1F89

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.4 Å
  • R-Value Free: 0.258 
  • R-Value Work: 0.229 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

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: 10.1002/prot.10417

  • 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 san ...

    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.


    Related Citations: 
    • Catalysis in the nitrilase superfamily.
      Brenner, C.
      (2002) CURR.OPIN.STRUCT.BIOL. 12: 775


    Organizational Affiliation

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




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
32.5 KDA PROTEIN YLR351C
A, B
291Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Gene Names: NIT3
EC: 3.5.-.-
Find proteins for P49954 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P49954
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.4 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 = 90.00
b = 53.492β = 112.43
c = 80.985γ = 90.00
Software Package:
Software NamePurpose
DENZOdata reduction
SHARPphasing
PHASESphasing
CNSrefinement
SCALEPACKdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2001-10-04
    Type: Initial release
  • Version 1.1: 2008-04-27
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance