scene name='User:Udayan_Shevade/Sandbox1/Helicase_atp_water/1'>A water molecule</scene> near the ATP is present for stability and nucleophilic attack during hydrolysis. <scene name='User:Udayan_Shevade/Sandbox1/Helicase_trans_residues/1'>Six ''trans''-residues</scene>, 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 <scene name='User:Udayan_Shevade/Sandbox1/Taghelicase_betahairpin/1'>the "β hairpin,"</scene> 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 [http://www.sciencedirect.com/cache/MiamiImageURL/1-s2.0-S0092867404008906-gr7_lrg.jpg/0?wchp=dGLbVlk-zSkWb motion of the β hairpin] unwinds the DNA through the central channel <ref name='D'>PMID:15454080</ref>.<br /> <br /> <br /> ===== Tumorigenesis =====<br /> <br /> <br /> ==== References ====<br /> {{reflist}}</div>

Udayan Shevade https://proteopedia.org/index.php?title=User:Udayan_Shevade/Sandbox1&diff=1317446 User:Udayan Shevade/Sandbox1 2011-11-14T03:32:35Z

<p>Udayan Shevade: </p> <hr /> <div>= SV40 Large T Antigen =<br /> <br /> === Introduction ===<br /> <br /> The '''SV40 large tumor antigen''' is a multifunctional regulatory protein encoded by Simian Virus 40. It is classified under the AAA+ family of helicases <ref name="A">PMID:8946857</ref>. 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.<br /> <br /> <br /> === Structure ===<br /> 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 <ref name="B">PMID:15454080</ref>.<br /> <br /> <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'><br /> ===== The Origin Binding Domain =====<br /> 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>. <br /> [[Image:Tagobd_dna_interactions.jpg|200px|left|thumb]]<br /> 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><br /> <br /> {{STRUCTURE_1svm| PDB=1svm | SCENE= }}<br /> <br /> ===== Helicase =====<br /> 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 [http://www.sciencedirect.com/cache/MiamiImageURL/1-s2.0-S0092867404008906-gr3_lrg.jpg/0?wchp=dGLbVlV-zSkWA transitions in conformation] between these states enable the unwinding of viral dsDNA. There are both cis- and trans-monomer interactions involving ATP. <scene name='User:Udayan_Shevade/Sandbox1/Helicase_cis_residues/1'>''Cis''-residues</scene> 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. <scene name='User:Udayan_Shevade/Sandbox1/Helicase_atp_water/1'>A water molecule</scene> near the ATP is present for stability and nucleophilic attack during hydrolysis. <scene name='User:Udayan_Shevade/Sandbox1/Helicase_trans_residues/1'>Six ''trans''-residues</scene>, 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 <scene name='User:Udayan_Shevade/Sandbox1/Taghelicase_betahairpin/1'>the "β hairpin,"</scene> 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 [http://www.sciencedirect.com/cache/MiamiImageURL/1-s2.0-S0092867404008906-gr7_lrg.jpg/0?wchp=dGLbVlk-zSkWb motion of the β hairpin] unwinds the DNA through the central channel <ref name='D'>PMID:15454080</ref>.<br /> <br /> <br /> ===== Tumorigenesis =====<br /> <br /> <br /> ==== References ====<br /> {{reflist}}</div>

Udayan Shevade https://proteopedia.org/index.php?title=User:Udayan_Shevade/Sandbox1&diff=1317437 User:Udayan Shevade/Sandbox1 2011-11-14T03:18:43Z

<p>Udayan Shevade: </p> <hr /> <div>= SV40 Large T Antigen =<br /> <br /> === Introduction ===<br /> <br /> The '''SV40 large tumor antigen''' is a multifunctional regulatory protein encoded by Simian Virus 40. It is classified under the AAA+ family of helicases <ref name="A">PMID:8946857</ref>. 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.<br /> <br /> <br /> === Structure ===<br /> 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 <ref name="B">PMID:15454080</ref>.<br /> <br /> <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'><br /> ===== The Origin Binding Domain =====<br /> 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>. <br /> [[Image:Tagobd_dna_interactions.jpg|200px|left|thumb]]<br /> 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><br /> <br /> {{STRUCTURE_1svm| PDB=1svm | SCENE= }}<br /> <br /> ===== Helicase =====<br /> 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 [http://www.sciencedirect.com/cache/MiamiImageURL/1-s2.0-S0092867404008906-gr3_lrg.jpg/0?wchp=dGLbVlV-zSkWA transitions in conformation] between these states enable the unwinding of viral dsDNA. There are both cis- and trans-monomer interactions involving ATP. <scene name='User:Udayan_Shevade/Sandbox1/Helicase_cis_residues/1'>''Cis''-residues</scene> 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. <scene name='User:Udayan_Shevade/Sandbox1/Helicase_atp_water/1'>A water molecule</scene> near the ATP is present for stability and nucleophilic attack during hydrolysis. <scene name='User:Udayan_Shevade/Sandbox1/Helicase_trans_residues/1'>Six ''trans''-residues</scene>, 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 [http://www.sciencedirect.com/cache/MiamiImageURL/1-s2.0-S0092867404008906-gr7_lrg.jpg/0?wchp=dGLbVlk-zSkWb motion of the β hairpin] unwinds the DNA through the central channel <ref name='D'>PMID:15454080</ref>.<br /> <br /> <br /> ===== Tumorigenesis =====<br /> <br /> <br /> ==== References ====<br /> {{reflist}}</div>

Udayan Shevade https://proteopedia.org/index.php?title=User:Udayan_Shevade/Sandbox1&diff=1317435 User:Udayan Shevade/Sandbox1 2011-11-14T03:16:42Z

