PDBsum entry 5e6j

Hydrolase

PDB id: 5e6j

Contents

Protein chains

317 a.a.

76 a.a.

75 a.a.

Ligands

ACT

Metals

_NI

Waters ×55

PDB id:

5e6j

Name:

Hydrolase

Title:

Structure of sars plpro bound to a lys48-linked di-ubiquitin activity based probe

Structure:

Replicase polyprotein 1ab. Chain: a, d. Fragment: unp residues 1541-1856. 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. Ubiquitin. Chain: b, e.

Source:

Human sars coronavirus. Sars-cov. Organism_taxid: 227859. Gene: rep, 1a-1b. Expressed in: escherichia coli. Expression_system_taxid: 562. Synthetic: yes. Homo sapiens. Organism_taxid: 32630.

Resolution:

2.85Å R-factor: 0.234 R-free: 0.264

Authors:

C.D.Lima,M.Bekes

Key ref:

M.Békés et al. (2016). Recognition of Lys48-Linked Di-ubiquitin and Deubiquitinating Activities of the SARS Coronavirus Papain-like Protease. Mol Cell, 62, 572-585. PubMed id: 27203180

Date:

09-Oct-15 Release date: 18-May-16

Protein chains

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

Seq: 7073 a.a.

Struc: 317 a.a.*

Protein chains

P0CG48  (UBC_HUMAN) -  Polyubiquitin-C from Homo sapiens

Seq: 685 a.a.

Struc: 76 a.a.*

Protein chains

P0CG47  (UBB_HUMAN) -  Polyubiquitin-B from Homo sapiens

Seq: 229 a.a.

Struc: 75 a.a.

* PDB and UniProt seqs differ at 5 residue positions (black crosses)

Enzyme reactions

• Enzyme class 2: Chains A, D: E.C.2.1.1.- - ?????
• Enzyme class 3: Chains A, 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 A, 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 A, 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 A, 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 A, D: E.C.3.1.13.- - ?????
• Enzyme class 8: Chains A, 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 A, D: E.C.3.4.22.- - ?????
• Enzyme class 10: Chains A, D: E.C.3.4.22.69 - Sars coronavirus main proteinase.
• Enzyme class 11: Chains A, D: E.C.3.6.4.12 - Dna helicase.
• Reaction: ATP + H2O = ADP + phosphate + H⁺
• Enzyme class 12: Chains A, D: E.C.3.6.4.13 - Rna helicase.
• Reaction: ATP + H2O = ADP + phosphate + H⁺
• Enzyme class 13: Chains A, 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

Mol Cell 62:572-585 (2016)

PubMed id: 27203180

Recognition of Lys48-Linked Di-ubiquitin and Deubiquitinating Activities of the SARS Coronavirus Papain-like Protease.

M.Békés, G.J.van der Heden van Noort, R.Ekkebus, H.Ovaa, T.T.Huang, C.D.Lima.

ABSTRACT

Deubiquitinating enzymes (DUBs) recognize and cleave linkage-specific polyubiquitin (polyUb) chains, but mechanisms underlying specificity remain elusive in many cases. The severe acute respiratory syndrome (SARS) coronavirus papain-like protease (PLpro) is a DUB that cleaves ISG15, a two-domain Ub-like protein, and Lys48-linked polyUb chains, releasing diUb(Lys48) products. To elucidate this specificity, we report the 2.85 Å crystal structure of SARS PLpro bound to a diUb(Lys48) activity-based probe. SARS PLpro binds diUb(Lys48) in an extended conformation via two contact sites, S1 and S2, which are proximal and distal to the active site, respectively. We show that specificity for polyUb(Lys48) chains is predicated on contacts in the S2 site and enhanced by an S1-S1' preference for a Lys48 linkage across the active site. In contrast, ISG15 specificity is dominated by contacts in the S1 site. Determinants revealed for polyUb(Lys48) specificity should prove useful in understanding PLpro deubiquitinating activities in coronavirus infections.