5t6f: Difference between revisions

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'''Unreleased structure'''


The entry 5t6f is ON HOLD  until Paper Publication
==1.90 A resolution structure of Norovirus 3CL protease in complex with the dipeptidyl inhibitor 7l (orthorhombic P form)==
 
<StructureSection load='5t6f' size='340' side='right' caption='[[5t6f]], [[Resolution|resolution]] 1.90&Aring;' scene=''>
Authors: Lovell, S., Battaile, K.P., Mehzabeen, N., Kankanamalage, A.C.G., Kim, Y., Rathnayake, A.D., Damalanka, V.C., Weerawarna, P.M., Doyle, S.T., Alsoudi, A.F., Dissanayake, D.M.P., Chang, K.-O., Groutas, W.C.
== Structural highlights ==
 
<table><tr><td colspan='2'>[[5t6f]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5T6F OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5T6F FirstGlance]. <br>
Description: 1.90 A resolution structure of Norovirus 3CL protease in complex with the dipeptidyl inhibitor 6l (orthorhombic P form)
</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=N38:3-CYCLOHEXYL-N-{(2S)-1-HYDROXY-3-[(3S)-2-OXOPYRROLIDIN-3-YL]PROPAN-2-YL}-N~2~-{[3-(4-METHOXYPHENOXY)PROPYL]SULFONYL}-L-ALANINAMIDE'>N38</scene></td></tr>
[[Category: Unreleased Structures]]
<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[5t6d|5t6d]], [[5t6g|5t6g]]</td></tr>
[[Category: Chang, K.-O]]
<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=5t6f FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5t6f OCA], [http://pdbe.org/5t6f PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5t6f RCSB], [http://www.ebi.ac.uk/pdbsum/5t6f PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5t6f ProSAT]</span></td></tr>
[[Category: Alsoudi, A.F]]
</table>
[[Category: Doyle, S.T]]
== Function ==
[[Category: Kankanamalage, A.C.G]]
[[http://www.uniprot.org/uniprot/POLG_NVN68 POLG_NVN68]] Protein p48 may play a role in viral replication by interacting with host VAPA, a vesicle-associated membrane protein that plays a role in SNARE-mediated vesicle fusion. This interaction may target replication complex to intracellular membranes.<ref>PMID:569187</ref> <ref>PMID:11160659</ref>  NTPase presumably plays a role in replication. Despite having similarities with helicases, does not seem to display any helicase activity.<ref>PMID:569187</ref> <ref>PMID:11160659</ref>  Protein P22 may play a role in targeting replication complex to intracellular membranes.<ref>PMID:569187</ref> <ref>PMID:11160659</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.<ref>PMID:569187</ref> <ref>PMID:11160659</ref>  3C-like protease processes the polyprotein: 3CLpro-RdRp is first released by autocleavage, then all other proteins are cleaved. May cleave host polyadenylate-binding protein thereby inhibiting cellular translation (By similarity).<ref>PMID:569187</ref> <ref>PMID:11160659</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 encodes for structural proteins. Catalyzes the covalent attachment VPg with viral RNAs (By similarity).<ref>PMID:569187</ref> <ref>PMID:11160659</ref> 
[[Category: Dissanayake, D.M.P]]
== References ==
[[Category: Battaile, K.P]]
<references/>
[[Category: Weerawarna, P.M]]
__TOC__
</StructureSection>
[[Category: Alsoudi, A F]]
[[Category: Battaile, K P]]
[[Category: Chang, K O]]
[[Category: Damalanka, V C]]
[[Category: Dissanayake, D M.P]]
[[Category: Doyle, S T]]
[[Category: Groutas, W C]]
[[Category: Kankanamalage, A C.G]]
[[Category: Kim, Y]]
[[Category: Lovell, S]]
[[Category: Lovell, S]]
[[Category: Damalanka, V.C]]
[[Category: Groutas, W.C]]
[[Category: Mehzabeen, N]]
[[Category: Mehzabeen, N]]
[[Category: Kim, Y]]
[[Category: Rathnayake, A D]]
[[Category: Rathnayake, A.D]]
[[Category: Weerawarna, P M]]
[[Category: Antiviral inhibitor]]
[[Category: Dipeptidyl inhibitor]]
[[Category: Norovirus]]
[[Category: Norwalk virus]]
[[Category: Protease]]
[[Category: Protease-protease inhibitor complex]]