<p>Udayan Shevade: </p> <hr /> <div>= SV40 Large T Antigen =<br /> <br /> === Introduction ===<br /> <br /> The '''SV40 large tumor antigen''' is a multifunctional regulatory protein encoded by Simian Virus 40. It is classified under the AAA+ family of helicases <ref name="A">PMID:8946857</ref>. 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.<br /> <br /> <br /> === Structure ===<br /> 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 <ref name="B">PMID:15454080</ref>.<br /> <br /> <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'><br /> ===== The Origin Binding Domain =====<br /> 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>. <br /> [[Image:Tagobd_dna_interactions.jpg|200px|left|thumb]]<br /> 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><br /> <br /> {{STRUCTURE_1svm| PDB=1svm | SCENE= }}<br /> <br /> ===== Helicase =====<br /> 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 [http://www.sciencedirect.com/cache/MiamiImageURL/1-s2.0-S0092867404008906-gr3_lrg.jpg/0?wchp=dGLbVlV-zSkWA transitions in conformation] between these states enable the unwinding of viral dsDNA. There are both cis- and trans-monomer interactions involving ATP. <scene name='User:Udayan_Shevade/Sandbox1/Helicase_cis_residues/1'>''Cis''-residues</scene> 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. <scene name='User:Udayan_Shevade/Sandbox1/Helicase_atp_water/1'>A water molecule</scene> near the ATP is present for stability and nucleophilic attack during hydrolysis. <scene name='User:Udayan_Shevade/Sandbox1/Helicase_trans_residues/1'>Six ''trans''-residues</scene>, 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 [http://www.sciencedirect.com/cache/MiamiImageURL/1-s2.0-S0092867404008906-gr7_lrg.jpg/0?wchp=dGLbVlk-zSkWb motion of the β hairpin] unwinds the DNA through the central channel.<br /> <br /> <br /> ===== Tumorigenesis =====<br /> <br /> <br /> ==== References ====<br /> {{reflist}}</div>

Udayan Shevade https://proteopedia.org/index.php?title=User:Udayan_Shevade/Sandbox1&diff=1317434 User:Udayan Shevade/Sandbox1 2011-11-14T03:14:32Z

<p>Udayan Shevade: </p> <hr /> <div>= SV40 Large T Antigen =<br /> <br /> === Introduction ===<br /> <br /> The '''SV40 large tumor antigen''' is a multifunctional regulatory protein encoded by Simian Virus 40. It is classified under the AAA+ family of helicases <ref name="A">PMID:8946857</ref>. 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.<br /> <br /> <br /> === Structure ===<br /> 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 <ref name="B">PMID:15454080</ref>.<br /> <br /> <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'><br /> ===== The Origin Binding Domain =====<br /> 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>. <br /> [[Image:Tagobd_dna_interactions.jpg|200px|left|thumb]]<br /> 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><br /> <br /> {{STRUCTURE_1svm| PDB=1svm | SCENE= }}<br /> <br /> ===== Helicase =====<br /> 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. <scene name='User:Udayan_Shevade/Sandbox1/Helicase_cis_residues/1'>''Cis''-residues</scene> 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. <scene name='User:Udayan_Shevade/Sandbox1/Helicase_atp_water/1'>A water molecule</scene> near the ATP is present for stability and nucleophilic attack during hydrolysis. <scene name='User:Udayan_Shevade/Sandbox1/Helicase_trans_residues/1'>Six ''trans''-residues</scene>, 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 motion of the β hairpin unwinds the DNA through the channel.<br /> <br /> <br /> ===== Tumorigenesis =====<br /> <br /> <br /> ==== References ====<br /> {{reflist}}</div>

Udayan Shevade https://proteopedia.org/index.php?title=User:Udayan_Shevade/Sandbox1&diff=1317432 User:Udayan Shevade/Sandbox1 2011-11-14T03:13:49Z

<p>Udayan Shevade: </p> <hr /> <div>= SV40 Large T Antigen =<br /> <br /> === Introduction ===<br /> <br /> The '''SV40 large tumor antigen''' is a multifunctional regulatory protein encoded by Simian Virus 40. It is classified under the AAA+ family of helicases <ref name="A">PMID:8946857</ref>. 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.<br /> <br /> <br /> === Structure ===<br /> 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 <ref name="B">PMID:15454080</ref>.<br /> <br /> <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'><br /> ===== The Origin Binding Domain =====<br /> 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>. <br /> [[Image:Tagobd_dna_interactions.jpg|200px|left|thumb]]<br /> 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><br /> <br /> {{STRUCTURE_1svm| PDB=1svm | SCENE= }}<br /> <br /> ===== Helicase =====<br /> 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. <scene name='User:Udayan_Shevade/Sandbox1/Helicase_cis_residues/1'>''Cis''-residues</scene>''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. <scene name='User:Udayan_Shevade/Sandbox1/Helicase_atp_water/1'>A water molecule</scene> near the ATP is present for stability and nucleophilic attack during hydrolysis. <scene name='User:Udayan_Shevade/Sandbox1/Helicase_trans_residues/1'>Six ''trans''-residues</scene>, 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 motion of the β hairpin unwinds the DNA through the channel.<br /> <br /> <br /> ===== Tumorigenesis =====<br /> <br /> <br /> ==== References ====<br /> {{reflist}}</div>

Udayan Shevade https://proteopedia.org/index.php?title=User:Udayan_Shevade/Sandbox1&diff=1317405 User:Udayan Shevade/Sandbox1 2011-11-14T02:37:27Z

<p>Udayan Shevade: </p> <hr /> <div>= SV40 Large T Antigen =<br /> <br /> === Introduction ===<br /> <br /> The '''SV40 large tumor antigen''' is a multifunctional regulatory protein encoded by Simian Virus 40. It is classified under the AAA+ family of helicases <ref name="A">PMID:8946857</ref>. 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.<br /> <br /> <br /> === Structure ===<br /> 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 <ref name="B">PMID:15454080</ref>.<br /> <br /> <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'><br /> ===== The Origin Binding Domain =====<br /> 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>. <br /> [[Image:Tagobd_dna_interactions.jpg|200px|left|thumb]]<br /> 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><br /> <br /> {{STRUCTURE_1svm| PDB=1svm | SCENE= }}<br /> <br /> ===== Helicase =====<br /> 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. <scene name='User:Udayan_Shevade/Sandbox1/Helicase_cis_residues/1'>''Cis''-residues</scene>''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. <scene name='User:Udayan_Shevade/Sandbox1/Helicase_atp_water/1'>A water molecule</scene> near the ATP is present for stability and nucleophilic attack during hydrolysis. <scene name='User:Udayan_Shevade/Sandbox1/Helicase_trans_residues/1'>Six ''trans''-residues</scene>, 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.<br /> <br /> <br /> <br /> ==== References ====<br /> {{reflist}}</div>

