5hyo

From Proteopedia

(Difference between revisions)

Revision as of 11:00, 16 August 2023

X-Ray Structure of Unbound Porcine Epidemic Diarrhea Virus 3CLpro

Structural highlights

5hyo is a 2 chain structure with sequence from Porcine epidemic diarrhea virus. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	X-ray diffraction, Resolution 2.104Å
Ligands:	, ,
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

U6BPB2_9ALPC Nsp7-nsp8 hexadecamer may possibly confer processivity to the polymerase, maybe by binding to dsRNA or by producing primers utilized by the latter.[ARBA:ARBA00002928] Nsp9 is a ssRNA-binding protein.[ARBA:ARBA00003140] The papain-like proteinase 1 (PLP1) and papain-like proteinase 2 (PLP2) are responsible for the cleavages located at the N-terminus of the replicase polyprotein. In addition, PLP2 possesses a deubiquitinating/deISGylating activity and processes both 'Lys-48'- and 'Lys-63'-linked polyubiquitin chains from cellular substrates. PLP2 also antagonizes innate immune induction of type I interferon by blocking the nuclear translocation of host IRF-3.[ARBA:ARBA00025562]

Publication Abstract from PubMed

Porcine epidemic diarrhea virus (PEDV) is a coronavirus that infects pigs and can have mortality rates approaching 100% in piglets, causing serious economic impact. The 3C-like protease (3CL(pro)) is essential for the coronaviral life cycle and is an appealing target for the development of therapeutics. We report the expression, purification, crystallization and 2.10 A X-ray structure of 3CL(pro) from PEDV. Analysis of the PEDV 3CL(pro) structure and comparison to other coronaviral 3CL(pro)'s from the same alpha-coronavirus phylogeny shows that the overall structures and active site architectures across 3CL(pro)'s are conserved, with the exception of a loop that comprises the protease S2 pocket. We found a known inhibitor of severe acute respiratory syndrome coronavirus (SARS-CoV) 3CL(pro), (R)-16, to have inhibitor activity against PEDV 3CL(pro), despite that SARS-3CL(pro) and PEDV 3CL(pro) share only 45.4% sequence identity. Structural comparison reveals that the majority of residues involved in (R)-16 binding to SARS-3CL(pro) are conserved in PEDV-3CL(pro); however, the sequence variation and positional difference in the loop forming the S2 pocket may account for large observed difference in IC50 values. This work advances our understanding of the subtle, but important, differences in coronaviral 3CL(pro) architecture and contributes to the broader structural knowledge of coronaviral 3CL(pro)'s.

X-Ray Structure and Inhibition of 3C-like Protease from Porcine Epidemic Diarrhea Virus.,St John SE, Anson BJ, Mesecar AD Sci Rep. 2016 May 13;6:25961. doi: 10.1038/srep25961. PMID:27173881^[1]

From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.

References

↑ St John SE, Anson BJ, Mesecar AD. X-Ray Structure and Inhibition of 3C-like Protease from Porcine Epidemic Diarrhea Virus. Sci Rep. 2016 May 13;6:25961. doi: 10.1038/srep25961. PMID:27173881 doi:http://dx.doi.org/10.1038/srep25961

1 Structural highlights
2 Function
3 Publication Abstract from PubMed
4 See Also
5 References

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/5hyo"

Categories: Large Structures | Porcine epidemic diarrhea virus | Mesecar AD | St John SE

@@ Line 3: / Line 3: @@
 <StructureSection load='5hyo' size='340' side='right'caption='[[5hyo]], [[Resolution|resolution]] 2.10&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[5hyo]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Pedv Pedv]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5HYO OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5HYO FirstGlance]. <br>
+<table><tr><td colspan='2'>[[5hyo]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Porcine_epidemic_diarrhea_virus Porcine epidemic diarrhea virus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5HYO OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5HYO FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=DMS:DIMETHYL+SULFOXIDE'>DMS</scene>, <scene name='pdbligand=IPA:ISOPROPYL+ALCOHOL'>IPA</scene>, <scene name='pdbligand=MPD:(4S)-2-METHYL-2,4-PENTANEDIOL'>MPD</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]] 2.104&#8491;</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=5hyo FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5hyo OCA], [http://pdbe.org/5hyo PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5hyo RCSB], [http://www.ebi.ac.uk/pdbsum/5hyo PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5hyo ProSAT]</span></td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=DMS:DIMETHYL+SULFOXIDE'>DMS</scene>, <scene name='pdbligand=IPA:ISOPROPYL+ALCOHOL'>IPA</scene>, <scene name='pdbligand=MPD:(4S)-2-METHYL-2,4-PENTANEDIOL'>MPD</scene></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=5hyo FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5hyo OCA], [https://pdbe.org/5hyo PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5hyo RCSB], [https://www.ebi.ac.uk/pdbsum/5hyo PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5hyo ProSAT]</span></td></tr>
 </table>
+== Function ==
+[https://www.uniprot.org/uniprot/U6BPB2_9ALPC U6BPB2_9ALPC] Nsp7-nsp8 hexadecamer may possibly confer processivity to the polymerase, maybe by binding to dsRNA or by producing primers utilized by the latter.[ARBA:ARBA00002928]  Nsp9 is a ssRNA-binding protein.[ARBA:ARBA00003140]  The papain-like proteinase 1 (PLP1) and papain-like proteinase 2 (PLP2) are responsible for the cleavages located at the N-terminus of the replicase polyprotein. In addition, PLP2 possesses a deubiquitinating/deISGylating activity and processes both 'Lys-48'- and 'Lys-63'-linked polyubiquitin chains from cellular substrates. PLP2 also antagonizes innate immune induction of type I interferon by blocking the nuclear translocation of host IRF-3.[ARBA:ARBA00025562]
 <div style="background-color:#fffaf0;">
 == Publication Abstract from PubMed ==
@@ Line 18: / Line 21: @@
 ==See Also==
-*[[Virus protease|Virus protease]]
+*[[Virus protease 3D structures|Virus protease 3D structures]]
 == References ==
 <references/>
@@ Line 24: / Line 27: @@
 </StructureSection>
 [[Category: Large Structures]]
-[[Category: Pedv]]
+[[Category: Porcine epidemic diarrhea virus]]
-[[Category: John, S E.St]]
+[[Category: Mesecar AD]]
-[[Category: Mesecar, A D]]
+[[Category: St John SE]]
-[[Category: Coronavirus]]
-[[Category: Mpro]]
-[[Category: Viral protein]]

5hyo

From Proteopedia

Revision as of 11:00, 16 August 2023

X-Ray Structure of Unbound Porcine Epidemic Diarrhea Virus 3CLpro

Structural highlights

Function

Publication Abstract from PubMed

See Also

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

Views

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