1KMK

E. coli NifS/CsdB protein at 2.20A with the cysteine perselenide intermediate (residue CSZ).


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.2 Å
  • R-Value Free: 0.239 
  • R-Value Work: 0.196 

wwPDB Validation 3D Report Full Report


This is version 1.5 of the entry. See complete history

Literature

Analysis of the E. coli NifS CsdB protein at 2.0 A reveals the structural basis for perselenide and persulfide intermediate formation.

Lima, C.D.

(2002) J.Mol.Biol. 315: 1199-1208

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

  • 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 ...

    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




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
SELENOCYSTEINE LYASE
A
406Escherichia coli (strain K12)Gene Names: sufS (csdB, ynhB)
EC: 4.4.1.16, 2.8.1.7
Find proteins for P77444 (Escherichia coli (strain K12))
Go to UniProtKB:  P77444
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SEC
Query on SEC

Download SDF File 
Download CCD File 
A
SELENOCYSTEINE
C3 H7 N O2 Se
ZKZBPNGNEQAJSX-REOHCLBHSA-N
 Ligand Interaction
PLP
Query on PLP

Download SDF File 
Download CCD File 
A
PYRIDOXAL-5'-PHOSPHATE
VITAMIN B6 Phosphate
C8 H10 N O6 P
NGVDGCNFYWLIFO-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
CSZ
Query on CSZ
A
L-PEPTIDE LINKINGC3 H7 N O2 S SeCYS
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.2 Å
  • R-Value Free: 0.239 
  • R-Value Work: 0.196 
  • Space Group: P 43 21 2
Unit Cell:
Length (Å)Angle (°)
a = 125.855α = 90.00
b = 125.855β = 90.00
c = 133.200γ = 90.00
Software Package:
Software NamePurpose
SCALEPACKdata scaling
DENZOdata reduction
REFMACrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2001-12-21
    Type: Initial release
  • Version 1.1: 2008-04-27
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Derived calculations, Version format compliance
  • Version 1.3: 2012-09-05
    Type: Database references
  • Version 1.4: 2014-04-09
    Type: Non-polymer description
  • Version 1.5: 2017-10-11
    Type: Refinement description