Udayan Shevade https://proteopedia.org/index.php?title=User:Udayan_Shevade/Sandbox1&diff=1317258 User:Udayan Shevade/Sandbox1 2011-11-13T23:59:12Z

<p>Udayan Shevade: </p> <hr /> <div>= SV40 Large T Antigen =<br /> <br /> === Introduction ===<br /> <br /> The '''SV40 large tumor antigen''' is a multifunctional regulatory protein encoded by Simian Virus 40. It is classified under the AAA+ family of helicases <ref name="A">PMID:8946857</ref>. 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.<br /> <br /> <br /> === Structure ===<br /> 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 <ref name="B">PMID:15454080</ref>.<br /> <br /> <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'><br /> ===== The Origin Binding Domain =====<br /> 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>. <br /> [[Image:Tagobd_dna_interactions.jpg|200px|left|thumb]]<br /> 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><br /> <br /> {{STRUCTURE_1svm| PDB=1svm | SCENE= }}<br /> <br /> ===== Helicase =====<br /> 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.<br /> <br /> <br /> <br /> ==== References ====<br /> {{reflist}}</div>

Udayan Shevade https://proteopedia.org/index.php?title=User:Udayan_Shevade/Sandbox1&diff=1317255 User:Udayan Shevade/Sandbox1 2011-11-13T23:58:14Z

<p>Udayan Shevade: </p> <hr /> <div>= SV40 Large T Antigen =<br /> <br /> === Introduction ===<br /> <br /> The '''SV40 large tumor antigen''' is a multifunctional regulatory protein encoded by Simian Virus 40. It is classified under the AAA+ family of helicases <ref name="A">PMID:8946857</ref>. 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.<br /> <br /> <br /> === Structure ===<br /> 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 <ref name="B">PMID:15454080</ref>.<br /> <br /> <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'><br /> ==== The Origin Binding Domain ====<br /> 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>. <br /> [[Image:Tagobd_dna_interactions.jpg|200px|left|thumb]]<br /> 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><br /> <br /> <br /> {{STRUCTURE_1svm| PDB=1svm | SCENE= }}<br /> <br /> <br /> ==== Helicase ====<br /> 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.<br /> <br /> <br /> <br /> ==== References ====<br /> {{reflist}}</div>

Udayan Shevade https://proteopedia.org/index.php?title=User:Udayan_Shevade/Sandbox1&diff=1316901 User:Udayan Shevade/Sandbox1 2011-11-12T23:28:40Z

<p>Udayan Shevade: </p> <hr /> <div>= SV40 Large T Antigen =<br /> <br /> === Introduction ===<br /> <br /> The '''SV40 large tumor antigen''' is a multifunctional regulatory protein encoded by Simian Virus 40. It is classified under the AAA+ family of helicases <ref name="A">PMID:8946857</ref>. 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.<br /> <br /> <br /> === Structure ===<br /> 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 <ref name="B">PMID:15454080</ref>. The activities of each are covered briefly below.<br /> <br /> <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'><br /> ==== The Origin Binding Domain ====<br /> 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 fully assembled 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>. <br /> [[Image:Tagobd_dna_interactions.jpg|200px|left|thumb]]<br /> Binding of large T antigen at the origin of replication allows replicative machinery to unwind and synthesize new DNA. Residues necessary for DNA binding also bind with single-stranded DNA 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><br /> <br /> <br /> {{STRUCTURE_1svm| PDB=1svm | SCENE= }}<br /> <br /> <br /> ==== Helicase ====<br /> The helicase monomer consists of 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.<br /> <br /> <br /> <br /> ==== References ====<br /> {{reflist}}</div>

Udayan Shevade https://proteopedia.org/index.php?title=User:Udayan_Shevade/Sandbox1&diff=1316900 User:Udayan Shevade/Sandbox1 2011-11-12T23:28:02Z

<p>Udayan Shevade: </p> <hr /> <div>= SV40 Large T Antigen =<br /> <br /> === Introduction ===<br /> <br /> The '''SV40 large tumor antigen''' is a multifunctional regulatory protein encoded by Simian Virus 40. It is classified under the AAA+ family of helicases <ref name="A">PMID:8946857</ref>. 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.<br /> <br /> <br /> === Structure ===<br /> 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 <ref name="B">PMID:15454080</ref>. The activities of each are covered briefly below.<br /> <br /> <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'><br /> ==== The Origin Binding Domain ====<br /> 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 fully assembled 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>. <br /> [[Image:Tagobd_dna_interactions.jpg|200px|left|thumb]]<br /> Binding of large T antigen at the origin of replication allows replicative machinery to unwind and synthesize new DNA. Residues necessary for DNA binding also bind with single-stranded DNA 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><br /> <br /> <br /> {{STRUCTURE_1svm| PDB=1svm | SCENE= }}<br /> <br /> <br /> ==== Helicase ====<br /> The helicase monomer consists of 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.<br /> <br /> <br /> <br /> ==== References ====<br /> {{reflist}}</div>

Udayan Shevade https://proteopedia.org/index.php?title=User:Udayan_Shevade/Sandbox1&diff=1316899 User:Udayan Shevade/Sandbox1 2011-11-12T23:27:22Z

