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| | ==Crystal Structure of Rabbit Hemorrhagic Disease Virus RNA-dependent RNA polymerase complexed with Mn2+== | | ==Crystal Structure of Rabbit Hemorrhagic Disease Virus RNA-dependent RNA polymerase complexed with Mn2+== |
| - | <StructureSection load='1khw' size='340' side='right' caption='[[1khw]], [[Resolution|resolution]] 2.70Å' scene=''> | + | <StructureSection load='1khw' size='340' side='right'caption='[[1khw]], [[Resolution|resolution]] 2.70Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[1khw]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Rhdv Rhdv]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1KHW OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1KHW FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[1khw]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Rabbit_hemorrhagic_disease_virus Rabbit hemorrhagic disease virus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1KHW OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1KHW FirstGlance]. <br> |
| - | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</scene></td></tr> | + | </td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.7Å</td></tr> |
| - | <tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[1khv|1khv]]</td></tr> | + | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</scene></td></tr> |
| - | <tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/RNA-directed_RNA_polymerase RNA-directed RNA polymerase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.7.7.48 2.7.7.48] </span></td></tr>
| + | <tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1khw FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1khw OCA], [https://pdbe.org/1khw PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1khw RCSB], [https://www.ebi.ac.uk/pdbsum/1khw PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1khw ProSAT]</span></td></tr> |
| - | <tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1khw FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1khw OCA], [http://pdbe.org/1khw PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1khw RCSB], [http://www.ebi.ac.uk/pdbsum/1khw PDBsum]</span></td></tr> | + | |
| | </table> | | </table> |
| | == Function == | | == Function == |
| - | [[http://www.uniprot.org/uniprot/POLG_RHDVF POLG_RHDVF]] NTPase presumably plays a role in replication (By similarity).<ref>PMID:1887589</ref> <ref>PMID:15063122</ref> Viral genome-linked protein is covalently linked to the 5'-end of the positive-strand, negative-strand genomic RNAs and subgenomic RNA. Acts as a genome-linked replication primer. May recruit ribosome to viral RNA thereby promoting viral proteins translation (By similarity).<ref>PMID:1887589</ref> <ref>PMID:15063122</ref> 3C-like protease processes the polyprotein: 3CLpro-RdRp (p72) is first released by autocleavage, then all other proteins are cleaved (By similarity).<ref>PMID:1887589</ref> <ref>PMID:15063122</ref> RNA-directed RNA polymerase replicates genomic and antigenomic RNA by recognizing replications specific signals. Transcribes also a subgenomic mRNA by initiating RNA synthesis internally on antigenomic RNA. This sgRNA codes for structural proteins. Catalyzes the covalent attachment VPg with viral RNAs (By similarity).<ref>PMID:1887589</ref> <ref>PMID:15063122</ref> Capsid protein VP60 self assembles to form an icosahedral capsid with a T=3 symmetry, about 35 nm in diameter, and consisting of 180 capsid proteins. A smaller form of capsid with a diameter of 23 nm might be capsid proteins assembled as icosahedron with T=1 symmetry. The capsid encapsulate VP2 proteins and genomic or subgenomic RNA. Attaches virion to target cells by binding histo-blood group antigens, inducing endocytosis of the viral particle. Acidification of the endosome induces conformational change of capsid protein thereby injecting virus genomic RNA into host cytoplasm (By similarity).<ref>PMID:1887589</ref> <ref>PMID:15063122</ref> | + | [https://www.uniprot.org/uniprot/POLG_RHDVF POLG_RHDVF] NTPase presumably plays a role in replication (By similarity).<ref>PMID:1887589</ref> <ref>PMID:15063122</ref> Viral genome-linked protein is covalently linked to the 5'-end of the positive-strand, negative-strand genomic RNAs and subgenomic RNA. Acts as a genome-linked replication primer. May recruit ribosome to viral RNA thereby promoting viral proteins translation (By similarity).<ref>PMID:1887589</ref> <ref>PMID:15063122</ref> 3C-like protease processes the polyprotein: 3CLpro-RdRp (p72) is first released by autocleavage, then all other proteins are cleaved (By similarity).