4EKF

Structure of the Inactive Adenovirus Proteinase at 0.98 Angstrom Resolution


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 0.98 Å
  • R-Value Free: 0.168 

wwPDB Validation 3D Report Full Report


This is version 1.4 of the entry. See complete history

Literature

Regulation of a Viral Proteinase by a Peptide and DNA in One-dimensional Space: III. ATOMIC RESOLUTION STRUCTURE OF THE NASCENT FORM OF THE ADENOVIRUS PROTEINASE.

Baniecki, M.L.McGrath, W.J.Mangel, W.F.

(2013) J.Biol.Chem. 288: 2081-2091

  • DOI: 10.1074/jbc.M112.407429

  • PubMed Abstract: 
  • The adenovirus proteinase (AVP), the first member of a new class of cysteine proteinases, is essential for the production of infectious virus, and here we report its structure at 0.98 Å resolution. AVP, initially synthesized as an inactive enzyme, re ...

    The adenovirus proteinase (AVP), the first member of a new class of cysteine proteinases, is essential for the production of infectious virus, and here we report its structure at 0.98 Å resolution. AVP, initially synthesized as an inactive enzyme, requires two cofactors for maximal activity: pVIc, an 11-amino acid peptide, and the viral DNA. Comparison of the structure of AVP with that of an active form, the AVP-pVIc complex, reveals why AVP is inactive. Both forms have an α + β fold; the major structural differences between them lie in the β-sheet domain. In AVP-pVIc, the general base His-54 Nδ1 is 3.9 Å away from the Cys-122 Sγ, thereby rendering it nucleophilic. In AVP, however, His-54 Nδ1 is 7.0 Å away from Cys-122 Sγ, too far away to be able to abstract the proton from Cys-122. In AVP-pVIc, Tyr-84 forms a cation-π interaction with His-54 that should raise the pK(a) of His-54 and freeze the imidazole ring in the place optimal for forming an ion pair with Cys-122. In AVP, however, Tyr-84 is more than 11 Å away from its position in AVP-pVIc. Based on the structural differences between AVP and AVP-pVIc, we present a model that postulates that activation of AVP by pVIc occurs via a 62-amino acid-long activation pathway in which the binding of pVIc initiates contiguous conformational changes, analogous to falling dominos. There is a common pathway that branches into a pathway that leads to the repositioning of His-54 and another pathway that leads to the repositioning of Tyr-84.


    Related Citations: 
    • Regulation of a viral proteinase by a peptide and DNA in one-dimensional space. IV. viral proteinase slides along DNA to locate and process its substrates.
      Blainey, P.C.,Graziano, V.,Perez-Berna, A.J.,McGrath, W.J.,Flint, S.J.,San Martin, C.,Xie, X.S.,Mangel, W.F.
      (2012) J.Biol.Chem. 15: 1778
    • Viral DNA and a viral peptide can act as cofactors of adenovirus virion proteinase activity.
      Mangel, W.F.,McGrath, W.J.,Toledo, D.L.,Anderson, C.W.
      (1993) Nature 361: 274
    • Regulation of a viral proteinase by a peptide and DNA in one-dimensional space. II. adenovirus proteinase is activated in an unusual one-dimensional biochemical reaction.
      Graziano, V.,Luo, G.,Blainey, P.C.,Perez-Berna, A.J.,McGrath, W.J.,Flint, S.J.,San Martin, C.,Xie, X.S.,Mangel, W.F.
      (2012) J.Biol.Chem. 58: 1462
    • Regulation of a viral proteinase by a peptide and DNA in one-dimensional space. I. binding to DNA and to hexon of the precursor to protein VI, pVI, of human adenovirus.
      Graziano, V.,McGrath, W.J.,Suomalainen, M.,Greber, U.F.,Freimuth, P.,Blainey, P.C.,Luo, G.,Xie, X.S.,Mangel, W.F.
      (2012) J.Biol.Chem. --: --
    • Crystallographic structure at 1.6-A resolution of the human adenovirus proteinase in a covalent complex with its 11-amino-acid peptide cofactor: insights on a new fold.
      McGrath, W.J.,Ding, J.,Didwania, A.,Sweet, R.M.,Mangel, W.F.
      (2003) Biochim.Biophys.Acta 1648: 1
    • Crystal structure of the human adenovirus proteinase with its 11 amino acid cofactor.
      Ding, J.,McGrath, W.J.,Sweet, R.M.,Mangel, W.F.
      (1996) Embo J. 15: 1778
    • Adenovirus proteinase: crystallization and preliminary X-ray diffraction studies to atomic resolution.
      Baniecki, M.L.,McGrath, W.J.,Dauter, Z.,Mangel, W.F.
      (2002) Acta Crystallogr.,Sect.D 58: 1462


    Organizational Affiliation

    Biology Department, Brookhaven National Laboratory, Upton, New York 11973, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Adenain
A
204Human adenovirus C serotype 2EC: 3.4.22.39
Find proteins for P03252 (Human adenovirus C serotype 2)
Go to UniProtKB:  P03252
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NA
Query on NA

Download SDF File 
Download CCD File 
A
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
CSD
Query on CSD
A
L-PEPTIDE LINKINGC3 H7 N O4 SCYS
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 0.98 Å
  • R-Value Free: 0.168 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 36.270α = 90.00
b = 54.540β = 100.10
c = 42.410γ = 90.00
Software Package:
Software NamePurpose
PDB_EXTRACTdata extraction
HKL-2000data scaling
DENZOdata reduction
AMoREphasing
SHELXL-97refinement
SHELXrefinement
SCALEPACKdata scaling
HKL-2000data reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2012-10-10
    Type: Initial release
  • Version 1.1: 2012-10-24
    Type: Database references
  • Version 1.2: 2012-12-12
    Type: Database references
  • Version 1.3: 2013-02-06
    Type: Database references
  • Version 1.4: 2017-11-15
    Type: Advisory, Refinement description