<p>Udayan Shevade: </p> <hr /> <div>= SV40 Large T Antigen =<br /> <br /> === Introduction ===<br /> <br /> The '''SV40 large tumor antigen''' is a multifunctional regulatory protein encoded by Simian Virus 40. It is classified under the AAA+ family of helicases <ref name="A">PMID:8946857</ref>. 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.<br /> <br /> <br /> === Structure ===<br /> 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 <ref name="B">PMID:15454080</ref>. The activities of each are covered briefly below.<br /> <br /> <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'><br /> ==== The Origin Binding Domain ====<br /> 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 fully assembled 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>. <br /> [[Image:Tagobd_dna_interactions.jpg|200px|left|thumb]]<br /> Binding of large T antigen at the origin of replication entails conformational changes and allows replicative machinery to unwind and synthesize new DNA. Residues necessary for DNA binding also bind with single-stranded DNA 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><br /> <br /> <br /> {{STRUCTURE_1svm| PDB=1svm | SCENE= }}<br /> <br /> <br /> ==== Helicase ====<br /> The helicase monomer consists of 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.<br /> <br /> <br /> <br /> ==== References ====<br /> {{reflist}}</div>

Udayan Shevade https://proteopedia.org/index.php?title=User:Udayan_Shevade/Sandbox1&diff=1316898 User:Udayan Shevade/Sandbox1 2011-11-12T23:26:55Z

<p>Udayan Shevade: </p> <hr /> <div>= SV40 Large T Antigen =<br /> <br /> === Introduction ===<br /> <br /> The '''SV40 large tumor antigen''' is a multifunctional regulatory protein encoded by Simian Virus 40. It is classified under the AAA+ family of helicases <ref name="A">PMID:8946857</ref>. 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.<br /> <br /> <br /> === Structure ===<br /> 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 <ref name="B">PMID:15454080</ref>. The activities of each are covered briefly below.<br /> <br /> <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'><br /> ==== The Origin Binding Domain ====<br /> 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 fully assembled 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>. <br /> [[Image:Tagobd_dna_interactions.jpg|200px|left|thumb]]<br /> Binding of large T antigen at the origin of replication entails conformational changes and allows replicative machinery to unwind and synthesize new DNA. Residues necessary for DNA binding also bind with single-stranded DNA binding protein human RPA<ref>PMID:2600586</ref>. It 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><br /> <br /> <br /> {{STRUCTURE_1svm| PDB=1svm | SCENE= }}<br /> <br /> <br /> ==== Helicase ====<br /> The helicase monomer consists of 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.<br /> <br /> <br /> <br /> ==== References ====<br /> {{reflist}}</div>

Udayan Shevade https://proteopedia.org/index.php?title=User:Udayan_Shevade/Sandbox1&diff=1316897 User:Udayan Shevade/Sandbox1 2011-11-12T23:12:23Z

<p>Udayan Shevade: </p> <hr /> <div>= SV40 Large T Antigen =<br /> <br /> === Introduction ===<br /> <br /> The '''SV40 large tumor antigen''' is a multifunctional regulatory protein encoded by Simian Virus 40. It is classified under the AAA+ family of helicases <ref name="A">PMID:8946857</ref>. 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.<br /> <br /> <br /> === Structure ===<br /> 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 <ref name="B">PMID:15454080</ref>. The activities of each are covered briefly below.<br /> <br /> <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'><br /> ==== The Origin Binding Domain ====<br /> 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 fully assembled 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>. <br /> [[Image:Tagobd_dna_interactions.jpg|200px|left|thumb]] <br /> Binding of large T antigen at the origin of replication allows replicative machinery to unwind and synthesize new DNA. 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><br /> <br /> <br /> {{STRUCTURE_1svm| PDB=1svm | SCENE= }}<br /> <br /> <br /> ==== Helicase ====<br /> The helicase monomer consists of 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.<br /> <br /> <br /> <br /> ==== References ====<br /> {{reflist}}</div>

Udayan Shevade https://proteopedia.org/index.php?title=User:Udayan_Shevade/Sandbox1&diff=1316896 User:Udayan Shevade/Sandbox1 2011-11-12T23:03:48Z

<p>Udayan Shevade: </p> <hr /> <div>= SV40 Large T Antigen =<br /> <br /> === Introduction ===<br /> <br /> The '''SV40 large tumor antigen''' is a multifunctional regulatory protein encoded by Simian Virus 40. It is classified under the AAA+ family of helicases <ref name="A">PMID:8946857</ref>. 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.<br /> <br /> <br /> === Structure ===<br /> 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 <ref name="B">PMID:15454080</ref>. The activities of each are covered briefly below.<br /> <br /> <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'><br /> ==== The Origin Binding Domain ====<br /> 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>. <br /> [[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. 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><br /> <br /> <br /> {{STRUCTURE_1svm| PDB=1svm | SCENE= }}<br /> <br /> <br /> ==== Helicase ====<br /> The helicase monomer consists of a AAA+ domain. As with the origin-binding domain, these monomers also hexamerize. However the complex does not form a spiral, but a flat ring. Each monomer binds and hydrolyzes an ATP in the presence of magnesium ion and drives an overall conformational change in the hexamer.<br /> <br /> <br /> <br /> ==== References ====<br /> {{reflist}}</div>

Udayan Shevade https://proteopedia.org/index.php?title=User:Udayan_Shevade/Sandbox1&diff=1316893 User:Udayan Shevade/Sandbox1 2011-11-12T22:51:02Z

<p>Udayan Shevade: </p> <hr /> <div>= SV40 Large T Antigen =<br /> <br /> === Introduction ===<br /> <br /> The '''SV40 large tumor antigen''' is a multifunctional regulatory protein encoded by Simian Virus 40. It is classified under the AAA+ family of helicases <ref name="A">PMID:8946857</ref>. 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.<br /> <br /> <br /> === Structure ===<br /> 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 <ref name="B">PMID:15454080</ref>. The activities of each are covered briefly below.<br /> <br /> <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'><br /> ==== The Origin Binding Domain ====<br /> 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>. <br /> [[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. 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><br /> <br /> <br /> {{STRUCTURE_1svm| PDB=1svm | SCENE= }}<br /> <br /> <br /> ==== Helicase ====<br /> 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.</div>

Udayan Shevade https://proteopedia.org/index.php?title=User:Udayan_Shevade/Sandbox1&diff=1316892 User:Udayan Shevade/Sandbox1 2011-11-12T22:25:21Z

