PDBsum entry 2fe8

Hydrolase

PDB id: 2fe8

Contents

Protein chains

315 a.a. *

Ligands

SO4 ×3

Metals

_ZN ×3

_BR ×9

Waters ×530

* Residue conservation analysis

PDB id:

2fe8

Name:

Hydrolase

Title:

Sars coronavirus papain-like protease: structure of a viral deubiquitinating enzyme

Structure:

Replicase polyprotein 1ab. Chain: a, b, c. Fragment: papain like proteinase, residues 1541-1854. Synonym: pp1ab, orf1ab. Engineered: yes

Source:

Sars coronavirus. Organism_taxid: 227859. Strain: sars. Expressed in: escherichia coli bl21. Expression_system_taxid: 511693.

Biol. unit:

Hexamer (from PQS)

Resolution:

1.85Å R-factor: 0.201 R-free: 0.229

Authors:

K.Ratia,B.D.Santarsiero,A.D.Mesecar

Key ref:

K.Ratia et al. (2006). Severe acute respiratory syndrome coronavirus papain-like protease: structure of a viral deubiquitinating enzyme. Proc Natl Acad Sci U S A, 103, 5717-5722. PubMed id: 16581910 DOI: 10.1073/pnas.0510851103

Date:

15-Dec-05 Release date: 21-Mar-06

Protein chains

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

Seq: 7073 a.a.

Struc: 315 a.a.*

* PDB and UniProt seqs differ at 1 residue position (black cross)

Enzyme reactions

• Enzyme class 2: E.C.2.1.1.- - ?????
• Enzyme class 3: 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: 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: E.C.2.7.7.48 - RNA-directed Rna polymerase.
• Reaction: RNA(n) + a ribonucleoside 5'-triphosphate = RNA(n+1) + diphosphate
• Enzyme class 6: 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: E.C.3.1.13.- - ?????
• Enzyme class 8: 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: E.C.3.4.22.- - ?????
• Enzyme class 10: E.C.3.4.22.69 - Sars coronavirus main proteinase.
• Enzyme class 11: E.C.3.6.4.12 - Dna helicase.
• Reaction: ATP + H2O = ADP + phosphate + H⁺
• Enzyme class 12: E.C.3.6.4.13 - Rna helicase.
• Reaction: ATP + H2O = ADP + phosphate + H⁺
• Enzyme class 13: 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: 10.1073/pnas.0510851103

Proc Natl Acad Sci U S A 103:5717-5722 (2006)

PubMed id: 16581910

Severe acute respiratory syndrome coronavirus papain-like protease: structure of a viral deubiquitinating enzyme.

K.Ratia, K.S.Saikatendu, B.D.Santarsiero, N.Barretto, S.C.Baker, R.C.Stevens, A.D.Mesecar.

ABSTRACT

Replication of severe acute respiratory syndrome (SARS) coronavirus (SARS-CoV) requires proteolytic processing of the replicase polyprotein by two viral cysteine proteases, a chymotrypsin-like protease (3CLpro) and a papain-like protease (PLpro). These proteases are important targets for development of antiviral drugs that would inhibit viral replication and reduce mortality associated with outbreaks of SARS-CoV. In this work, we describe the 1.85-A crystal structure of the catalytic core of SARS-CoV PLpro and show that the overall architecture adopts a fold closely resembling that of known deubiquitinating enzymes. Key features, however, distinguish PLpro from characterized deubiquitinating enzymes, including an intact zinc-binding motif, an unobstructed catalytically competent active site, and the presence of an intriguing, ubiquitin-like N-terminal domain. To gain insight into the active-site recognition of the C-terminal tail of ubiquitin and the related LXGG motif, we propose a model of PLpro in complex with ubiquitin-aldehyde that reveals well defined sites within the catalytic cleft that help to account for strict substrate-recognition motifs.

Selected figure(s)

Figure 4.
Fig. 4. The SARS-CoV PLpro and USP14 active sites. (A) SARS-CoV PLpro catalytic triad residues, C112, H273, and D287, and other important active-site residues. Distances between residues are indicated in angstroms. The hydrogen bond between D109 and W97 is indicated by an arrow. (B) Comparison of USP14 and SARS-CoV PLpro BL1 and BL2 loop regions. Corresponding regions of unbound USP14 (red), Ubal-complexed USP14 (yellow), and PLpro (blue) are shown superimposed. The BL1 and BL2 loop regions are indicated. The BL1 loop region of PLpro is colored in green. The catalytic triad residues are shown by a ball-and-stick representation.

Figure 5.
Fig. 5. Comparison of the ubiquitin-binding surfaces of HAUSP, USP14, and PLpro based on modeling studies. For modeling ubiquitin into the SARS-CoV PLpro active site, the structures of the Ubal-bound forms of HAUSP (1nbf) and USP14 (2ayo) were superimposed onto the PLpro structure and analyzed. Contacts at the C-terminal tail of ubiquitin and two interacting surfaces of the PLpro palm domain were manually edited and minimized by using CNS. The ubiquitin molecule is shown as a ribbon diagram.

Figures were selected by an automated process.