PDBsum entry 2g9t

Viral protein

PDB id

2g9t

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Contents

			Protein chains

					(+ 18 more) 118 a.a. *

			Metals

					_ZN ×48

			Waters ×1507

* Residue conservation analysis

PDB id:

2g9t

Links

Name:

Viral protein

Title:

Crystal structure of the sars coronavirus nsp10 at 2.1a

Structure:

Orf1a polyprotein. Chain: a, b, c, d, e, f, g, h, i, j, k, l, m, n, o, p, q, r, s, t, u, v, w, x. Fragment: nsp10 protein. Engineered: yes

Source:

Severe acute respiratory syndrome-related coronavirus. Organism_taxid: 694009. Expressed in: escherichia coli. Expression_system_taxid: 562.

Biol. unit:

Dodecamer (from PQS)

Resolution:

2.10Å

R-factor:

0.217

R-free:

0.247

Authors:

D.Su,Z.Lou,H.Yang,F.Sun,Z.Rao

Key ref:

D.Su et al. (2006). Dodecamer structure of severe acute respiratory syndrome coronavirus nonstructural protein nsp10. J Virol, 80, 7902-7908. PubMed id: 16873247

Date:

07-Mar-06

Release date:

15-Aug-06

PROCHECK

	Headers

	References

Protein chains

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

Seq: Struc:

Seq: Struc:

Seq: Struc:

Seq: Struc:

Seq: Struc:

Seq: Struc:

Seq: Struc:

Seq: Struc:

Seq: Struc:					4382 a.a. 118 a.a.

Key:

PfamA domain

Secondary structure



		Enzyme reactions

Enzyme class 1:

E.C.2.7.7.50 - mRNA guanylyltransferase.

[IntEnz] [ExPASy] [KEGG] [BRENDA]

Reaction:

a 5'-end diphospho-ribonucleoside in mRNA + GTP + H⁺ = a 5'-end (5'-triphosphoguanosine)-ribonucleoside in mRNA + diphosphate

5'-end diphospho-ribonucleoside in mRNA	+	GTP	+	H(+)	=	5'-end (5'-triphosphoguanosine)-ribonucleoside in mRNA	+	diphosphate

Enzyme class 2:

E.C.3.4.19.12 - ubiquitinyl hydrolase 1.

[IntEnz] [ExPASy] [KEGG] [BRENDA]

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.- - ?????

[IntEnz] [ExPASy] [KEGG] [BRENDA]

Enzyme class 4:

E.C.3.4.22.69 - Sars coronavirus main proteinase.

[IntEnz] [ExPASy] [KEGG] [BRENDA]

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 Virol 80:7902-7908 (2006)
PubMed id: 16873247

Dodecamer structure of severe acute respiratory syndrome coronavirus nonstructural protein nsp10.
D.Su, Z.Lou, F.Sun, Y.Zhai, H.Yang, R.Zhang, A.Joachimiak, X.C.Zhang, M.Bartlam, Z.Rao.

ABSTRACT

The severe acute respiratory syndrome coronavirus (SARS-CoV) nonstructural proteins nsp1 to nsp16 have been implicated by genetic analysis in the assembly of a functional replication/transcription complex. We report the crystal structure of nsp10 from SARS-CoV at 2.1-A resolution. The nsp10 structure has a novel fold, and 12 identical subunits assemble to form a unique spherical dodecameric architecture. Two zinc fingers have been identified from the nsp10 monomer structure with the sequence motifs C-(X)2-C-(X)5-H-(X)6-C and C-(X)2-C-(X)7-C-(X)-C. The nsp10 crystal structure is the first of a new class of zinc finger protein three-dimensional structures to be revealed experimentally. The zinc finger sequence motifs are conserved among all three coronavirus antigenic groups, implicating an essential function for nsp10 in all coronaviruses. Based on the structure, we propose that nsp10 is a transcription factor for coronavirus replication/transcription.

Literature references that cite this PDB file's key reference

PubMed id

Reference

19875418

A.J.te Velthuis, J.J.Arnold, C.E.Cameron, S.H.van den Worm, and E.J.Snijder (2010).
The RNA polymerase activity of SARS-coronavirus nsp12 is primer dependent.

Nucleic Acids Res, 38, 203-214.

20668085

H.L.Stokes, S.Baliji, C.G.Hui, S.G.Sawicki, S.C.Baker, and S.G.Siddell (2010).
A new cistron in the murine hepatitis virus replicase gene.

J Virol, 84, 10148-10158.

20421945

M.Bouvet, C.Debarnot, I.Imbert, B.Selisko, E.J.Snijder, B.Canard, and E.Decroly (2010).
In vitro reconstitution of SARS-coronavirus mRNA cap methylation.

