PDBsum entry 2idy

Viral protein

PDB id

2idy

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Contents

			Protein chain

					112 a.a. *

* Residue conservation analysis

PDB id:

2idy

Links
- PDBe
- RCSB
- MMDB
- JenaLib
- Proteopedia
- CATH
- SCOP
- PDBSWS
- ProSAT

Name:

Viral protein

Title:

Nmr structure of the sars-cov non-structural protein nsp3a

Structure:

Nsp3. Chain: a. Engineered: yes

Source:

Sars coronavirus. Organism_taxid: 227859. Expressed in: escherichia coli. Expression_system_taxid: 562.

NMR struc:

1 models

Authors:

P.Serrano,M.S.Almeida,M.A.Johnson,R.Horst,T.Herrmann,J.Joseph, K.Saikatendu,V.Subramanian,R.C.Stevens,P.Kuhn,K.Wuthrich,Joint Center For Structural Genomics (Jcsg)

Key ref:

P.Serrano et al. (2007). Nuclear magnetic resonance structure of the N-terminal domain of nonstructural protein 3 from the severe acute respiratory syndrome coronavirus. J Virol, 81, 12049-12060. PubMed id: 17728234

Date:

15-Sep-06

Release date:

05-Dec-06

PROCHECK

	Headers

	References

Protein chain

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

Seq: Struc:

Seq: Struc:

Seq: Struc:

Seq: Struc:

Seq: Struc:

Seq: Struc:

Seq: Struc:

Seq: Struc:

Seq: Struc:

Seq: Struc:

Seq: Struc:

Seq: Struc:

Seq: Struc:

Seq: Struc:

Seq: Struc:					7073 a.a. 112 a.a.

Key:

PfamA domain

Secondary structure

CATH domain



		Enzyme reactions

Enzyme class 2:

E.C.2.1.1.- - ?????

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

Enzyme class 3:

E.C.2.1.1.56 - mRNA (guanine-N(7))-methyltransferase.

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

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

5'-end (5'-triphosphoguanosine)-ribonucleoside in mRNA	+	S-adenosyl-L- methionine	=	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.

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

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⁺

5'-end (N(7)-methyl 5'-triphosphoguanosine)-ribonucleoside in mRNA	+	S-adenosyl-L-methionine	=	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.

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

Reaction:

RNA(n) + a ribonucleoside 5'-triphosphate = RNA(n+1) + diphosphate

RNA(n)	+	ribonucleoside 5'-triphosphate	=	RNA(n+1)	+	diphosphate

Enzyme class 6:

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 7:

E.C.3.1.13.- - ?????

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

Enzyme class 8:

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 9:

E.C.3.4.22.- - ?????

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

Enzyme class 10:

E.C.3.4.22.69 - Sars coronavirus main proteinase.

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

Enzyme class 11:

E.C.3.6.4.12 - Dna helicase.

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

Reaction:

ATP + H2O = ADP + phosphate + H⁺

ATP	+	H2O	=	ADP	+	phosphate	+	H(+)

Enzyme class 12:

E.C.3.6.4.13 - Rna helicase.

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

Reaction:

ATP + H2O = ADP + phosphate + H⁺

ATP	+	H2O	=	ADP	+	phosphate	+	H(+)

Enzyme class 13:

E.C.4.6.1.- - ?????

[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

reference

	J Virol 81:12049-12060 (2007)
PubMed id: 17728234

Nuclear magnetic resonance structure of the N-terminal domain of nonstructural protein 3 from the severe acute respiratory syndrome coronavirus.
P.Serrano, M.A.Johnson, M.S.Almeida, R.Horst, T.Herrmann, J.S.Joseph, B.W.Neuman, V.Subramanian, K.S.Saikatendu, M.J.Buchmeier, R.C.Stevens, P.Kuhn, K.Wüthrich.

ABSTRACT

This paper describes the structure determination of nsp3a, the N-terminal domain of the severe acute respiratory syndrome coronavirus (SARS-CoV) nonstructural protein 3. nsp3a exhibits a ubiquitin-like globular fold of residues 1 to 112 and a flexibly extended glutamic acid-rich domain of residues 113 to 183. In addition to the four beta-strands and two alpha-helices that are common to ubiquitin-like folds, the globular domain of nsp3a contains two short helices representing a feature that has not previously been observed in these proteins. Nuclear magnetic resonance chemical shift perturbations showed that these unique structural elements are involved in interactions with single-stranded RNA. Structural similarities with proteins involved in various cell-signaling pathways indicate possible roles of nsp3a in viral infection and persistence.

Literature references that cite this PDB file's key reference

PubMed id

Reference

20660183

K.R.Hurst, R.Ye, S.J.Goebel, P.Jayaraman, and P.S.Masters (2010).
An interaction between the nucleocapsid protein and a component of the replicase-transcriptase complex is crucial for the infectivity of coronavirus genomic RNA.

J Virol, 84, 10276-10288.

19052085

A.Chatterjee, M.A.Johnson, P.Serrano, B.Pedrini, J.S.Joseph, B.W.Neuman, K.Saikatendu, M.J.Buchmeier, P.Kuhn, and K.Wüthrich (2009).
Nuclear magnetic resonance structure shows that the severe acute respiratory syndrome coronavirus-unique domain contains a macrodomain fold.

J Virol, 83, 1823-1836.

PDB codes:

2jzd 2jze 2jzf 2rnk

19436709

J.Tan, C.Vonrhein, O.S.Smart, G.Bricogne, M.Bollati, Y.Kusov, G.Hansen, J.R.Mesters, C.L.Schmidt, and R.Hilgenfeld (2009).
The SARS-Unique Domain (SUD) of SARS Coronavirus Contains Two Macrodomains That Bind G-Quadruplexes.

PLoS Pathog, 5, e1000428.

PDB codes:

2w2g 2wct

19828617

P.Serrano, M.A.Johnson, A.Chatterjee, B.W.Neuman, J.S.Joseph, M.J.Buchmeier, P.Kuhn, and K.Wüthrich (2009).
Nuclear magnetic resonance structure of the nucleic acid-binding domain of severe acute respiratory syndrome coronavirus nonstructural protein 3.

J Virol, 83, 12998-13008.

PDB code:

2k87

19430490

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

Nat Rev Microbiol, 7, 439-450.

18367524

B.W.Neuman, J.S.Joseph, K.S.Saikatendu, P.Serrano, A.Chatterjee, M.A.Johnson, L.Liao, J.P.Klaus, J.R.Yates, K.Wüthrich, R.C.Stevens, M.J.Buchmeier, and P.Kuhn (2008).
Proteomics analysis unravels the functional repertoire of coronavirus nonstructural protein 3.

J Virol, 82, 5279-5294.

19636888

P.Serrano, M.A.Johnson, A.Chatterjee, B.Pedrini, and K.Wüthrich (2008).
NMR assignment of the nonstructural protein nsp3(1066-1181) from SARS-CoV.

Biomol NMR Assign, 2, 135-138.

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 codes are shown on the right.