Crystal structure of Saccharomyces cerevisiae Nit3, a member of branch 10 of the nitrilase superfamily

Experimental Data Snapshot

  • Resolution: 2.40 Å
  • R-Value Free: 0.258 
  • R-Value Work: 0.229 

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Crystal structure of a putative CN hydrolase from yeast

Kumaran, D.Eswaramoorthy, S.Gerchman, S.E.Kycia, H.Studier, F.W.Swaminathan, S.

(2003) Proteins 52: 283-291

  • DOI: https://doi.org/10.1002/prot.10417
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    The crystal structure of a yeast hypothetical protein with sequence similarity to CN hydrolases has been determined to 2.4 A resolution by the multiwavelength anomalous dispersion (MAD) method. The protein folds as a four-layer alphabetabetaalpha sandwich and exists as a dimer in the crystal and in solution. It was selected in a structural genomics project as representative of CN hydrolases at a time when no structures had been determined for members of this family. Structures for two other members of the family have since been reported and the three proteins have similar topology and dimerization modes, which are distinct from those of other alphabetabetaalpha proteins whose structures are known. The dimers form an unusual eight-layer alphabetabetaalpha:alphabetabetaalpha structure. Although the precise enzymatic reactions catalyzed by the yeast protein are not known, considerable information about the active site may be deduced from conserved sequence motifs, comparative biochemical information, and comparison with known structures of hydrolase active sites. As with serine hydrolases, the active-site nucleophile (cysteine in this case) is positioned on a nucleophile elbow.

  • Organizational Affiliation

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

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
A, B
291Saccharomyces cerevisiaeMutation(s): 0 
Find proteins for P49954 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P49954 
Go to UniProtKB:  P49954
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP49954
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 2.40 Å
  • R-Value Free: 0.258 
  • R-Value Work: 0.229 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 73.523α = 90
b = 53.492β = 112.43
c = 80.985γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling

Structure Validation

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Entry History 

Revision History  (Full details and data files)

  • Version 1.0: 2001-10-04
    Type: Initial release
  • Version 1.1: 2008-04-27
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2021-02-03
    Changes: Structure summary
  • Version 1.4: 2024-02-07
    Changes: Data collection, Database references