PDBsum entry 2acf

Viral protein

PDB id: 2acf

Contents

Protein chains

172 a.a. *

Ligands

GOL ×12

Waters ×950

* Residue conservation analysis

PDB id:

2acf

Name:

Viral protein

Title:

Nmr structure of sars-cov non-structural protein nsp3a (sars1) from sars coronavirus

Structure:

Replicase polyprotein 1ab. Chain: a, b, c, d. Fragment: adrp domain of nsp-3. Engineered: yes

Source:

Sars coronavirus tor2. Organism_taxid: 227984. Strain: tor-2. Expressed in: escherichia coli. Expression_system_taxid: 562

Resolution:

1.40Å R-factor: 0.165 R-free: 0.189

Authors:

K.S.Saikatendu,J.S.Joseph,V.Subramanian,B.W.Neuman,M.J.Buchmeier, R.C.Stevens,P.Kuhn,Joint Center For Structural Genomics (Jcsg)

Key ref:

K.S.Saikatendu et al. (2005). Structural basis of severe acute respiratory syndrome coronavirus ADP-ribose-1''-phosphate dephosphorylation by a conserved domain of nsP3. Structure (Camb), 13, 1665-1675. PubMed id: 16271890 DOI: 10.1016/j.str.2005.07.022

Date:

18-Jul-05 Release date: 14-Feb-06

Protein chains

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

Seq: 7073 a.a.

Struc: 172 a.a.*

* PDB and UniProt seqs differ at 4 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/j.str.2005.07.022

Structure (Camb) 13:1665-1675 (2005)

PubMed id: 16271890

Structural basis of severe acute respiratory syndrome coronavirus ADP-ribose-1''-phosphate dephosphorylation by a conserved domain of nsP3.

K.S.Saikatendu, J.S.Joseph, V.Subramanian, T.Clayton, M.Griffith, K.Moy, J.Velasquez, B.W.Neuman, M.J.Buchmeier, R.C.Stevens, P.Kuhn.

ABSTRACT

The crystal structure of a conserved domain of nonstructural protein 3 (nsP3) from severe acute respiratory syndrome coronavirus (SARS-CoV) has been solved by single-wavelength anomalous dispersion to 1.4 A resolution. The structure of this "X" domain, seen in many single-stranded RNA viruses, reveals a three-layered alpha/beta/alpha core with a macro-H2A-like fold. The putative active site is a solvent-exposed cleft that is conserved in its three structural homologs, yeast Ymx7, Archeoglobus fulgidus AF1521, and Er58 from E. coli. Its sequence is similar to yeast YBR022W (also known as Poa1P), a known phosphatase that acts on ADP-ribose-1''-phosphate (Appr-1''-p). The SARS nsP3 domain readily removes the 1'' phosphate group from Appr-1''-p in in vitro assays, confirming its phosphatase activity. Sequence and structure comparison of all known macro-H2A domains combined with available functional data suggests that proteins of this superfamily form an emerging group of nucleotide phosphatases that dephosphorylate Appr-1''-p.

Selected figure(s)

Figure 2.
Figure 2. Structure of SARS ADRP
(A) Ribbon representation of the SARS nsP3 ADRP monomer. The two glycine-rich loops are shown in yellow. Secondary structures are colored from blue (N) to red (C terminus). Helices are numbered H1-H6, and b strands are numbered from 1 to 8.
(B) The SARS ADRP dimer observed between the B and D subunits in the asymmetric unit. The four conserved segments are colored red in each subunit; the conserved histidines and asparagines at the active site are shown as ball-and-sticks.

The above figure is reprinted by permission from Cell Press: Structure (Camb) (2005, 13, 1665-1675) copyright 2005.

Figure was selected by an automated process.