<p>Udayan Shevade: </p> <hr /> <div>= SV40 Large T Antigen =<br /> <br /> === Introduction ===<br /> <br /> The '''SV40 large tumor antigen''' is a multifunctional regulatory protein encoded by Simian Virus 40. It is classified under the AAA+ family of helicases <ref name="A">PMID:8946857</ref>. 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.<br /> <br /> <br /> === Structure ===<br /> 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 <ref name="B">PMID:15454080</ref>. The activities of each are covered briefly below.<br /> <br /> <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'><br /> ==== The Origin Binding Domain ====<br /> 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>. <br /> [[Image:Tagobd_dna_interactions.jpg|200px|left|thumb]] Binding of T antigen at the origin of replication allows replicative machinery to unwind and synthesize new DNA. It also acts as a repressor of early gene transcription. When increased amounts of T antigen are present, T antigen binds DNA and blocks the overlapping promoter sequence, thus behaving as its own regulator.</Structuresection><br /> <br /> <br /> {{STRUCTURE_1svm| PDB=1svm | SCENE= }}<br /> <br /> <br /> ==== Helicase ====<br /> 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.</div>

Udayan Shevade https://proteopedia.org/index.php?title=User:Udayan_Shevade/Sandbox1&diff=1316891 User:Udayan Shevade/Sandbox1 2011-11-12T22:20:16Z

<p>Udayan Shevade: </p> <hr /> <div>= SV40 Large T Antigen =<br /> <br /> === Introduction ===<br /> <br /> The '''SV40 large tumor antigen''' is a multifunctional regulatory protein encoded by Simian Virus 40. It is classified under the AAA+ family of helicases <ref name="A">PMID:8946857</ref>. 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.<br /> <br /> <br /> === Structure ===<br /> 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 <ref name="B">PMID:15454080</ref>. The activities of each are covered briefly below.<br /> <br /> <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'><br /> ==== The Origin Binding Domain ====<br /> 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>. <br /> [[Image:Tagobd_dna_interactions.jpg|200px|left|thumb]]</Structuresection><br /> <br /> <br /> {{STRUCTURE_1svm| PDB=1svm | SCENE= }}<br /> <br /> <br /> ==== Helicase ====<br /> 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.</div>

Udayan Shevade https://proteopedia.org/index.php?title=User:Udayan_Shevade/Sandbox1&diff=1316890 User:Udayan Shevade/Sandbox1 2011-11-12T22:12:26Z

<p>Udayan Shevade: </p> <hr /> <div>= SV40 Large T Antigen =<br /> <br /> === Introduction ===<br /> <br /> The '''SV40 large tumor antigen''' is a multifunctional regulatory protein encoded by Simian Virus 40. It is classified under the AAA+ family of helicases <ref name="A">PMID:8946857</ref>. 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.<br /> <br /> <br /> === Structure ===<br /> 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 <ref name="B">PMID:15454080</ref>. The activities of each are covered briefly below.<br /> <br /> <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'><br /> ==== The Origin Binding Domain ====<br /> 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>. <br /> [[Image:Tagobd_dna_interactions.jpg|200px|left|thumb]]</Structuresection><br /> <br /> <br /> {{STRUCTURE_1svm| PDB=1svm | SCENE= }}<br /> <br /> <br /> ==== Helicase ====<br /> 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.</div>

Udayan Shevade https://proteopedia.org/index.php?title=User:Udayan_Shevade/Sandbox1&diff=1316888 User:Udayan Shevade/Sandbox1 2011-11-12T21:57:12Z

<p>Udayan Shevade: </p> <hr /> <div>= SV40 Large T Antigen =<br /> <br /> === Introduction ===<br /> <br /> The '''SV40 large tumor antigen''' is a multifunctional regulatory protein encoded by Simian Virus 40. It is classified under the AAA+ family of helicases <ref name="A">PMID:8946857</ref>. 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.<br /> <br /> <br /> === Structure ===<br /> 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 <ref name="B">PMID:15454080</ref>. The activities of each are covered briefly below.<br /> <br /> <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'><br /> ==== The Origin Binding Domain ====<br /> 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. The hexamer 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 primarily make the base-specific interactions with DNA, whereas residues from the B2 loop interact mainly with the phosphate backbone. These interactions bury a large area of the protein and give rise to a 60nM K<sub>d</sub>.<ref name="C">PMID:1779811</ref>. <br /> [[Image:Tagobd_dna_interactions.jpg|200px|left|thumb]]</Structuresection><br /> <br /> <br /> {{STRUCTURE_1svm| PDB=1svm | SCENE= }}<br /> <br /> <br /> ==== Helicase ====<br /> 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.</div>

Udayan Shevade https://proteopedia.org/index.php?title=User:Udayan_Shevade/Sandbox1&diff=1316886 User:Udayan Shevade/Sandbox1 2011-11-12T21:51:56Z

<p>Udayan Shevade: </p> <hr /> <div>= SV40 Large T Antigen =<br /> <br /> === Introduction ===<br /> <br /> The '''SV40 large tumor antigen''' is a multifunctional regulatory protein encoded by Simian Virus 40. It is classified under the AAA+ family of helicases <ref name="A">PMID:8946857</ref>. 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.<br /> <br /> <br /> === Structure ===<br /> 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 <ref name="B">PMID:15454080</ref>. The activities of each are covered briefly below.<br /> <br /> <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'><br /> ==== The Origin Binding Domain ====<br /> 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. The hexamer 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 primarily make the base-specific interactions with DNA, whereas residues from the B2 loop interact mainly with the phosphate backbone<ref name="C">PMID:1779811</ref>. <br /> [[Image:Tagobd_dna_interactions.jpg|200px|left|thumb]]</Structuresection><br /> <br /> <br /> {{STRUCTURE_1svm| PDB=1svm | SCENE= }}<br /> <br /> <br /> ==== Helicase ====<br /> 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.</div>

Udayan Shevade https://proteopedia.org/index.php?title=User:Udayan_Shevade/Sandbox1&diff=1316885 User:Udayan Shevade/Sandbox1 2011-11-12T21:48:28Z

