1I29

CRYSTAL STRUCTURE OF CSDB COMPLEXED WITH L-PROPARGYLGLYCINE


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.8 Å
  • R-Value Free: 0.233 
  • R-Value Work: 0.209 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Structure of external aldimine of Escherichia coli CsdB, an IscS/NifS homolog: implications for its specificity toward selenocysteine.

Mihara, H.Fujii, T.Kato, S.Kurihara, T.Hata, Y.Esaki, N.

(2002) J.BIOCHEM.(TOKYO) 131: 679-685


  • PubMed Abstract: 
  • Escherichia coli CsdB is a pyridoxal 5'-phosphate (PLP)-dependent enzyme that catalyzes both cysteine desulfuration and selenocysteine deselenation. The enzyme has a high specific activity for L-selenocysteine relative to L-cysteine. On the other han ...

    Escherichia coli CsdB is a pyridoxal 5'-phosphate (PLP)-dependent enzyme that catalyzes both cysteine desulfuration and selenocysteine deselenation. The enzyme has a high specific activity for L-selenocysteine relative to L-cysteine. On the other hand, its paralog, IscS, exhibits higher activity for L-cysteine, which acts as a sulfur donor during the biosynthesis of the iron-sulfur cluster and 4-thiouridine. The structure of CsdB complexed with L-propargylglycine was determined by X-ray crystallography at 2.8 A resolution. The overall polypeptide fold of the complex is similar to that of the uncomplexed enzyme, indicating that no significant structural change occurs upon formation of the complex. In the complex, propargylglycine forms a Schiff base with PLP, providing the features of the external aldimine formed in the active site. The Cys364 residue, which is essential for the activity of CsdB toward L-cysteine but not toward L-selenocysteine, is clearly visible on a loop of the extended lobe (Thr362-Arg375) in all enzyme forms studied, in contrast to the corresponding disordered loop (Ser321-Arg332) of the Thermotoga maritima NifS-like protein, which is closely related to IscS. The extended lobe of CsdB has an 11-residue deletion compared with that of the NifS-like protein. These facts suggest that the restricted flexibility of the Cys364-anchoring extended lobe in CsdB may be responsible for the ability of the enzyme to discriminate between selenium and sulfur.


    Related Citations: 
    • A NifS-like Gene, CsdB, Encodes an Escherichia coli Counterpart of Mammalian Selenocysteine Lyase: Gene Cloning, Purification, Characterization and Preliminary X-ray Crystallographic Studies
      Mihara, H.,Maeda, M.,Fujii, T.,Kurihara, T.,Hata, Y.,Esaki, N.
      (1999) J.Biol.Chem. 274: 14768
    • Structure of a NifS Homologue: X-ray Structure Analysis of CsdB, An Escherichia coli Counterpart of Mammalian Selenocysteine Lyase
      Fujii, T.,Maeda, M.,Mihara, H.,Kurihara, T.,Esaki, N.,Hata, Y.
      (2000) Biochemistry 39: 1263


    Organizational Affiliation

    Institute for Chemical Research, Kyoto University, Uji, Kyoto 611-0011, Japan.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
CSDB
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
LPG
Query on LPG

Download SDF File 
Download CCD File 
A
L-PROPARGYLGLYCINE
2-AMINO-BUT-3-YNOIC ACID
C4 H5 N O2
DSUAJFIEKRKPEE-VKHMYHEASA-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
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.8 Å
  • R-Value Free: 0.233 
  • R-Value Work: 0.209 
  • Space Group: P 43 21 2
Unit Cell:
Length (Å)Angle (°)
a = 128.459α = 90.00
b = 128.459β = 90.00
c = 136.830γ = 90.00
Software Package:
Software NamePurpose
CNSrefinement
CNSphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2003-07-01
    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: 2017-10-04
    Type: Refinement description