<ref>PMID:1887589</ref> <ref>PMID:15063122</ref> RNA-directed RNA polymerase replicates genomic and antigenomic RNA by recognizing replications specific signals. Transcribes also a subgenomic mRNA by initiating RNA synthesis internally on antigenomic RNA. This sgRNA codes for structural proteins. Catalyzes the covalent attachment VPg with viral RNAs (By similarity).<ref>PMID:1887589</ref> <ref>PMID:15063122</ref> Capsid protein VP60 self assembles to form an icosahedral capsid with a T=3 symmetry, about 35 nm in diameter, and consisting of 180 capsid proteins. A smaller form of capsid with a diameter of 23 nm might be capsid proteins assembled as icosahedron with T=1 symmetry. The capsid encapsulate VP2 proteins and genomic or subgenomic RNA. Attaches virion to target cells by binding histo-blood group antigens, inducing endocytosis of the viral particle. Acidification of the endosome induces conformational change of capsid protein thereby injecting virus genomic RNA into host cytoplasm (By similarity).<ref>PMID:1887589</ref> <ref>PMID:15063122</ref> |
| | == Evolutionary Conservation == | | == Evolutionary Conservation == |
| | [[Image:Consurf_key_small.gif|200px|right]] | | [[Image:Consurf_key_small.gif|200px|right]] |
| | Check<jmol> | | Check<jmol> |
| | <jmolCheckbox> | | <jmolCheckbox> |
| - | <scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/kh/1khw_consurf.spt"</scriptWhenChecked> | + | <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/kh/1khw_consurf.spt"</scriptWhenChecked> |
| - | <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked> | + | <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview03.spt</scriptWhenUnchecked> |
| | <text>to colour the structure by Evolutionary Conservation</text> | | <text>to colour the structure by Evolutionary Conservation</text> |
| | </jmolCheckbox> | | </jmolCheckbox> |
| - | </jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/chain_selection.php?pdb_ID=2ata ConSurf]. | + | </jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=1khw ConSurf]. |
| | <div style="clear:both"></div> | | <div style="clear:both"></div> |
| | <div style="background-color:#fffaf0;"> | | <div style="background-color:#fffaf0;"> |
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| | ==See Also== | | ==See Also== |
| - | *[[RNA polymerase|RNA polymerase]] | + | *[[RNA polymerase 3D structures|RNA polymerase 3D structures]] |
| | == References == | | == References == |
| | <references/> | | <references/> |
| | __TOC__ | | __TOC__ |
| | </StructureSection> | | </StructureSection> |
| - | [[Category: RNA-directed RNA polymerase]] | + | [[Category: Large Structures]] |
| - | [[Category: Rhdv]] | + | [[Category: Rabbit hemorrhagic disease virus]] |
| - | [[Category: Alonso, J M]] | + | [[Category: Alonso JM]] |
| - | [[Category: Cherney, M M]] | + | [[Category: Cherney MM]] |
| - | [[Category: James, M N]] | + | [[Category: James MN]] |
| - | [[Category: Machin, A]] | + | [[Category: Machin A]] |
| - | [[Category: Ng, K K]] | + | [[Category: Ng KK]] |
| - | [[Category: Parra, F]] | + | [[Category: Parra F]] |
| - | [[Category: Vazquez, A L]] | + | [[Category: Vazquez AL]] |
| - | [[Category: Rna-dependent rna polymerase]]
| + | |
| - | [[Category: Transferase]]
| + | |
| Structural highlights
Function
POLG_RHDVF NTPase presumably plays a role in replication (By similarity).[1] [2] Viral genome-linked protein is covalently linked to the 5'-end of the positive-strand, negative-strand genomic RNAs and subgenomic RNA. Acts as a genome-linked replication primer. May recruit ribosome to viral RNA thereby promoting viral proteins translation (By similarity).[3] [4] 3C-like protease processes the polyprotein: 3CLpro-RdRp (p72) is first released by autocleavage, then all other proteins are cleaved (By similarity).[5] [6] RNA-directed RNA polymerase replicates genomic and antigenomic RNA by recognizing replications specific signals. Transcribes also a subgenomic mRNA by initiating RNA synthesis internally on antigenomic RNA. This sgRNA codes for structural proteins. Catalyzes the covalent attachment VPg with viral RNAs (By similarity).[7] [8] Capsid protein VP60 self assembles to form an icosahedral capsid with a T=3 symmetry, about 35 nm in diameter, and consisting of 180 capsid proteins. A smaller form of capsid with a diameter of 23 nm might be capsid proteins assembled as icosahedron with T=1 symmetry. The capsid encapsulate VP2 proteins and genomic or subgenomic RNA. Attaches virion to target cells by binding histo-blood group antigens, inducing endocytosis of the viral particle. Acidification of the endosome induces conformational change of capsid protein thereby injecting virus genomic RNA into host cytoplasm (By similarity).[9] [10]
Evolutionary Conservation
Check, as determined by ConSurfDB. You may read the explanation of the method and the full data available from ConSurf.
