PDBsum entry 1lvo

Hydrolase

PDB id: 1lvo

Contents

Protein chains

(+ 0 more) 299 a.a. *

Ligands

SO4 ×27

DIO ×9

MRD ×6

Waters ×1003

* Residue conservation analysis

PDB id:

1lvo

Name:

Hydrolase

Title:

Structure of coronavirus main proteinase reveals combination of a chymotrypsin fold with an extra alpha-helical domain

Structure:

Replicase, hydrolase domain. Chain: a, b, c, d, e, f. Fragment: residues 2879-3180. Engineered: yes

Source:

Transmissible gastroenteritis virus. Organism_taxid: 11149. Gene: orf1a. Expressed in: escherichia coli. Expression_system_taxid: 562.

Biol. unit:

Dimer (from PQS)

Resolution:

1.96Å R-factor: 0.210 R-free: 0.256

Authors:

K.Anand,G.J.Palm,J.R.Mesters,S.G.Siddell,J.Ziebuhr,R.Hilgenfeld

Key ref:

K.Anand et al. (2002). Structure of coronavirus main proteinase reveals combination of a chymotrypsin fold with an extra alpha-helical domain. EMBO J, 21, 3213-3224. PubMed id: 12093723 DOI: 10.1093/emboj/cdf327

Date:

29-May-02 Release date: 17-Jul-02

Protein chains

P0C6Y5  (R1AB_CVPPU) -  Replicase polyprotein 1ab from Porcine transmissible gastroenteritis coronavirus (strain Purdue)

Seq: 6684 a.a.

Struc: 299 a.a.

Enzyme reactions

• Enzyme class 2: 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 3: E.C.2.7.7.48 - RNA-directed Rna polymerase.
• Reaction: RNA(n) + a ribonucleoside 5'-triphosphate = RNA(n+1) + diphosphate
• Enzyme class 4: 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 5: E.C.3.1.13.- - ?????
• Enzyme class 6: 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 7: E.C.3.4.22.- - ?????
• Enzyme class 8: E.C.3.6.4.12 - Dna helicase.
• Reaction: ATP + H2O = ADP + phosphate + H⁺
• Enzyme class 9: E.C.3.6.4.13 - Rna helicase.
• Reaction: ATP + H2O = ADP + phosphate + H⁺
• Enzyme class 10: 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: 10.1093/emboj/cdf327

EMBO J 21:3213-3224 (2002)

PubMed id: 12093723

Structure of coronavirus main proteinase reveals combination of a chymotrypsin fold with an extra alpha-helical domain.

K.Anand, G.J.Palm, J.R.Mesters, S.G.Siddell, J.Ziebuhr, R.Hilgenfeld.

ABSTRACT

The key enzyme in coronavirus polyprotein processing is the viral main proteinase, M(pro), a protein with extremely low sequence similarity to other viral and cellular proteinases. Here, the crystal structure of the 33.1 kDa transmissible gastroenteritis (corona)virus M(pro) is reported. The structure was refined to 1.96 A resolution and revealed three dimers in the asymmetric unit. The mutual arrangement of the protomers in each of the dimers suggests that M(pro) self-processing occurs in trans. The active site, comprised of Cys144 and His41, is part of a chymotrypsin-like fold that is connected by a 16 residue loop to an extra domain featuring a novel alpha-helical fold. Molecular modelling and mutagenesis data implicate the loop in substrate binding and elucidate S1 and S2 subsites suitable to accommodate the side chains of the P1 glutamine and P2 leucine residues of M(pro) substrates. Interactions involving the N-terminus and the alpha-helical domain stabilize the loop in the orientation required for trans-cleavage activity. The study illustrates that RNA viruses have evolved unprecedented variations of the classical chymotrypsin fold.

Selected figure(s)

Figure 7.
Figure 7 Stereo diagram of a P5−P1 substrate (Asn−Ser−Thr−Leu−Gln, red; corresponding to the TGEV M^pro N-terminal autoprocessing site) modelled into the active site cleft of the TGEV M^pro. Hydrogen bonds are depicted by dotted lines.

Figure 8.
Figure 8 Intra- and intermolecular contacts of the TGEV M^pro N-terminus. (A) MOLSCRIPT stereo representation of a TGEV M^pro dimer. Molecule A is coloured from blue at the N-terminus, via green (domain II), to red (C-terminus), while molecule B is shown in grey. The catalytic Cys144 and His41 residues are labelled in both monomers. (B) Detailed view of the interactions made by the N-terminal segment (blue) and domains II/III of monomer A as well as domains II/III of monomer B. Residues critically involved in these interactions are designated by the single-letter code and shown in ball-and-stick representation (see text for details). The N- and C-termini of molecule A are indicated.

The above figures are reprinted from an Open Access publication published by Macmillan Publishers Ltd: EMBO J (2002, 21, 3213-3224) copyright 2002.

Figures were selected by an automated process.