PLoS Pathog, 6, e1000863.

20444893

S.Fang, H.Shen, J.Wang, F.P.Tay, and D.X.Liu (2010).
Functional and genetic studies of the substrate specificity of coronavirus infectious bronchitis virus 3C-like proteinase.

J Virol, 84, 7325-7336.

19430490

S.Perlman, and J.Netland (2009).
Coronaviruses post-SARS: update on replication and pathogenesis.

Nat Rev Microbiol, 7, 439-450.

19153232

Z.J.Miknis, E.F.Donaldson, T.C.Umland, R.A.Rimmer, R.S.Baric, and L.W.Schultz (2009).
Severe acute respiratory syndrome coronavirus nsp9 dimerization is essential for efficient viral growth.

J Virol, 83, 3007-3018.

PDB code:

3ee7

18054092

B.Canard, J.S.Joseph, and P.Kuhn (2008).
International research networks in viral structural proteomics: again, lessons from SARS.

Antiviral Res, 78, 47-50.

18827877

J.Pan, X.Peng, Y.Gao, Z.Li, X.Lu, Y.Chen, M.Ishaq, D.Liu, M.L.Dediego, L.Enjuanes, and D.Guo (2008).
Genome-wide analysis of protein-protein interactions and involvement of viral proteins in SARS-CoV replication.

PLoS ONE, 3, e3299.

18156685

M.Bartlam, X.Xue, and Z.Rao (2008).
The search for a structural basis for therapeutic intervention against the SARS coronavirus.

Acta Crystallogr A, 64, 204-213.

17397959

R.L.Graham, J.S.Sparks, L.D.Eckerle, A.C.Sims, and M.R.Denison (2008).
SARS coronavirus replicase proteins in pathogenesis.

Virus Res, 133, 88.

18032506

R.Züst, T.B.Miller, S.J.Goebel, V.Thiel, and P.S.Masters (2008).
Genetic interactions between an essential 3' cis-acting RNA pseudoknot, replicase gene products, and the extreme 3' end of the mouse coronavirus genome.

J Virol, 82, 1214-1228.

17634238

D.J.Deming, R.L.Graham, M.R.Denison, and R.S.Baric (2007).
Processing of open reading frame 1a replicase proteins nsp7 to nsp10 in murine hepatitis virus strain A59 replication.

J Virol, 81, 10280-10291.

17392363

E.F.Donaldson, A.C.Sims, R.L.Graham, M.R.Denison, and R.S.Baric (2007).
Murine hepatitis virus replicase protein nsp10 is a critical regulator of viral RNA synthesis.

J Virol, 81, 6356-6368.

17680348

M.Bartlam, Y.Xu, and Z.Rao (2007).
Structural proteomics of the SARS coronavirus: a model response to emerging infectious diseases.

J Struct Funct Genomics, 8, 85-97.

17855519

M.Oostra, E.G.te Lintelo, M.Deijs, M.H.Verheije, P.J.Rottier, and C.A.de Haan (2007).
Localization and membrane topology of coronavirus nonstructural protein 4: involvement of the early secretory pathway in replication.

J Virol, 81, 12323-12336.

17202208

M.S.Almeida, M.A.Johnson, T.Herrmann, M.Geralt, and K.Wüthrich (2007).
Novel beta-barrel fold in the nuclear magnetic resonance structure of the replicase nonstructural protein 1 from the severe acute respiratory syndrome coronavirus.

J Virol, 81, 3151-3161.

PDB codes:

2gdt 2hsx

16928755

S.G.Sawicki, D.L.Sawicki, and S.G.Siddell (2007).
A contemporary view of coronavirus transcription.

J Virol, 81, 20-29.

17934078

V.C.Cheng, S.K.Lau, P.C.Woo, and K.Y.Yuen (2007).
Severe acute respiratory syndrome coronavirus as an agent of emerging and reemerging infection.

Clin Microbiol Rev, 20, 660-694.

16987966

H.Schütze, R.Ulferts, B.Schelle, S.Bayer, H.Granzow, B.Hoffmann, T.C.Mettenleiter, and J.Ziebuhr (2006).
Characterization of White bream virus reveals a novel genetic cluster of nidoviruses.

J Virol, 80, 11598-11609.

17085042

J.R.Mesters, J.Tan, and R.Hilgenfeld (2006).
Viral enzymes.

Curr Opin Struct Biol, 16, 776-786.

The most recent references are shown first. Citation data come partly from CiteXplore and partly from an automated harvesting procedure. Note that this is likely to be only a partial list as not all journals are covered by either method. However, we are continually building up the citation data so more and more references will be included with time. Where a reference describes a PDB structure, the PDB code is shown on the right.