Crystal structure of N392L mutant of yeast bleomycin hydrolase

Experimental Data Snapshot

  • Resolution: 2.00 Å
  • R-Value Free: 0.248 
  • R-Value Work: 0.212 
  • R-Value Observed: 0.212 

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Mutagenesis and crystallographic studies of the catalytic residues of the papain family protease bleomycin hydrolase: new insights into active-site structure

O'Farrell, P.A.Joshua-Tor, L.

(2007) Biochem J 401: 421-428

  • DOI: https://doi.org/10.1042/BJ20060641
  • Primary Citation of Related Structures:  
    2DZY, 2DZZ, 2E00, 2E01, 2E02, 2E03

  • PubMed Abstract: 

    Bleomycin hydrolase (BH) is a hexameric papain family cysteine protease which is involved in preparing peptides for antigen presentation and has been implicated in tumour cell resistance to bleomycin chemotherapy. Structures of active-site mutants of yeast BH yielded unexpected results. Replacement of the active-site asparagine with alanine, valine or leucine results in the destabilization of the histidine side chain, demonstrating unambiguously the role of the asparagine residue in correctly positioning the histidine for catalysis. Replacement of the histidine with alanine or leucine destabilizes the asparagine position, indicating a delicate arrangement of the active-site residues. In all of the mutants, the C-terminus of the protein, which lies in the active site, protrudes further into the active site. All mutants were compromised in their catalytic activity. The structures also revealed the importance of a tightly bound water molecule which stabilizes a loop near the active site and which is conserved throughout the papain family. It is displaced in a number of the mutants, causing destabilization of this loop and a nearby loop, resulting in a large movement of the active-site cysteine. The results imply that this water molecule plays a key structural role in this family of enzymes.

  • Organizational Affiliation

    W.M. Keck Structural Biology Laboratory, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Cysteine proteinase 1457Saccharomyces cerevisiaeMutation(s): 1 
Find proteins for Q01532 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore Q01532 
Go to UniProtKB:  Q01532
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ01532
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 2.00 Å
  • R-Value Free: 0.248 
  • R-Value Work: 0.212 
  • R-Value Observed: 0.212 
  • Space Group: P 63 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 150.878α = 90
b = 150.878β = 90
c = 89.84γ = 120
Software Package:
Software NamePurpose
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2007-11-06
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Derived calculations, Version format compliance
  • Version 1.2: 2021-11-10
    Changes: Database references
  • Version 1.3: 2024-05-29
    Changes: Data collection