Revision as of 13:58, 10 December 2016

1.90 A resolution structure of Norovirus 3CL protease in complex with the dipeptidyl inhibitor 7l (orthorhombic P form)1.90 A resolution structure of Norovirus 3CL protease in complex with the dipeptidyl inhibitor 7l (orthorhombic P form)

Structural highlights

5t6f is a 2 chain structure. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Ligands:
Resources:FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

[POLG_NVN68] Protein p48 may play a role in viral replication by interacting with host VAPA, a vesicle-associated membrane protein that plays a role in SNARE-mediated vesicle fusion. This interaction may target replication complex to intracellular membranes.[1] [2] NTPase presumably plays a role in replication. Despite having similarities with helicases, does not seem to display any helicase activity.[3] [4] Protein P22 may play a role in targeting replication complex to intracellular membranes.[5] [6] 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.[7] [8] 3C-like protease processes the polyprotein: 3CLpro-RdRp is first released by autocleavage, then all other proteins are cleaved. May cleave host polyadenylate-binding protein thereby inhibiting cellular translation (By similarity).[9] [10] 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 encodes for structural proteins. Catalyzes the covalent attachment VPg with viral RNAs (By similarity).[11] [12]

References

  1. ↑ Burroughs JN, Brown F. Presence of a covalently linked protein on calicivirus RNA. J Gen Virol. 1978 Nov;41(2):443-6. PMID:569187
  2. ↑ Pfister T, Wimmer E. Polypeptide p41 of a Norwalk-like virus is a nucleic acid-independent nucleoside triphosphatase. J Virol. 2001 Feb;75(4):1611-9. PMID:11160659 doi:10.1128/JVI.75.4.1611-1619.2001
  3. ↑ Burroughs JN, Brown F. Presence of a covalently linked protein on calicivirus RNA. J Gen Virol. 1978 Nov;41(2):443-6. PMID:569187
  4. ↑ Pfister T, Wimmer E. Polypeptide p41 of a Norwalk-like virus is a nucleic acid-independent nucleoside triphosphatase. J Virol. 2001 Feb;75(4):1611-9. PMID:11160659 doi:10.1128/JVI.75.4.1611-1619.2001
  5. ↑ Burroughs JN, Brown F. Presence of a covalently linked protein on calicivirus RNA. J Gen Virol. 1978 Nov;41(2):443-6. PMID:569187
  6. ↑ Pfister T, Wimmer E. Polypeptide p41 of a Norwalk-like virus is a nucleic acid-independent nucleoside triphosphatase. J Virol. 2001 Feb;75(4):1611-9. PMID:11160659 doi:10.1128/JVI.75.4.1611-1619.2001
  7. ↑ Burroughs JN, Brown F. Presence of a covalently linked protein on calicivirus RNA. J Gen Virol. 1978 Nov;41(2):443-6. PMID:569187
  8. ↑ Pfister T, Wimmer E. Polypeptide p41 of a Norwalk-like virus is a nucleic acid-independent nucleoside triphosphatase. J Virol. 2001 Feb;75(4):1611-9. PMID:11160659 doi:10.1128/JVI.75.4.1611-1619.2001
  9. ↑ Burroughs JN, Brown F. Presence of a covalently linked protein on calicivirus RNA. J Gen Virol. 1978 Nov;41(2):443-6. PMID:569187
  10. ↑ Pfister T, Wimmer E. Polypeptide p41 of a Norwalk-like virus is a nucleic acid-independent nucleoside triphosphatase. J Virol. 2001 Feb;75(4):1611-9. PMID:11160659 doi:10.1128/JVI.75.4.1611-1619.2001
  11. ↑ Burroughs JN, Brown F. Presence of a covalently linked protein on calicivirus RNA. J Gen Virol. 1978 Nov;41(2):443-6. PMID:569187
  12. ↑ Pfister T, Wimmer E. Polypeptide p41 of a Norwalk-like virus is a nucleic acid-independent nucleoside triphosphatase. J Virol. 2001 Feb;75(4):1611-9. PMID:11160659 doi:10.1128/JVI.75.4.1611-1619.2001

5t6f, resolution 1.90Å

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