1NLN

CRYSTAL STRUCTURE OF HUMAN ADENOVIRUS 2 PROTEINASE WITH ITS 11 AMINO ACID COFACTOR AT 1.6 ANGSTROM RESOLUTION


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.60 Å
  • R-Value Free: 0.179 
  • R-Value Work: 0.136 

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This is version 1.2 of the entry. See complete history


Literature

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: 1-11

  • DOI: 10.1016/s1570-9639(03)00024-4
  • Primary Citation of Related Structures:  
    1NLN

  • PubMed Abstract: 
  • The crystal structure of the human adenovirus proteinase (AVP), a cysteine proteinase covalently bound to its 11-amino-acid peptide cofactor pVIc, has been solved to 1.6-A resolution with a crystallographic R-factor of 0.136, R(free)=0.179. The fold of AVP-pVIc is new and the structural basis for it is described in detail ...

    The crystal structure of the human adenovirus proteinase (AVP), a cysteine proteinase covalently bound to its 11-amino-acid peptide cofactor pVIc, has been solved to 1.6-A resolution with a crystallographic R-factor of 0.136, R(free)=0.179. The fold of AVP-pVIc is new and the structural basis for it is described in detail. The polypeptide chain of AVP folds into two domains. One domain contains a five-strand beta-sheet with two peripheral alpha-helices; this region represents the hydrophobic core of the protein. A second domain contains the N terminus, several C-terminal alpha-helices, and a small peripheral anti-parallel beta-sheet. The domains interact through an extended polar interface. pVIc spans the two domains like a strap, its C-terminal portion forming a sixth strand on the beta-sheet. The active site is in a long, deep groove located between the two domains. Portions are structurally similar to the active site of the prototypical cysteine proteinase papain, especially some of the Calpha backbone atoms (r.m.s. deviation of 0.354 A for 12 Calpha atoms). The active-site nucleophile of AVP, the conserved Cys(122), was shown to have a pK(a) of 4.5, close to the pK(a) of 3.0 for the nucleophile of papain, suggesting that a similar ion pair arrangement with His(54) may be present in AVP-pVIc. The interactions between AVP and pVIc include 24 non-beta-strand hydrogen bonds, six beta-strand hydrogen bonds and one covalent bond. Of the 204 amino acid residues in AVP, 33 are conserved among the many serotypes of adenovirus, and these aid in forming the active site groove, are involved in substrate specificity or interact between secondary structure elements.


    Related Citations: 
    • 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
    • Characterization of Three Components of Human Adenovirus Proteinase Activity in vitro
      (1996) J Biol Chem 271: 536
    • Viral DNA and a Viral Peptide can act as Cofactors of Adenovirus Virion Proteinase Activity
      (1993) Nature 361: 274

    Organizational Affiliation

    Biology Department, Brookhaven National Laboratory, 50 Bell Avenue, Upton, NY 11973-5000, USA.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
AdenainA204Human adenovirus 2Mutation(s): 0 
Gene Names: L3-23kL3
EC: 3.4.22.39
UniProt
Find proteins for P03252 (Human adenovirus C serotype 2)
Explore P03252 
Go to UniProtKB:  P03252
Protein Feature View
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  • Reference Sequence
  • Find similar proteins by:  Sequence   |   Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
PVICB11N/AMutation(s): 0 
UniProt
Find proteins for P03274 (Human adenovirus C serotype 2)
Explore P03274 
Go to UniProtKB:  P03274
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ACY
Query on ACY

Download Ideal Coordinates CCD File 
C [auth A]ACETIC ACID
C2 H4 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.60 Å
  • R-Value Free: 0.179 
  • R-Value Work: 0.136 
  • Space Group: P 61
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 111.5α = 90
b = 111.5β = 90
c = 50.9γ = 120
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
X-PLORmodel building
X-PLORrefinement
X-PLORphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2003-08-26
    Type: Initial release
  • Version 1.1: 2008-04-29
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance