spacer
spacer

PDBsum entry 1nln

Go to PDB code: 
protein ligands Protein-protein interface(s) links
Hydrolase PDB id
1nln
Jmol
Contents
Protein chains
203 a.a. *
11 a.a. *
Ligands
ACY
Waters ×238
* Residue conservation analysis
PDB id:
1nln
Name: Hydrolase
Title: Crystal structure of human adenovirus 2 proteinase with its 11 amino acid cofactor at 1.6 angstrom resolution
Structure: Adenain. Chain: a. Fragment: adenovirus proteinase. Synonym: endoprotease, late l3 23 kda protein. Engineered: yes. Pvic. Chain: b. Fragment: pvic peptide. Engineered: yes
Source: Human adenovirus 2. Organism_taxid: 10515. Gene: l3-23k. Expressed in: escherichia coli bl21. Expression_system_taxid: 511693. Synthetic: yes. Other_details: chemically synthesized c-terminal 11 amino acids from human adenovirus serotype 2 pvi molecule
Biol. unit: Dimer (from PQS)
Resolution:
1.60Å     R-factor:   0.136     R-free:   0.179
Authors: W.J.Mcgrath,J.Ding,R.M.Sweet,W.F.Mangel
Key ref: W.J.McGrath et al. (2003). 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. Biochim Biophys Acta, 1648, 1. PubMed id: 12758141 DOI: 10.1016/S1570-9639(03)00024-4
Date:
07-Jan-03     Release date:   26-Aug-03    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
P03252  (ADEN_ADE02) -  Protease
Seq:
Struc:
204 a.a.
203 a.a.
Protein chain
Pfam   ArchSchema ?
P03274  (PIV6_ADE02) -  Pre-protein VI
Seq:
Struc:
250 a.a.
11 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Enzyme reactions 
   Enzyme class: Chain A: E.C.3.4.22.39  - Adenain.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: Cleaves proteins of the adenovirus and its host cell at two consensus sites: -Yaa-Xaa-Gly-Gly-|-Xaa- and -Yaa-Xaa-Gly-Xaa-|-Gly- (in which Yaa is Met, Ile or Leu, and Xaa is any amino acid).
 Gene Ontology (GO) functional annotation 
  GO annot!
  Cellular component     virion   2 terms 
  Biological process     proteolysis   1 term 
  Biochemical function     hydrolase activity     5 terms  

 

 
DOI no: 10.1016/S1570-9639(03)00024-4 Biochim Biophys Acta 1648:1 (2003)
PubMed id: 12758141  
 
 
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.
W.J.McGrath, J.Ding, A.Didwania, R.M.Sweet, W.F.Mangel.
 
  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 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.
 

Literature references that cite this PDB file's key reference

  PubMed id Reference
  20376613 J.G.Smith, C.M.Wiethoff, P.L.Stewart, and G.R.Nemerow (2010).
Adenovirus.
  Curr Top Microbiol Immunol, 343, 195-224.  
18852458 K.Ratia, S.Pegan, J.Takayama, K.Sleeman, M.Coughlin, S.Baliji, R.Chaudhuri, W.Fu, B.S.Prabhakar, M.E.Johnson, S.C.Baker, A.K.Ghosh, and A.D.Mesecar (2008).
A noncovalent class of papain-like protease/deubiquitinase inhibitors blocks SARS virus replication.
  Proc Natl Acad Sci U S A, 105, 16119-16124.  
16689636 K.Takamoto, and M.R.Chance (2006).
Radiolytic protein footprinting with mass spectrometry to probe the structure of macromolecular complexes.
  Annu Rev Biophys Biomol Struct, 35, 251-276.  
17005667 S.D.Saban, M.Silvestry, G.R.Nemerow, and P.L.Stewart (2006).
Visualization of alpha-helices in a 6-angstrom resolution cryoelectron microscopy structure of adenovirus allows refinement of capsid protein assignments.
  J Virol, 80, 12049-12059.  
16913834 T.Sulea, H.A.Lindner, and R.Ménard (2006).
Structural aspects of recently discovered viral deubiquitinating activities.
  Biol Chem, 387, 853-862.  
16537396 V.V.Kapitonov, and J.Jurka (2006).
Self-synthesizing DNA transposons in eukaryotes.
  Proc Natl Acad Sci U S A, 103, 4540-4545.  
16126388 J.Q.Guan, and M.R.Chance (2005).
Structural proteomics of macromolecular assemblies using oxidative footprinting and mass spectrometry.
  Trends Biochem Sci, 30, 583-592.  
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.