Publication Abstract from PubMed
The structure of the RNA-dependent RNA polymerase (RdRP) from the rabbit hemorrhagic disease virus has been determined by x-ray crystallography to a 2.5-A resolution. The overall structure resembles a "right hand," as seen before in other polymerases, including the RdRPs of polio virus and hepatitis C virus. Two copies of the polymerase are present in the asymmetric unit of the crystal, revealing active and inactive conformations within the same crystal form. The fingers and palm domains form a relatively rigid unit, but the thumb domain can adopt either "closed" or "open" conformations differing by a rigid body rotation of approximately 8 degrees. Metal ions bind at different positions in the two conformations and suggest how structural changes may be important to enzymatic function in RdRPs. Comparisons between the structures of the alternate conformational states of rabbit hemorrhagic disease virus RdRP and the structures of RdRPs from hepatitis C virus and polio virus suggest novel structure-function relationships in this medically important class of enzymes.
Crystal structures of active and inactive conformations of a caliciviral RNA-dependent RNA polymerase.,Ng KK, Cherney MM, Vazquez AL, Machin A, Alonso JM, Parra F, James MN J Biol Chem. 2002 Jan 11;277(2):1381-7. Epub 2001 Oct 24. PMID:11677245[11]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
See Also
References
- ↑ Meyers G, Wirblich C, Thiel HJ. Genomic and subgenomic RNAs of rabbit hemorrhagic disease virus are both protein-linked and packaged into particles. Virology. 1991 Oct;184(2):677-86. PMID:1887589
- ↑ Barcena J, Verdaguer N, Roca R, Morales M, Angulo I, Risco C, Carrascosa JL, Torres JM, Caston JR. The coat protein of Rabbit hemorrhagic disease virus contains a molecular switch at the N-terminal region facing the inner surface of the capsid. Virology. 2004 Apr 25;322(1):118-34. PMID:15063122 doi:http://dx.doi.org/10.1016/j.virol.2004.01.021
- ↑ Meyers G, Wirblich C, Thiel HJ. Genomic and subgenomic RNAs of rabbit hemorrhagic disease virus are both protein-linked and packaged into particles. Virology. 1991 Oct;184(2):677-86. PMID:1887589
- ↑ Barcena J, Verdaguer N, Roca R, Morales M, Angulo I, Risco C, Carrascosa JL, Torres JM, Caston JR. The coat protein of Rabbit hemorrhagic disease virus contains a molecular switch at the N-terminal region facing the inner surface of the capsid. Virology. 2004 Apr 25;322(1):118-34. PMID:15063122 doi:http://dx.doi.org/10.1016/j.virol.2004.01.021
- ↑ Meyers G, Wirblich C, Thiel HJ. Genomic and subgenomic RNAs of rabbit hemorrhagic disease virus are both protein-linked and packaged into particles. Virology. 1991 Oct;184(2):677-86. PMID:1887589
- ↑ Barcena J, Verdaguer N, Roca R, Morales M, Angulo I, Risco C, Carrascosa JL, Torres JM, Caston JR. The coat protein of Rabbit hemorrhagic disease virus contains a molecular switch at the N-terminal region facing the inner surface of the capsid. Virology. 2004 Apr 25;322(1):118-34. PMID:15063122 doi:http://dx.doi.org/10.1016/j.virol.2004.01.021
- ↑ Meyers G, Wirblich C, Thiel HJ. Genomic and subgenomic RNAs of rabbit hemorrhagic disease virus are both protein-linked and packaged into particles. Virology. 1991 Oct;184(2):677-86. PMID:1887589
- ↑ Barcena J, Verdaguer N, Roca R, Morales M, Angulo I, Risco C, Carrascosa JL, Torres JM, Caston JR. The coat protein of Rabbit hemorrhagic disease virus contains a molecular switch at the N-terminal region facing the inner surface of the capsid. Virology. 2004 Apr 25;322(1):118-34. PMID:15063122 doi:http://dx.doi.org/10.1016/j.virol.2004.01.021
- ↑ Meyers G, Wirblich C, Thiel HJ. Genomic and subgenomic RNAs of rabbit hemorrhagic disease virus are both protein-linked and packaged into particles. Virology. 1991 Oct;184(2):677-86. PMID:1887589
- ↑ Barcena J, Verdaguer N, Roca R, Morales M, Angulo I, Risco C, Carrascosa JL, Torres JM, Caston JR. The coat protein of Rabbit hemorrhagic disease virus contains a molecular switch at the N-terminal region facing the inner surface of the capsid. Virology. 2004 Apr 25;322(1):118-34. PMID:15063122 doi:http://dx.doi.org/10.1016/j.virol.2004.01.021
- ↑ Ng KK, Cherney MM, Vazquez AL, Machin A, Alonso JM, Parra F, James MN. Crystal structures of active and inactive conformations of a caliciviral RNA-dependent RNA polymerase. J Biol Chem. 2002 Jan 11;277(2):1381-7. Epub 2001 Oct 24. PMID:11677245 doi:10.1074/jbc.M109261200
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