Brand  (β version)

PDB ID: 5E6J

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Ligands
Code Name Style Show Link
ACT Acetate ion PoSSuM
NI Nickel (II) ion PoSSuM
Non-standard Residues
Code Name Show
5MW (2~{S})-5-[4-(aminomethyl)-1,2,3-triazol-1-yl]-2-azanyl-pentanoic acid
Glycosylation
Code Name Emphasize
Modification
Code Name Show
AYE Prop-2-en-1-amine

Structure summary

Code : 5E6J   PDBj   RCSB PDB   PDBe
Header : HYDROLASE
Title : Structure of SARS PLpro bound to a Lys48-linked di-ubiquitin activity based probe
Release Data : 2016-05-18
Compound :
mol_id molecule chains synonym
1 Replicase polyprotein 1ab A,D 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.-.-
fragment: UNP Residues 1541-1856
mol_id molecule chains
2 ubiquitin B,E
mutation: K48LYQ, G76AYE
mol_id molecule chains
3 Polyubiquitin-B C,F
Source :
mol_id organism_scientific organism_common expression_system
1 Human SARS coronavirus  (taxid:227859) SARS-CoV Escherichia coli  (taxid:562)
gene: rep, 1a-1b
expression_system_strain: BL-21(DE3) RIL Codon Plus
expression_system_vector_type: plasmid
expression_system_plasmid: pET28
mol_id organism_scientific
2 Homo sapiens  (taxid:32630)
synthetic: yes
mol_id organism_scientific
3 Homo sapiens  (taxid:32630)
synthetic: yes
Authors : Lima, C.D., Bekes, M.
Keywords : SARS PLpro, deubiquitinating enzyme, ubiquitin, activity based probe, K48-linkage, HYDROLASE
Exp. method : X-RAY DIFFRACTION ( 2.850 Å )
Citation :

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

Bekes, M.,van der Heden van Noort, G.J.,Ekkebus, R.  et al.
(2016)  Mol. Cell  62 : 572 - 585

PubMed: 27203180
DOI: 10.1016/j.molcel.2016.04.016

Reaction

Chain : A, D
UniProt : P0C6X7 (R1AB_SARS)
Reaction: EC: Evidence:
Physiological Direction:
[RNA-directed RNA polymerase nsp12]
a ribonucleoside 5'-triphosphate + RNA(n) = diphosphate + RNA(n+1) 		2.7.7.48 PROSITE-ProRule:PRU00539, PubMed:14561748
-
[Helicase nsp13]
ATP + H2O = ADP + H(+) + phosphate 		3.6.4.12 PubMed:22615777
-
[Helicase nsp13]
ATP + H2O = ADP + H(+) + phosphate 		3.6.4.13 PubMed:22615777
-
[3C-like proteinase nsp5]
TSAVLQ-|-SGFRK-NH2 and SGVTFQ-|-GKFKK the two peptides corresponding to the two self-cleavage sites of the SARS 3C-like proteinase are the two most reactive peptide substrates. The enzyme exhibits a strong preference for substrates containing Gln at P1 position and Leu at P2 position. 		3.4.22.69 PubMed:12917450, PubMed:14561748
-
[Papain-like protease nsp3]
Thiol-dependent hydrolysis of ester, thioester, 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). 		3.4.19.12 PubMed:12917450, PubMed:17692280
-
[2'-O-methyltransferase nsp16]
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 + H(+) + S- adenosyl-L-homocysteine 		2.1.1.57 PubMed:22022266, PubMed:28158275
-
[Uridylate-specific endoribonuclease nsp15]
uridylyl-uridylyl-ribonucleotide-RNA = a 3'-end uridylyl- 2',3'-cyclophospho-uridine-RNA + a 5'-end dephospho-ribonucleoside- RNA 		- PubMed:16828802
-
[Guanine-N7 methyltransferase nsp14]
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 		2.1.1.56 PubMed:34845015
-
[RNA-directed RNA polymerase nsp12]
a 5'-end diphospho-ribonucleoside in mRNA + GTP + H(+) = a 5'- end (5'-triphosphoguanosine)-(ribonucleoside) in mRNA + diphosphate 		2.7.7.50 UniProtKB:P0DTD1
-
Chain : B, E
UniProt : P0CG48 (UBC_HUMAN)
Reaction : -
Chain : C, F
UniProt : P0CG47 (UBB_HUMAN)
Reaction : -