PDBsum entry 1uw7

Viral protein

PDB id: 1uw7

Contents

Protein chain

122 a.a. *

* Residue conservation analysis

PDB id:

1uw7

Name:

Viral protein

Title:

Nsp9 protein from sars-coronavirus.

Structure:

Nsp9. Chain: a. Fragment: nsp9, residues 3925-4037. Synonym: pp1ab, orf1ab, replicase polyprotein 1ab. Engineered: yes

Source:

Sars coronavirus hku-39849. Organism_taxid: 228404. Cell_line: vero e6. Expressed in: escherichia coli. Expression_system_taxid: 562.

Biol. unit:

Dimer (from PDB file)

Resolution:

2.80Å R-factor: 0.228 R-free: 0.314

Authors:

G.Sutton,E.Fry,L.Carter,S.Sainsbury,T.Walter,J.Nettleship,N.Berrow, R.Owens,R.Gilbert,A.Davidson,S.Siddell,L.L.M.Poon,J.Diprose, D.Alderton,M.Walsh,J.M.Grimes,D.I.Stuart

Key ref:

G.Sutton et al. (2004). The nsp9 replicase protein of SARS-coronavirus, structure and functional insights. Structure, 12, 341-353. PubMed id: 14962394 DOI: 10.1016/S0969-2126(04)00026-7

Date:

30-Jan-04 Release date: 20-Feb-04

Protein chain

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

Seq: 7073 a.a.

Struc: 122 a.a.*

* PDB and UniProt seqs differ at 9 residue positions (black crosses)

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: 10.1016/S0969-2126(04)00026-7

Structure 12:341-353 (2004)

PubMed id: 14962394

The nsp9 replicase protein of SARS-coronavirus, structure and functional insights.

G.Sutton, E.Fry, L.Carter, S.Sainsbury, T.Walter, J.Nettleship, N.Berrow, R.Owens, R.Gilbert, A.Davidson, S.Siddell, L.L.Poon, J.Diprose, D.Alderton, M.Walsh, J.M.Grimes, D.I.Stuart.

ABSTRACT

As part of a high-throughput structural analysis of SARS-coronavirus (SARS-CoV) proteins, we have solved the structure of the non-structural protein 9 (nsp9). This protein, encoded by ORF1a, has no designated function but is most likely involved with viral RNA synthesis. The protein comprises a single beta-barrel with a fold previously unseen in single domain proteins. The fold superficially resembles an OB-fold with a C-terminal extension and is related to both of the two subdomains of the SARS-CoV 3C-like protease (which belongs to the serine protease superfamily). nsp9 has, presumably, evolved from a protease. The crystal structure suggests that the protein is dimeric. This is confirmed by analytical ultracentrifugation and dynamic light scattering. We show that nsp9 binds RNA and interacts with nsp8, activities that may be essential for its function(s).

Selected figure(s)

Figure 1.
Figure 1. Structure of SARS-CoV nsp9(A) A stereo a carbon trace colored blue to red from the N to the C terminus. The nine residues of the N-terminal tag are shown dashed. Every tenth residue is labeled.(B) A stereo ribbon depiction colored as in (A) with the main secondary structure elements labeled according to Figure 2C. The N-terminal tag residues are shown transparent. Figures are produced using BOBSCRIPT (Esnouf, 1997) and RASTER3D (Merrit and Murphy, 1994).(C) Stereo diagram of the 2F[o] - F[c] electron density for the C-terminal a helix residues 101-111, contoured at 1s. The electron density is shown as a green mesh with the residues depicted in red ball-and-stick.

The above figure is reprinted by permission from Cell Press: Structure (2004, 12, 341-353) copyright 2004.

Figure was selected by an automated process.