<p>Udayan Shevade: </p> <hr /> <div>= SV40 Large T Antigen =<br /> <br /> === Introduction ===<br /> <br /> The '''SV40 large tumor antigen''' is a multifunctional regulatory protein encoded by Simian Virus 40. It is classified under the AAA+ family of helicases <ref name="A">PMID:8946857</ref>. 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.<br /> <br /> <br /> === Structure ===<br /> 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 <ref name="B">PMID:15454080</ref>. The activities of each are covered briefly below.<br /> <br /> <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'><br /> ==== The Origin Binding Domain ====<br /> 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. The hexamer 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, despite varying protein sequences, suggesting a mechanism of recognition distinct to the virus. The Asn and Arg within the A1 motif primarily make the base-specific interactions with DNA, whereas residues from the B2 loop interact mainly with the phosphate backbone<ref name="C">PMID:1779811</ref>. <br /> [[Image:Tagobd_dna_interactions.jpg|200px|left|thumb]]</Structuresection><br /> <br /> <br /> {{STRUCTURE_1svm| PDB=1svm | SCENE= }}<br /> <br /> <br /> ==== Helicase ====<br /> 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.</div>

Udayan Shevade https://proteopedia.org/index.php?title=User:Udayan_Shevade/Sandbox1&diff=1316884 User:Udayan Shevade/Sandbox1 2011-11-12T21:47:53Z

<p>Udayan Shevade: </p> <hr /> <div>= SV40 Large T Antigen =<br /> <br /> === Introduction ===<br /> <br /> The '''large tumor antigen''' is a multifunctional regulatory protein encoded by Simian Virus 40. It is classified under the AAA+ family of helicases <ref name="A">PMID:8946857</ref>. 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.<br /> <br /> <br /> === Structure ===<br /> 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 <ref name="B">PMID:15454080</ref>. The activities of each are covered briefly below.<br /> <br /> <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'><br /> ==== The Origin Binding Domain ====<br /> 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. The hexamer 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, despite varying protein sequences, suggesting a mechanism of recognition distinct to the virus. The Asn and Arg within the A1 motif primarily make the base-specific interactions with DNA, whereas residues from the B2 loop interact mainly with the phosphate backbone<ref name="C">PMID:1779811</ref>. <br /> [[Image:Tagobd_dna_interactions.jpg|200px|left|thumb]]</Structuresection><br /> <br /> <br /> {{STRUCTURE_1svm| PDB=1svm | SCENE= }}<br /> <br /> <br /> ==== Helicase ====<br /> 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.</div>

Udayan Shevade https://proteopedia.org/index.php?title=File:Tagobd_dna_interactions.jpg&diff=1316883 File:Tagobd dna interactions.jpg 2011-11-12T21:39:40Z

<p>Udayan Shevade: Taken from "The Crystal Structure of the SV40 T Antigen Origin Binding Domain in Complex with DNA" by Meinke, G. et al. (PLoS Biology 2007), this figure shows the interaction of the sequence-specific origin binding domain residues with GAGGC pentanucleoti</p> <hr /> <div>== Summary ==<br /> Taken from "The Crystal Structure of the SV40 T Antigen Origin Binding Domain in Complex with DNA" by Meinke, G. et al. (PLoS Biology 2007), this figure shows the interaction of the sequence-specific origin binding domain residues with GAGGC pentanucleotides at the origin of replication on SV40 DNA<br /> == Licensing ==<br /> {{cc-by-3.0}}</div>

Udayan Shevade https://proteopedia.org/index.php?title=User:Udayan_Shevade/Sandbox1&diff=1316833 User:Udayan Shevade/Sandbox1 2011-11-12T06:23:45Z

<p>Udayan Shevade: </p> <hr /> <div>= SV40 Large T Antigen =<br /> <br /> === Introduction ===<br /> <br /> The large tumor antigen is a multifunctional regulatory protein encoded by Simian Virus 40. It is classified under the AAA+ family of helicases <ref name="A">PMID:8946857</ref>. Noteworthy for its versatility, the protein is responsible for initiation of viral DNA replication, regulation of viral transcription and alteration of the host cell cycle to promote viral infectivity. Large T-antigen is an early gene product of SV40 and is produced via differential mRNA splicing.<br /> <br /> <br /> === Structure ===<br /> <br /> T-antigen consists of an N-terminal J domain, a central origin-binding domain, and a C-terminal helicase domain <ref name="A"/>.<br /> <br /> <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'><br /> <br /> ==== The Origin Binding Domain ====<br /> 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. The hexamer forms a central pore 40 Angstroms wide, large enough for double stranded DNA, and carries a positive charge. The monomers bind a series of GAGGC pentanucleotide sequences P1 through P4, collectively known as Site II. <scene name='User:Udayan_Shevade/Sandbox1/Obd_residues/1'>The residues</scene> implicated in DNA binding along the inner surface of the pore are <scene name='User:Udayan_Shevade/Sandbox1/Obd_153_154_155/5'>Asn 153, Arg 154, Thr 155 from the A 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"/>.</Structuresection><br /> <br /> <br /> {{STRUCTURE_1svm| PDB=1svm | SCENE= }}<br /> <br /> <br /> ==== Helicase ====<br /> 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.</div>

Udayan Shevade https://proteopedia.org/index.php?title=User:Udayan_Shevade/Sandbox1&diff=1316828 User:Udayan Shevade/Sandbox1 2011-11-12T05:54:57Z

