1KMJ

E. coli NifS/CsdB protein at 2.0A with the cysteine persulfide intermediate (residue CSS).


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.208 
  • R-Value Work: 0.178 

wwPDB Validation   3D Report Full Report


This is version 1.4 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:  
    1KMJ, 1KMK, 1JF9

  • 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 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:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Selenocysteine lyaseA406Escherichia coliMutation(s): 1 
EC: 4.4.1.16 (PDB Primary Data), 2.8.1.7 (UniProt)
Find proteins for P77444 (Escherichia coli (strain K12))
Explore P77444 
Go to UniProtKB:  P77444
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
PLP
Query on PLP

Download Ideal Coordinates CCD File 
B [auth A]PYRIDOXAL-5'-PHOSPHATE
C8 H10 N O6 P
NGVDGCNFYWLIFO-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
CSS
Query on CSS
AL-PEPTIDE LINKINGC3 H7 N O2 S2CYS
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.208 
  • R-Value Work: 0.178 
  • Space Group: P 43 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 126.418α = 90
b = 126.418β = 90
c = 133.547γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
REFMACrefinement

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2001-12-21
    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: 2013-10-23
    Changes: Database references
  • Version 1.4: 2021-02-03
    Changes: Database references, Derived calculations, Structure summary