1IBJ

Crystal structure of cystathionine beta-lyase from Arabidopsis thaliana

Summary for 1IBJ

• Entry DOI: 10.2210/pdb1ibj/pdb
• Related: 1CL1 1CL2 1CS1 1QGN
• Descriptor: CYSTATHIONINE BETA-LYASE, CARBONATE ION, SULFATE ION, ... (5 entities in total)
• Functional Keywords: plp-dependent enzyme, methionine biosynthesis, transsulfuration, lyase
• Biological source: Arabidopsis thaliana (thale cress)
• Total number of polymer chains: 2
• Total formula weight: 101691.32

Authors

Breitinger, U.,Clausen, T.,Messerschmidt, A. (deposition date: 2001-03-28, release date: 2001-04-04, Last modification date: 2023-08-09)

Primary citation

Breitinger, U.,Clausen, T.,Ehlert, S.,Huber, R.,Laber, B.,Schmidt, F.,Pohl, E.,Messerschmidt, A.
The three-dimensional structure of cystathionine beta-lyase from Arabidopsis and its substrate specificity
Plant Physiol., 126:631-642, 2001

PubMed Abstract: The pyridoxal 5'-phosphate-dependent enzyme cystathionine beta-lyase (CBL) catalyzes the penultimate step in the de novo biosynthesis of Met in microbes and plants. Absence of CBL in higher organisms makes it an important target for the development of antibiotics and herbicides. The three-dimensional structure of cystathionine beta-lyase from Arabidopsis was determined by Patterson search techniques, using the structure of tobacco (Nicotiana tabacum) cystathionine gamma-synthase as starting point. At a resolution of 2.3 A, the model was refined to a final crystallographic R-factor of 24.9%. The overall structure is very similar to other pyridoxal 5'-phosphate-dependent enzymes of the gamma-family. Exchange of a few critical residues within the active site causes the different substrate preferences between Escherichia coli and Arabidopsis CBL. Loss of interactions at the alpha-carboxyl site is the reason for the poorer substrate binding of Arabidopsis CBL. In addition, the binding pocket of Arabidopsis CBL is larger than that of E. coli CBL, explaining the similar binding of L-cystathionine and L-djenkolate in Arabidopsis CBL in contrast to E. coli CBL, where the substrate binding site is optimized for the natural substrate cystathionine.

PubMed: 11402193
DOI: 10.1104/pp.126.2.631

Experimental method

X-RAY DIFFRACTION (2.3 Å)