PDBsum entry 5tl7

Signaling protein/hydrolase

PDB id: 5tl7

Contents

Protein chains

77 a.a.

316 a.a.

Metals

_ZN ×2

Waters ×122

PDB id:

5tl7

Name:

Signaling protein/hydrolase

Title:

Crystal structure of sars-cov papain-like protease in complex with c- terminal domain mouse isg15

Structure:

Ubiquitin-like protein isg15. Chain: a, c. Fragment: c-terminal domain (unp residues 78-155. Synonym: interferon-induced 15 kda protein,interferon-induced 17 kda protein,ip17,ubiquitin cross-reactive protein. Engineered: yes. Replicase polyprotein 1ab. Chain: b, d. Fragment: unp residues 1541-1855.

Source:

Mus musculus. Mouse. Organism_taxid: 10090. Gene: isg15, g1p2, ucrp. Expressed in: escherichia coli bl21(de3). Expression_system_taxid: 469008. Sars coronavirus. Sars-cov. Organism_taxid: 227859.

Resolution:

2.44Å R-factor: 0.196 R-free: 0.267

Authors:

C.D.Daczkowski,J.V.Dzimianski,S.D.Pegan

Key ref:

C.M.Daczkowski et al. (2017). Structural Insights into the Interaction of Coronavirus Papain-Like Proteases and Interferon-Stimulated Gene Product 15 from Different Species. J Mol Biol, 429, 1661-1683. PubMed id: 28438633

Date:

10-Oct-16 Release date: 03-May-17

Protein chains

Q64339  (ISG15_MOUSE) -  Ubiquitin-like protein ISG15 from Mus musculus

Seq: 161 a.a.

Struc: 77 a.a.*

Protein chains

P0C6X7  (R1AB_CVHSA) -  Replicase polyprotein 1ab from Severe acute respiratory syndrome coronavirus

Seq: 7073 a.a.

Struc: 316 a.a.*

* PDB and UniProt seqs differ at 2 residue positions (black crosses)

Enzyme reactions

• Enzyme class 2: Chains B, D: E.C.2.1.1.- - ?????
• Enzyme class 3: Chains B, D: 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 4: Chains B, D: 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 5: Chains B, D: E.C.2.7.7.48 - RNA-directed Rna polymerase.
• Reaction: RNA(n) + a ribonucleoside 5'-triphosphate = RNA(n+1) + diphosphate
• Enzyme class 6: Chains B, D: 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 7: Chains B, D: E.C.3.1.13.- - ?????
• Enzyme class 8: Chains B, D: 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 9: Chains B, D: E.C.3.4.22.- - ?????
• Enzyme class 10: Chains B, D: E.C.3.4.22.69 - Sars coronavirus main proteinase.
• Enzyme class 11: Chains B, D: E.C.3.6.4.12 - Dna helicase.
• Reaction: ATP + H2O = ADP + phosphate + H⁺
• Enzyme class 12: Chains B, D: E.C.3.6.4.13 - Rna helicase.
• Reaction: ATP + H2O = ADP + phosphate + H⁺
• Enzyme class 13: Chains B, D: 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

J Mol Biol 429:1661-1683 (2017)

PubMed id: 28438633

Structural Insights into the Interaction of Coronavirus Papain-Like Proteases and Interferon-Stimulated Gene Product 15 from Different Species.

C.M.Daczkowski, J.V.Dzimianski, J.R.Clasman, O.Goodwin, A.D.Mesecar, S.D.Pegan.

ABSTRACT

Severe acute respiratory syndrome coronavirus (SARS-CoV) and Middle East respiratory syndrome coronavirus (MERS-CoV) encode multifunctional papain-like proteases (PLPs) that have the ability to process the viral polyprotein to facilitate RNA replication and antagonize the host innate immune response. The latter function involves reversing the post-translational modification of cellular proteins conjugated with either ubiquitin (Ub) or Ub-like interferon-stimulated gene product 15 (ISG15). Ub is known to be highly conserved among eukaryotes, but surprisingly, ISG15 is highly divergent among animals. The ramifications of this sequence divergence to the recognition of ISG15 by coronavirus PLPs at a structural and biochemical level are poorly understood. Therefore, the activity of PLPs from SARS-CoV, MERS-CoV, and mouse hepatitis virus was evaluated against seven ISG15s originating from an assortment of animal species susceptible, and not, to certain coronavirus infections. Excitingly, our kinetic, thermodynamic, and structural analysis revealed an array of different preferences among PLPs. Included in these studies is the first insight into a coronavirus PLP's interface with ISG15 via SARS-CoV PLpro in complex with the principle binding domain of human ISG15 (hISG15) and mouse ISG15s (mISG15s). The first X-ray structure of the full-length mISG15 protein is also reported and highlights a unique, twisted hinge region of ISG15 that is not conserved in hISG15, suggesting a potential role in differential recognition. Taken together, this new information provides a structural and biochemical understanding of the distinct specificities among coronavirus PLPs observed and addresses a critical gap of how PLPs can interact with ISG15s from a wide variety of species.