PDBsum entry 4wur

Hydrolase

PDB id: 4wur

Contents

Protein chains

317 a.a.

74 a.a.

Ligands

IPA ×2

Metals

_ZN

PDB id:

4wur

Name:

Hydrolase

Title:

The crystal structure of the mers-cov papain-like protease (c111s) with human ubiquitin

Structure:

Papain-like protease. Chain: a. Fragment: unp residues 1482-1801. Synonym: pp1ab,orf1ab polyprotein. Ec: 3.4.19.12,3.4.22.69,3.4.22.-,2.7.7.48,3.6.4.12,3.6.4.13,2.1.1.-, 3.1.13.-,3.1.-.-. Engineered: yes. Mutation: yes. Polyubiquitin-b.

Source:

Human coronavirus emc. Hcov-emc. Organism_taxid: 1263720. Strain: isolate united kingdom/h123990006/2012. Gene: rep, 1a-1b. Expressed in: escherichia coli bl21(de3). Expression_system_taxid: 469008. Expression_system_variant: tuner placi. Homo sapiens.

Resolution:

3.16Å R-factor: 0.210 R-free: 0.252

Authors:

J.Lei,R.Hilgenfeld

Key ref:

J.Lei and R.Hilgenfeld (2016). Structural and mutational analysis of the interaction between the Middle-East respiratory syndrome coronavirus (MERS-CoV) papain-like protease and human ubiquitin. Virol Sin, 31, 288-299. PubMed id: 27245450 DOI: 10.1007/s12250-016-3742-4

Date:

03-Nov-14 Release date: 26-Nov-14

Protein chain

K9N7C7  (R1AB_CVEMC) -  Replicase polyprotein 1ab from Middle East respiratory syndrome-related coronavirus (isolate United Kingdom/H123990006/2012)

Seq: 7078 a.a.

Struc: 317 a.a.*

Protein chain

P0CG47  (UBB_HUMAN) -  Polyubiquitin-B from Homo sapiens

Seq: 229 a.a.

Struc: 74 a.a.

* PDB and UniProt seqs differ at 3 residue positions (black crosses)

Enzyme reactions

• Enzyme class 2: Chain A: E.C.2.1.1.56 - mRNA (guanine-N(7))-methyltransferase.
• Reaction: a 5'-end (5'-triphosphoguanosine)-ribonucleoside in mRNA + S-adenosyl-L- methionine = a 5'-end (N(7)-methyl 5'-triphosphoguanosine)-ribonucleoside in mRNA + S-adenosyl-L-homocysteine
• Enzyme class 3: 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 4: Chain A: E.C.2.7.7.48 - RNA-directed Rna polymerase.
• Reaction: RNA(n) + a ribonucleoside 5'-triphosphate = RNA(n+1) + diphosphate
• Enzyme class 5: 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 6: Chain A: E.C.3.1.13.- - ?????
• Enzyme class 7: 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 8: Chain A: E.C.3.4.22.- - ?????
• Enzyme class 9: Chain A: E.C.3.6.4.12 - Dna helicase.
• Reaction: ATP + H2O = ADP + phosphate + H⁺
• Enzyme class 10: Chain A: E.C.3.6.4.13 - Rna helicase.
• Reaction: ATP + H2O = ADP + phosphate + H⁺
• Enzyme class 11: Chain A: E.C.4.6.1.- - ?????

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: 10.1007/s12250-016-3742-4

Virol Sin 31:288-299 (2016)

PubMed id: 27245450

Structural and mutational analysis of the interaction between the Middle-East respiratory syndrome coronavirus (MERS-CoV) papain-like protease and human ubiquitin.

J.Lei, R.Hilgenfeld.

ABSTRACT

The papain-like protease (PL(pro)) of Middle-East respiratory syndrome coronavirus (MERS-CoV) has proteolytic, deubiquitinating, and deISGylating activities. The latter two are involved in the suppression of the antiviral innate immune response of the host cell. To contribute to an understanding of this process, we present here the X-ray crystal structure of a complex between MERS-CoV PL(pro) and human ubiquitin (Ub) that is devoid of any covalent linkage between the two proteins. Five regions of the PL(pro) bind to two areas of the Ub. The C-terminal five residues of Ub, RLRGG, are similar to the P5-P1 residues of the polyprotein substrates of the PL(pro) and are responsible for the major part of the interaction between the two macromolecules. Through sitedirected mutagenesis, we demonstrate that conserved Asp165 and non-conserved Asp164 are important for the catalytic activities of MERS-CoV PL(pro). The enzyme appears not to be optimized for catalytic efficiency; thus, replacement of Phe269 by Tyr leads to increased peptidolytic and deubiquitinating activities. Ubiquitin binding by MERS-CoV PL(pro) involves remarkable differences compared to the corresponding complex with SARS-CoV PL(pro). The structure and the mutational study help understand common and unique features of the deubiquitinating activity of MERS-CoV PL(pro).