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4ypt

From Proteopedia

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X-ray structural of three tandemly linked domains of nsp3 from murine hepatitis virus at 2.60 Angstroms resolution

Structural highlights

4ypt is a 1 chain structure with sequence from Murine hepatitis virus strain A59. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	X-ray diffraction, Resolution 2.6009Å
Ligands:	, ,
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

R1AB_CVMA5 The replicase polyprotein of coronaviruses is a multifunctional protein: it contains the activities necessary for the transcription of negative stranded RNA, leader RNA, subgenomic mRNAs and progeny virion RNA as well as proteinases responsible for the cleavage of the polyprotein into functional products. The papain-like proteinase 1 (PL1-PRO) and papain-like proteinase 2 (PL2-PRO) 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. Antagonizes innate immune induction of type I interferon by blocking the phosphorylation, dimerization and subsequent nuclear translocation of host IRF-3 (By similarity). The main proteinase 3CL-PRO is responsible for the majority of cleavages as it cleaves the C-terminus of replicase polyprotein at 11 sites. Recognizes substrates containing the core sequence [ILMVF]-Q-|-[SGACN]. Inhibited by the substrate-analog Cbz-Val-Asn-Ser-Thr-Leu-Gln-CMK. Also contains an ADP-ribose-1-phosphate (ADRP)-binding function (By similarity). The helicase which contains a zinc finger structure displays RNA and DNA duplex-unwinding activities with 5' to 3' polarity. ATPase activity is strongly stimulated by poly(U), poly(dT), poly(C), poly(dA), but not by poly(G) (By similarity). The exoribonuclease acts on both ssRNA and dsRNA in a 3' to 5' direction (By similarity). Nsp7-nsp8 hexadecamer may possibly confer processivity to the polymerase, maybe by binding to dsRNA or by producing primers utilized by the latter (By similarity). Nsp9 is a ssRNA-binding protein (By similarity). NendoU is a Mn(2+)-dependent, uridylate-specific enzyme, which leaves 2'-3'-cyclic phosphates 5' to the cleaved bond (By similarity).

Publication Abstract from PubMed

Murine Hepatitis Virus (MHV) has long served as a model system for the study of coronaviruses (CoVs). Non-structural protein 3 (nsp3) is the largest nsp in the coronavirus genome and it contains multiple functional domains that are required for coronavirus replication. Despite the numerous functional studies on MHV and its nsp3 domain, the structure of only one domain in nsp3, the small ubiquitin-like domain 1 (Ubl1), has been determined. We report here the X-ray structure of three, tandemly-linked domains of MHV nsp3 including the papain-like protease 2 (PLP2) catalytic domain, the ubiquitin-like domain 2 (Ubl2) and a third domain that we call the "Domain Preceding Ubl2 and PLP2 (DPUP)" domain. DPUP has close structural similarity to the Severe Acute Respiratory Syndrome coronavirus unique domain C (SUD-C), suggesting that this domain may not be unique to SARS-CoV. The PLP2 catalytic domain was found to have both deubiquitinating and deISGylating isopeptidase activities in addition to proteolytic activity. A computationally-derived model of MHV PLP2 bound to ubiquitin was generated and the potential interactions between ubiquitin and PLP2 were probed by site-directed mutagenesis. These studies extend substantially our structural knowledge of MHV nsp3, providing a platform for further investigation of the role of nsp3 domains in MHV viral replication.

X-ray Structural and Functional Studies of the Three Tandemly-Linked Domains of Nsp3 from Murine Hepatitis Virus Reveal Conserved Functions.,Chen Y, Savinov SN, Mielech AM, Cao T, Baker SC, Mesecar AD J Biol Chem. 2015 Aug 19. pii: jbc.M115.662130. PMID:26296883^[1]

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

References

↑ Chen Y, Savinov SN, Mielech AM, Cao T, Baker SC, Mesecar AD. X-ray Structural and Functional Studies of the Three Tandemly-Linked Domains of Nsp3 from Murine Hepatitis Virus Reveal Conserved Functions. J Biol Chem. 2015 Aug 19. pii: jbc.M115.662130. PMID:26296883 doi:http://dx.doi.org/10.1074/jbc.M115.662130

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

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/4ypt"

@@ Line 4: / Line 4: @@
 == Structural highlights ==
 <table><tr><td colspan='2'>[[4ypt]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Murine_hepatitis_virus_strain_A59 Murine hepatitis virus strain A59]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4YPT OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4YPT FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=OCS:CYSTEINESULFONIC+ACID'>OCS</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</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]] 2.6009&#8491;</td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=OCS:CYSTEINESULFONIC+ACID'>OCS</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</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=4ypt FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4ypt OCA], [https://pdbe.org/4ypt PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4ypt RCSB], [https://www.ebi.ac.uk/pdbsum/4ypt PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4ypt ProSAT]</span></td></tr>
 </table>

4ypt

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Current revision

X-ray structural of three tandemly linked domains of nsp3 from murine hepatitis virus at 2.60 Angstroms resolution

Structural highlights

Function

Publication Abstract from PubMed

References

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Proteopedia Page Contributors and Editors (what is this?)

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