1I29

CRYSTAL STRUCTURE OF CSDB COMPLEXED WITH L-PROPARGYLGLYCINE

Summary for 1I29

• Entry DOI: 10.2210/pdb1i29/pdb
• Related: 1C0N 1I28
• Descriptor: CSDB, (2S)-2-aminobut-3-ynoic acid, PYRIDOXAL-5'-PHOSPHATE (3 entities in total)
• Functional Keywords: external aldimine, lyase
• Biological source: Escherichia coli
• Total number of polymer chains: 1
• Total formula weight: 44826.82

Authors

Mihara, H.,Fujii, T.,Kurihara, T.,Hata, Y.,Esaki, N. (deposition date: 2001-02-07, release date: 2003-07-01, Last modification date: 2023-08-09)

Primary citation

Mihara, H.,Fujii, T.,Kato, S.,Kurihara, T.,Hata, Y.,Esaki, N.
Structure of external aldimine of Escherichia coli CsdB, an IscS/NifS homolog: implications for its specificity toward selenocysteine.
J.BIOCHEM.(TOKYO), 131:679-685, 2002

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 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.

PubMed: 11983074

Experimental method

X-RAY DIFFRACTION (2.8 Å)