PDBsum entry 4rf1

Protein binding

PDB id: 4rf1

Contents

Protein chains

319 a.a.

75 a.a.

Ligands

PGO ×5

3CN

Metals

_ZN

Waters ×176

PDB id:

4rf1

Name:

Protein binding

Title:

Crystal structure of the middle-east respiratory syndrome coronavirus papain-like protease in complex with ubiquitin (space group p63)

Structure:

Orf1ab protein. Chain: a. Fragment: unp residues 1480-1803. Engineered: yes. Ubiquitin-60s ribosomal protein l40. Chain: b. Fragment: unp residues 1-75. Synonym: cep52, ubiquitin a-52 residue ribosomal protein fusion product 1, ubiquitin, 60s ribosomal protein l40.

Source:

Human betacoronavirus 2c jordan-n3/2012. Organism_taxid: 1306931. Gene: orf1ab. Expressed in: escherichia coli. Expression_system_taxid: 562. Homo sapiens. Human. Organism_taxid: 9606. Gene: uba52, ubcep2.

Resolution:

2.15Å R-factor: 0.202 R-free: 0.231

Authors:

B.A.Bailey-Elkin,G.G.Johnson,B.L.Mark

Key ref:

B.A.Bailey-Elkin et al. (2014). Crystal structure of the Middle East respiratory syndrome coronavirus (MERS-CoV) papain-like protease bound to ubiquitin facilitates targeted disruption of deubiquitinating activity to demonstrate its role in innate immune suppression. J Biol Chem, 289, 34667-34682. PubMed id: 25320088 DOI: 10.1074/jbc.M114.609644

Date:

24-Sep-14 Release date: 22-Oct-14

Protein chain

M4STU1  (M4STU1_MERS) -  ORF1ab polyprotein from Human betacoronavirus 2c Jordan-N3/2012

Seq: 7078 a.a.

Struc: 319 a.a.

Protein chain

P62987  (RL40_HUMAN) -  Ubiquitin-ribosomal protein eL40 fusion protein from Homo sapiens

Seq: 128 a.a.

Struc: 75 a.a.

Enzyme reactions

• Enzyme class 2: Chain A: E.C.2.1.1.57 - methyltransferase cap1.
• Reaction: a 5'-end (N(7)-methyl 5'-triphosphoguanosine)-ribonucleoside in mRNA + S-adenosyl-L-methionine = a 5'-end (N(7)-methyl 5'-triphosphoguanosine)- (2'-O-methyl-ribonucleoside) in mRNA + S-adenosyl-L-homocysteine + H⁺
• Enzyme class 3: Chain A: E.C.2.7.7.50 - mRNA guanylyltransferase.
• Reaction: a 5'-end diphospho-ribonucleoside in mRNA + GTP + H⁺ = a 5'-end (5'-triphosphoguanosine)-ribonucleoside in mRNA + diphosphate
• Enzyme class 4: Chain A: E.C.3.4.19.12 - ubiquitinyl hydrolase 1.
• Reaction: Thiol-dependent hydrolysis of ester, thiolester, amide, peptide and isopeptide bonds formed by the C-terminal Gly of ubiquitin (a 76-residue protein attached to proteins as an intracellular targeting signal).
• Enzyme class 5: Chain A: E.C.3.6.4.12 - Dna helicase.
• Reaction: ATP + H2O = ADP + phosphate + H⁺
• Enzyme class 6: Chain A: E.C.3.6.4.13 - Rna helicase.
• Reaction: ATP + H2O = ADP + phosphate + H⁺

Note, where more than one E.C. class is given (as above), each may correspond to a different protein domain or, in the case of polyprotein precursors, to a different mature protein.

Molecule diagrams generated from .mol files obtained from the KEGG ftp site

reference

DOI no: 10.1074/jbc.M114.609644

J Biol Chem 289:34667-34682 (2014)

PubMed id: 25320088

Crystal structure of the Middle East respiratory syndrome coronavirus (MERS-CoV) papain-like protease bound to ubiquitin facilitates targeted disruption of deubiquitinating activity to demonstrate its role in innate immune suppression.

B.A.Bailey-Elkin, R.C.Knaap, G.G.Johnson, T.J.Dalebout, D.K.Ninaber, P.B.van Kasteren, P.J.Bredenbeek, E.J.Snijder, M.Kikkert, B.L.Mark.

ABSTRACT

Middle East respiratory syndrome coronavirus (MERS-CoV) is a newly emerging human pathogen that was first isolated in 2012. MERS-CoV replication depends in part on a virus-encoded papain-like protease (PL(pro)) that cleaves the viral replicase polyproteins at three sites releasing non-structural protein 1 (nsp1), nsp2, and nsp3. In addition to this replicative function, MERS-CoV PL(pro) was recently shown to be a deubiquitinating enzyme (DUB) and to possess deISGylating activity, as previously reported for other coronaviral PL(pro) domains, including that of severe acute respiratory syndrome coronavirus. These activities have been suggested to suppress host antiviral responses during infection. To understand the molecular basis for ubiquitin (Ub) recognition and deconjugation by MERS-CoV PL(pro), we determined its crystal structure in complex with Ub. Guided by this structure, mutations were introduced into PL(pro) to specifically disrupt Ub binding without affecting viral polyprotein cleavage, as determined using an in trans nsp3↓4 cleavage assay. Having developed a strategy to selectively disable PL(pro) DUB activity, we were able to specifically examine the effects of this activity on the innate immune response. Whereas the wild-type PL(pro) domain was found to suppress IFN-β promoter activation, PL(pro) variants specifically lacking DUB activity were no longer able to do so. These findings directly implicate the DUB function of PL(pro), and not its proteolytic activity per se, in the inhibition of IFN-β promoter activity. The ability to decouple the DUB activity of PL(pro) from its role in viral polyprotein processing now provides an approach to further dissect the role(s) of PL(pro) as a viral DUB during MERS-CoV infection.