PDBsum entry 2kaf

Viral protein, RNA binding protein

PDB id: 2kaf

Contents

Protein chain

67 a.a.

PDB id:

2kaf

Name:

Viral protein, RNA binding protein

Title:

Solution structure of the sars-unique domain-c from the nonstructural protein 3 (nsp3) of the severe acute respiratory syndrome coronavirus

Structure:

Non-structural protein 3. Chain: a. Fragment: sars-unique domain-c, residues 1473-1532. Synonym: replicase polyprotein 1a, pp1a, orf1a polyprotein, nsp3, papain-like proteinase, pl-pro, pl2-pro. Engineered: yes

Source:

Sars coronavirus. Sars-cov. Organism_taxid: 227859. Gene: 1a. Expressed in: escherichia coli. Expression_system_taxid: 562.

NMR struc:

20 models

Authors:

M.A.Johnson,B.Mohanty,B.Pedrini,P.Serrano,A.Chatterjee,T.Herrmann, J.Joseph,K.Saikatendu,I.A.Wilson,M.J.Buchmeier,P.Kuhn,K.Wuthrich, Joint Center For Structural Genomics (Jcsg)

Key ref:

M.A.Johnson et al. (2010). SARS coronavirus unique domain: three-domain molecular architecture in solution and RNA binding. J Mol Biol, 400, 724-742. PubMed id: 20493876

Date:

05-Nov-08 Release date: 25-Nov-08

Protein chain

P0C6U8  (R1A_CVHSA) -  Replicase polyprotein 1a from Severe acute respiratory syndrome coronavirus

Seq: 4382 a.a.

Struc: 67 a.a.*

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

Enzyme reactions

• Enzyme class 1: 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 2: 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 3: E.C.3.4.22.- - ?????
• Enzyme class 4: E.C.3.4.22.69 - Sars coronavirus main proteinase.

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

Added reference

J Mol Biol 400:724-742 (2010)

PubMed id: 20493876

SARS coronavirus unique domain: three-domain molecular architecture in solution and RNA binding.

M.A.Johnson, A.Chatterjee, B.W.Neuman, K.Wüthrich.

ABSTRACT

The nonstructural protein 3 (nsp3) of the severe acute respiratory syndrome coronavirus (SARS-CoV) includes a "SARS-unique region" (SUD) consisting of three globular domains separated by short linker peptide segments. This paper reports NMR structure determinations of the C-terminal domain (SUD-C) and of a two-domain construct (SUD-MC) containing the middle domain (SUD-M) and the C-terminal domain, and NMR data on the conformational states of the N-terminal domain (SUD-N) and the SUD-NM two-domain construct. Both SUD-N and SUD-NM are monomeric and globular in solution, and in SUD-NM there is high mobility in the two-residue interdomain linking sequence, with no preferred relative orientation of the two domains. SUD-C adopts a frataxin-like fold and has structural similarity to DNA-binding domains of DNA-modifying enzymes. The structures of both SUD-M (previously determined) and SUD-C (from the present study) are maintained in SUD-MC, where the two domains are flexibly linked. Gel shift experiments showed that both SUD-C and SUD-MC bind to single-stranded RNA and recognize purine bases more strongly than pyrimidine bases, whereby SUD-MC binds to a more restricted set of purine-containing RNA sequences than SUD-M. NMR chemical shift perturbation experiments with observation of the (15)N-labeled proteins further resulted in the delineation of the RNA binding sites, i.e., in SUD-M a positively charged surface area with a pronounced cavity, and in SUD-C several residues of an antiparallel beta-sheet. Overall, the present data provide evidence for molecular mechanisms involving concerted actions of SUD-M and SUD-C, which result in specific RNA-binding that might be unique to the SUD, and thus to the SARS-CoV.