<p>Udayan Shevade: </p> <hr /> <div>= SV40 Large T Antigen =<br /> <br /> === Introduction ===<br /> <br /> The SV40 large tumor antigen is a multifunctional regulatory protein encoded by Simian Virus 40, belonging to the AAA+ family of helicases <ref name="A">PMID:8946857</ref>. Noteworthy for its versatility, the protein is responsible for initiation of viral DNA replication, regulation of viral transcription and alteration of the host cell cycle to promote viral infectivity. Large T-antigen is an early gene product of SV40 and is translated after differential mRNA splicing.<br /> <br /> <br /> === Structure ===<br /> <br /> T-antigen consists of an N-terminal J domain, a central origin-binding domain, and a C-terminal helicase domain <ref name="A"/>.<br /> <br /> <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'><br /> <br /> ==== The Origin Binding Domain ====<br /> The obd monomer consists of five anti-parallel beta sheets flanked on either side by a pair of alpha helices. These monomers arrange tightly into a [http://www.pdb.org/pdb/explore/jmol.do?structureId=2FUF&bionumber=1 hexameric left-handed spiral], with 6 obd's per turn. Side-side interaction is necessary in hexamerization, for which residues <scene name='User:Udayan_Shevade/Sandbox1/Obd_183_185/1'>Phe 183 and Ser 185</scene> are crucial. The hexameric conformation creates a central channel 40 Angstroms wide, large enough for double stranded DNA, and positively charged. The pitch of the spiral complements that of DNA, allowing the specific assembly of a double hexamer at the origin of replication. Along the inner surface of the channel, <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 A 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"/>.</Structuresection><br /> <br /> {{STRUCTURE_1svm| PDB=1svm | SCENE= }}<br /> <br /> <br /> ==== Helicase ====<br /> 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.</div>

Udayan Shevade https://proteopedia.org/index.php?title=User:Udayan_Shevade/Sandbox1&diff=1316798 User:Udayan Shevade/Sandbox1 2011-11-12T02:47:31Z

<p>Udayan Shevade: </p> <hr /> <div>= SV40 Large T Antigen =<br /> <br /> === Introduction ===<br /> <br /> The SV40 large tumor antigen is a multifunctional regulatory protein encoded by Simian Virus 40. It belongs to the AAA+ family of helicases <ref name="A">PMID:8946857</ref>. Noteworthy for its versatility, the protein is responsible for initiation of viral DNA replication, regulation of viral transcription and alteration of the host cell cycle to promote viral infectivity. Large T-antigen is an early gene product of SV40 and is translated after differential mRNA splicing.<br /> <br /> <br /> === Structure ===<br /> <br /> T-antigen consists of an N-terminal J domain, a central origin-binding domain, and a C-terminal helicase domain <ref name="A"/>.<br /> <br /> <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'><br /> <br /> ==== The Origin Binding Domain ====<br /> The obd monomer consists of five anti-parallel beta sheets flanked on either side by a pair of alpha helices. These monomers arrange tightly into a [http://www.pdb.org/pdb/explore/jmol.do?structureId=2FUF&bionumber=1 hexameric left-handed spiral], with 6 obd's per turn. Side-side interaction is necessary in hexamerization, for which residues <scene name='User:Udayan_Shevade/Sandbox1/Obd_183_185/1'>Phe 183 and Ser 185</scene> are crucial. The hexameric conformation creates a central channel 40 Angstroms wide, large enough for double stranded DNA, and positively charged. The pitch of the spiral complements that of DNA, allowing the specific assembly of a double hexamer at the origin of replication. Along the inner surface of the channel, <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 A 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"/>.</Structuresection><br /> <br /> {{STRUCTURE_1svm| PDB=1svm | SCENE= }}<br /> <br /> <br /> ==== Helicase ====<br /> 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.</div>

Udayan Shevade https://proteopedia.org/index.php?title=User:Udayan_Shevade/Sandbox1&diff=1316797 User:Udayan Shevade/Sandbox1 2011-11-12T02:32:20Z

<p>Udayan Shevade: </p> <hr /> <div>= SV40 Large T Antigen =<br /> <br /> === Introduction ===<br /> <br /> The SV40 large T antigen is a multifunctional regulatory protein encoded by Simian Virus 40. It belongs to the AAA+ family of helicases <ref name="A">PMID:8946857</ref>. The protein is responsible for initiation of DNA replication, regulation of transcription and alteration of the host cell cycle to promote infectivity. Large T antigen is an early gene product of SV40 and is translated via differential mRNA splicing.<br /> <br /> <br /> === Structure ===<br /> <br /> T-antigen consists of an N-terminal J domain, a central origin-binding domain, and a C-terminal helicase domain <ref name="A"/>.<br /> <br /> <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'><br /> <br /> ==== The Origin Binding Domain ====<br /> The obd monomer consists of a five-stranded anti-parallel beta sheet flanked on either side by a pair of alpha helices. These monomers arrange tightly into a [http://www.pdb.org/pdb/explore/jmol.do?structureId=2FUF&bionumber=1 hexameric left-handed spiral] with 6 obd's per turn. Side-side interaction is crucial in hexamerization, for which residues <scene name='User:Udayan_Shevade/Sandbox1/Obd_183_185/1'>Phe 183 and Ser 185</scene> are crucial. The hexameric conformation creates a central channel 40 Angstroms wide, large enough for double stranded DNA, and is positively charged. The pitch of the spiral complements that of DNA, allowing a specific assembly of a double hexamer at the origin of replication. Along the inner surface of the channel, <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 A 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"/>.</Structuresection><br /> <br /> {{STRUCTURE_1svm| PDB=1svm | SCENE= }}<br /> <br /> <br /> ==== Helicase ====<br /> The monomer of the helicase contains a AAA+ domain. Each monomer binds and hydrolyzes an ATP in the presence of magnesium and drives an overall conformational change in the hexamer.</div>

Udayan Shevade https://proteopedia.org/index.php?title=User:Udayan_Shevade/Sandbox1&diff=1316796 User:Udayan Shevade/Sandbox1 2011-11-12T02:31:19Z

