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PDBsum entry 3ejg

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protein links
Hydrolase PDB id
3ejg
Jmol PyMol
Contents
Protein chain
165 a.a. *
Waters ×146
* Residue conservation analysis
PDB id:
3ejg
Name: Hydrolase
Title: Crystal structure of hcov-229e x-domain
Structure: Non-structural protein 3. Chain: a. Fragment: macro domain, unp residues 1270-1434. Synonym: nsp3, pp1ab, orf1ab polyprotein. Engineered: yes
Source: Human coronavirus 229e. Hcov-229e. Organism_taxid: 11137. Gene: 1a. Expressed in: escherichia coli. Expression_system_taxid: 562.
Resolution:
1.78Å     R-factor:   0.167     R-free:   0.205
Authors: Y.Piotrowski,G.Hansen,R.Hilgenfeld
Key ref:
Y.Piotrowski et al. (2009). Crystal structures of the X-domains of a Group-1 and a Group-3 coronavirus reveal that ADP-ribose-binding may not be a conserved property. Protein Sci, 18, 6. PubMed id: 19177346 DOI: 10.1002/pro.15
Date:
18-Sep-08     Release date:   30-Sep-08    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
P0C6X1  (R1AB_CVH22) -  Replicase polyprotein 1ab
Seq:
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Seq:
Struc:
6758 a.a.
165 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Enzyme reactions 
   Enzyme class 2: E.C.2.7.7.48  - RNA-directed Rna polymerase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: Nucleoside triphosphate + RNA(n) = diphosphate + RNA(n+1)
Nucleoside triphosphate
+ RNA(n)
= diphosphate
+ RNA(n+1)
   Enzyme class 3: 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 4: E.C.3.6.4.12  - Dna helicase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: ATP + H2O = ADP + phosphate
ATP
+ H(2)O
= ADP
+ phosphate
   Enzyme class 5: E.C.3.6.4.13  - Rna helicase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: ATP + H2O = ADP + phosphate
ATP
+ H(2)O
= ADP
+ phosphate
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: 10.1002/pro.15 Protein Sci 18:6 (2009)
PubMed id: 19177346  
 
 
Crystal structures of the X-domains of a Group-1 and a Group-3 coronavirus reveal that ADP-ribose-binding may not be a conserved property.
Y.Piotrowski, G.Hansen, A.L.Boomaars-van der Zanden, E.J.Snijder, A.E.Gorbalenya, R.Hilgenfeld.
 
  ABSTRACT  
 
The polyproteins of coronaviruses are cleaved by viral proteases into at least 15 nonstructural proteins (Nsps). Consisting of five domains, Nsp3 is the largest of these (180-210 kDa). Among these domains, the so-called X-domain is believed to act as ADP-ribose-1''-phosphate phosphatase or to bind poly(ADP-ribose). However, here we show that the X-domain of Infectious Bronchitis Virus (strain Beaudette), a Group-3 coronavirus, fails to bind ADP-ribose. This is explained on the basis of the crystal structure of the protein, determined at two different pH values. For comparison, we also describe the crystal structure of the homologous X-domain from Human Coronavirus 229E, a Group-1 coronavirus, which does bind ADP-ribose.
 
  Selected figure(s)  
 
Figure 3.
Ribbon-representation of the superimposed X-domains of HCoV 229E (blue) and IBV (strain Beaudette) (green, pH 8.5; red, pH 5.6). N- and C-termini are indicated; the symbol "N" is framed for IBV-X.
Figure 4.
A: Stereo representation showing the binding of ADP-ribose to the X-domain of SARS-CoV,19 compared with the equivalent site in IBV-X8.5. The ADP-ribose molecule and the amino acid residues involved in the binding are represented as sticks. Carbon atoms of the ADP-ribose are colored white, carbon atoms of the protein are colored yellow and green, for SARS-X and IBV-X, respectively. Nitrogens and oxygens are colored blue and red, respectively. B: Residues [42]GGG[44] and [122]SCGIFG[127] (L11) of 229E-X (sticks, blue carbon atoms), likely involved in binding ADP-ribose, superimposed onto the corresponding site ([46]GSG[48] and [128]SLGIFG[133]) in IBV-X8.5 (transparent surface colored according to electrostatic potential, green sticks). Residue labels for 229E-X are framed. Note that Ile 131, and with it, the entire loop L11, in IBV-X is "pushed away" (red arrows) due to steric hindrance from Ser 47, thereby destroying the binding site for ADP-ribose.
 
  The above figures are reprinted from an Open Access publication published by the Protein Society: Protein Sci (2009, 18, 6) copyright 2009.  
  Figures were selected by an automated process.  

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.  
20369302 S.J.Bender, and S.R.Weiss (2010).
Pathogenesis of murine coronavirus in the central nervous system.
  J Neuroimmune Pharmacol, 5, 336-354.  
19386706 H.Malet, B.Coutard, S.Jamal, H.Dutartre, N.Papageorgiou, M.Neuvonen, T.Ahola, N.Forrester, E.A.Gould, D.Lafitte, F.Ferron, J.Lescar, A.E.Gorbalenya, X.de Lamballerie, and B.Canard (2009).
The crystal structures of Chikungunya and Venezuelan equine encephalitis virus nsP3 macro domains define a conserved adenosine binding pocket.
  J Virol, 83, 6534-6545.
PDB codes: 3gpg 3gpo 3gpq 3gqe 3gqo
19966415 J.A.Wojdyla, I.Manolaridis, E.J.Snijder, A.E.Gorbalenya, B.Coutard, Y.Piotrowski, R.Hilgenfeld, and P.A.Tucker (2009).
Structure of the X (ADRP) domain of nsp3 from feline coronavirus.
  Acta Crystallogr D Biol Crystallogr, 65, 1292-1300.
PDB codes: 3eti 3ew5 3jzt
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
20221421 K.M.Rose, and S.R.Weiss (2009).
Murine Coronavirus Cell Type Dependent Interaction with the Type I Interferon Response.
  Viruses, 1, 689-712.  
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
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.

 

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