2d7s

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[[Image:2d7s.gif|left|200px]]
 
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{{Structure
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==Foot and Mouth Disease Virus RNA-dependent RNA polymerase in complex with VPg protein==
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|PDB= 2d7s |SIZE=350|CAPTION= <scene name='initialview01'>2d7s</scene>, resolution 3.00&Aring;
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<StructureSection load='2d7s' size='340' side='right'caption='[[2d7s]], [[Resolution|resolution]] 3.00&Aring;' scene=''>
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|SITE=
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== Structural highlights ==
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|LIGAND=
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<table><tr><td colspan='2'>[[2d7s]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Foot_and_mouth_disease_virus_C Foot and mouth disease virus C] and [https://en.wikipedia.org/wiki/Foot-and-mouth_disease_virus_C-S8c1 Foot-and-mouth disease virus C-S8c1]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2D7S OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2D7S FirstGlance]. <br>
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|ACTIVITY= [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]
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</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 3&#8491;</td></tr>
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|GENE=
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<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=2d7s FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2d7s OCA], [https://pdbe.org/2d7s PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2d7s RCSB], [https://www.ebi.ac.uk/pdbsum/2d7s PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2d7s ProSAT]</span></td></tr>
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}}
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</table>
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== Function ==
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'''Foot and Mouth Disease Virus RNA-dependent RNA polymerase in complex with VPg protein'''
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[https://www.uniprot.org/uniprot/Q9QCE4_9PICO Q9QCE4_9PICO] Protein 3C is a cysteine protease that generates mature viral proteins from the precursor polyprotein. In addition to its proteolytic activity, it binds to viral RNA, and thus influences viral genome replication. RNA and substrate bind co-operatively to the protease (By similarity).[SAAS:SAAS000199_004_042266] RNA-directed RNA polymerase 3D-POL replicates genomic and antigenomic RNA by recognizing replications specific signals (By similarity).[SAAS:SAAS000199_004_010047]
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== Evolutionary Conservation ==
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[[Image:Consurf_key_small.gif|200px|right]]
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==Overview==
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Check<jmol>
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<jmolCheckbox>
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<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/d7/2d7s_consurf.spt"</scriptWhenChecked>
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<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
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<text>to colour the structure by Evolutionary Conservation</text>
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</jmolCheckbox>
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</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=2d7s ConSurf].
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<div style="clear:both"></div>
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<div style="background-color:#fffaf0;">
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== Publication Abstract from PubMed ==
Picornavirus RNA replication is initiated by the covalent attachment of a UMP molecule to the hydroxyl group of a tyrosine in the terminal protein VPg. This reaction is carried out by the viral RNA-dependent RNA polymerase (3D). Here, we report the X-ray structure of two complexes between foot-and-mouth disease virus 3D, VPg1, the substrate UTP and divalent cations, in the absence and in the presence of an oligoadenylate of 10 residues. In both complexes, VPg fits the RNA binding cleft of the polymerase and projects the key residue Tyr3 into the active site of 3D. This is achieved by multiple interactions with residues of motif F and helix alpha8 of the fingers domain and helix alpha13 of the thumb domain of the polymerase. The complex obtained in the presence of the oligoadenylate showed the product of the VPg uridylylation (VPg-UMP). Two metal ions and the catalytic aspartic acids of the polymerase active site, together with the basic residues of motif F, have been identified as participating in the priming reaction.
Picornavirus RNA replication is initiated by the covalent attachment of a UMP molecule to the hydroxyl group of a tyrosine in the terminal protein VPg. This reaction is carried out by the viral RNA-dependent RNA polymerase (3D). Here, we report the X-ray structure of two complexes between foot-and-mouth disease virus 3D, VPg1, the substrate UTP and divalent cations, in the absence and in the presence of an oligoadenylate of 10 residues. In both complexes, VPg fits the RNA binding cleft of the polymerase and projects the key residue Tyr3 into the active site of 3D. This is achieved by multiple interactions with residues of motif F and helix alpha8 of the fingers domain and helix alpha13 of the thumb domain of the polymerase. The complex obtained in the presence of the oligoadenylate showed the product of the VPg uridylylation (VPg-UMP). Two metal ions and the catalytic aspartic acids of the polymerase active site, together with the basic residues of motif F, have been identified as participating in the priming reaction.
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==About this Structure==
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The structure of a protein primer-polymerase complex in the initiation of genome replication.,Ferrer-Orta C, Arias A, Agudo R, Perez-Luque R, Escarmis C, Domingo E, Verdaguer N EMBO J. 2006 Feb 22;25(4):880-8. Epub 2006 Feb 2. PMID:16456546<ref>PMID:16456546</ref>
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2D7S is a [[Protein complex]] structure of sequences from [http://en.wikipedia.org/wiki/Foot_and_mouth_disease_virus Foot and mouth disease virus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2D7S OCA].
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==Reference==
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From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
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The structure of a protein primer-polymerase complex in the initiation of genome replication., Ferrer-Orta C, Arias A, Agudo R, Perez-Luque R, Escarmis C, Domingo E, Verdaguer N, EMBO J. 2006 Feb 22;25(4):880-8. Epub 2006 Feb 2. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/16456546 16456546]
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</div>
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[[Category: Foot and mouth disease virus]]
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<div class="pdbe-citations 2d7s" style="background-color:#fffaf0;"></div>
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[[Category: Protein complex]]
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[[Category: RNA-directed RNA polymerase]]
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[[Category: Arias, A.]]
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[[Category: Domingo, E.]]
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[[Category: Escarmis, C.]]
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[[Category: Ferrer-Orta, C.]]
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[[Category: Perez-Luque, R.]]
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[[Category: Verdaguer, N.]]
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[[Category: 3d polymerase]]
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[[Category: foot and mouth disease virus]]
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[[Category: protein-primer]]
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[[Category: rna-dependent rna polymerase]]
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[[Category: vpg]]
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''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Mar 20 16:24:07 2008''
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==See Also==
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*[[RNA polymerase 3D structures|RNA polymerase 3D structures]]
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== References ==
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<references/>
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__TOC__
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</StructureSection>
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[[Category: Foot and mouth disease virus C]]
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[[Category: Foot-and-mouth disease virus C-S8c1]]
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[[Category: Large Structures]]
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[[Category: Arias A]]
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[[Category: Domingo E]]
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[[Category: Escarmis C]]
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[[Category: Ferrer-Orta C]]
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[[Category: Perez-Luque R]]
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[[Category: Verdaguer N]]

Current revision

Foot and Mouth Disease Virus RNA-dependent RNA polymerase in complex with VPg protein

PDB ID 2d7s

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