<p>Udayan Shevade: </p> <hr /> <div>= SV40 Large T Antigen =<br /> <br /> === Introduction ===<br /> <br /> The SV40 large T antigen is a multifunctional regulatory protein encoded by Simian Virus 40. It belongs to the AAA+ family of helicases <ref name="A">PMID:8946857</ref>. The protein is responsible for initiation of DNA replication, regulation of transcription and alteration of the host cell cycle to promote infectivity. Large T antigen is an early gene product of SV40 and is translated via differential mRNA splicing.<br /> <br /> <br /> === Structure ===<br /> <br /> T-antigen consists of an N-terminal J domain, a central origin-binding domain, and a C-terminal helicase domain <ref name="A"/>.<br /> <br /> <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'><br /> <br /> ==== The Origin Binding Domain ====<br /> The obd monomer consists of a five-stranded anti-parallel beta sheet flanked on either side by a pair of alpha helices. These monomers arrange tightly into a [http://www.pdb.org/pdb/explore/jmol.do?structureId=2FUF&bionumber=1 hexameric left-handed spiral] with 6 obd's per turn. Side-side interaction is crucial in hexamerization, for which residues <scene name='User:Udayan_Shevade/Sandbox1/Obd_183_185/1'>Phe 183 and Ser 185</scene> are crucial. The conformation creates a central channel 40 Angstroms wide, large enough for double stranded DNA, and is positively charged. The pitch of the spiral complements that of DNA, allowing a specific assembly of a double hexamer at the origin of replication. Along the inner surface of the channel, <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 A 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"/>.</Structuresection><br /> <br /> {{STRUCTURE_1svm| PDB=1svm | SCENE= }}<br /> <br /> <br /> ==== Helicase ====<br /> The monomer of the helicase contains a AAA+ domain. Each monomer binds and hydrolyzes an ATP in the presence of magnesium and drives an overall conformational change in the hexamer.</div>

Udayan Shevade https://proteopedia.org/index.php?title=User:Udayan_Shevade/Sandbox1&diff=1316783 User:Udayan Shevade/Sandbox1 2011-11-11T22:05:05Z

<p>Udayan Shevade: </p> <hr /> <div>= SV40 Large T Antigen =<br /> <br /> === Introduction ===<br /> <br /> The SV40 large T antigen is a multifunctional regulatory protein encoded by Simian Virus 40. It belongs to the AAA+ family of helicases <ref name="A">PMID:8946857</ref>. The protein is responsible for initiation of DNA replication, regulation of transcription and alteration of the host cell cycle to promote infectivity. Large T antigen is an early gene product of SV40 and is translated via differential mRNA splicing.<br /> <br /> <br /> === Structure ===<br /> <br /> T-antigen consists of an N-terminal J domain, a central origin-binding domain, and a C-terminal helicase domain <ref name="A"/>.<br /> <br /> <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'><br /> <br /> ==== The Origin Binding Domain ====<br /> The obd monomer consists of a five-stranded anti-parallel beta sheet flanked on either side by a pair of alpha helices. These monomers arrange tightly into a [http://www.pdb.org/pdb/explore/jmol.do?structureId=2FUF&bionumber=1 hexameric left-handed spiral] with 6 obd's per turn. Side-side interaction is crucial in hexamerization, for which residues <scene name='User:Udayan_Shevade/Sandbox1/Obd_183_185/1'>Phe 183 and Ser 185</scene> are crucial. The conformation creates a central channel 60 Angstroms wide, large enough for double stranded DNA, and is positively charged. The pitch of the spiral complements that of DNA, allowing a specific assembly of a double hexamer at the origin of replication. Along the inner surface of the channel, residues implicated in DNA binding are <scene name='User:Udayan_Shevade/Sandbox1/Obd_153_154_155/5'>Asn 153, Arg 154, Thr 155 from the A motif</scene>; His 203, Arg 204 from the B2 motif; as well as His 201 and Arg 202. This region is specific for binding to the GAGGC pentanucleotide <ref name="A"/>.</Structuresection><br /> <br /> {{STRUCTURE_1svm| PDB=1svm | SCENE= }}<br /> <br /> <br /> ==== Helicase ====<br /> The monomer of the helicase contains a AAA+ domain. Each monomer binds and hydrolyzes an ATP in the presence of magnesium and drives an overall conformational change in the hexamer.</div>

Udayan Shevade https://proteopedia.org/index.php?title=User:Udayan_Shevade/Sandbox1&diff=1316781 User:Udayan Shevade/Sandbox1 2011-11-11T20:50:47Z

<p>Udayan Shevade: </p> <hr /> <div>= SV40 Large T Antigen =<br /> <br /> === Introduction ===<br /> <br /> The SV40 large T antigen is a multifunctional regulatory protein encoded by Simian Virus 40. It belongs to the AAA+ family of helicases <ref name="A">PMID:8946857</ref>. The protein is responsible for initiation of DNA replication, regulation of transcription and alteration of the host cell cycle to promote infectivity. Large T antigen is an early gene product of SV40 and is translated via differential mRNA splicing.<br /> <br /> <br /> === Structure ===<br /> <br /> T-antigen consists of an N-terminal J domain, a central origin-binding domain, and a C-terminal helicase domain <ref name="A"/>.<br /> <br /> <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'><br /> <br /> ==== The Origin Binding Domain ====<br /> The central obd monomer consists of a five-stranded anti-parallel beta sheet flanked by two pairs of alpha helices. These molecules arrange tightly into a [http://www.pdb.org/pdb/explore/jmol.do?structureId=2FUF&bionumber=1 hexameric left-handed spiral], with 6 obd's per turn. Side-side interaction is crucial in hexamerization, for which residues <scene name='User:Udayan_Shevade/Sandbox1/Obd_183_185/1'>Phe 183 and Ser 185</scene> are crucial. The conformation creates a central channel 60 Angstroms wide, large enough for double stranded DNA, and is positively charged. The pitch of the spiral complements that of the DNA, bringing the sequence-specific loops of the obd's near the GAGGC pentanucleotides of the origin. Along the inner surface of the channel, the residues implicated in DNA binding are Asn 153, Arg 154, Thr 155 from the A motif; His 203, Arg 204 from the B2 motif; as well as His 201 and Arg 202. <ref name="A"/>.</Structuresection><br /> <br /> {{STRUCTURE_1svm| PDB=1svm | SCENE= }}<br /> <br /> <br /> ==== Helicase ====<br /> The monomer of the helicase contains a AAA+ domain. Each monomer binds and hydrolyzes an ATP in the presence of magnesium and drives an overall conformational change in the hexamer.</div>

Udayan Shevade