Crystal Structure of selenocysteine lyase

Experimental Data Snapshot

  • Resolution: 2.00 Å
  • R-Value Free: 0.207 
  • R-Value Work: 0.178 

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Analysis of the E. coli NifS CsdB Protein at 2.0A Reveals the Structural Basis for Perselenide and Persulfide Intermediate Formation

Lima, C.D.

(2002) J Mol Biol 315: 1199-1208

  • DOI: https://doi.org/10.1006/jmbi.2001.5308
  • Primary Citation of Related Structures:  
    1JF9, 1KMJ, 1KMK

  • PubMed Abstract: 

    The Escherichia coli NifS CsdB protein is a member of the homodimeric pyridoxal 5'-phosphate (PLP)-dependent family of enzymes. These enzymes are capable of decomposing cysteine or selenocysteine into L-alanine and sulfur or selenium, respectively. E. coli NifS CsdB has a high specificity for L-selenocysteine in comparison to l-cysteine, suggesting a role for this enzyme is selenium metabolism. The 2.0 A crystal structure of E. coli NifS CsdB reveals a high-resolution view of the active site of this enzyme in apo-, persulfide, perselenide, and selenocysteine-bound intermediates, suggesting a mechanism for the stabilization of the enzyme persulfide and perselenide intermediates during catalysis, a necessary intermediate in the formation of sulfur and selenium containing metabolites.

  • Organizational Affiliation

    Biochemistry Department and Structural Biology Program, Weill Medical College of Cornell University, New York, NY 10021, USA. lima@pinky.med.cornell.edu

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
SELENOCYSTEINE LYASE408Escherichia coliMutation(s): 0 
Gene Names: NIFS/CSDB
Find proteins for P77444 (Escherichia coli (strain K12))
Explore P77444 
Go to UniProtKB:  P77444
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP77444
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on PLP

Download Ideal Coordinates CCD File 
C8 H10 N O6 P
Experimental Data & Validation

Experimental Data

  • Resolution: 2.00 Å
  • R-Value Free: 0.207 
  • R-Value Work: 0.178 
  • Space Group: P 43 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 126.375α = 90
b = 126.375β = 90
c = 133.578γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling

Structure Validation

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Ligand Structure Quality Assessment 

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2001-07-04
    Type: Initial release
  • Version 1.1: 2008-04-27
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Derived calculations, Version format compliance
  • Version 1.3: 2015-01-21
    Changes: Refinement description
  • Version 1.4: 2021-02-03
    Changes: Database references, Derived calculations, Structure summary