1U08

Crystal Structure and Reactivity of YbdL from Escherichia coli Identify a Methionine Aminotransferase Function.

Summary for 1U08

• Entry DOI: 10.2210/pdb1u08/pdb
• Related: 1DJU
• Descriptor: Hypothetical aminotransferase ybdL, PYRIDOXAL-5'-PHOSPHATE (3 entities in total)
• Functional Keywords: alpha beta protein, transferase
• Biological source: Escherichia coli
• Cellular location: Cytoplasm (By similarity): P77806
• Total number of polymer chains: 2
• Total formula weight: 86505.77

Authors

Dolzan, M.,Johansson, K.,Roig-Zamboni, V.,Campanacci, V.,Tegoni, M.,Schneider, G.,Cambillau, C. (deposition date: 2004-07-13, release date: 2004-07-27, Last modification date: 2023-10-25)

Primary citation

Dolzan, M.,Johansson, K.,Roig-Zamboni, V.,Campanacci, V.,Tegoni, M.,Schneider, G.,Cambillau, C.
Crystal structure and reactivity of YbdL from Escherichia coli identify a methionine aminotransferase function
FEBS Lett., 571:141-146, 2004

PubMed Abstract: The ybdL gene of Escherichia coli codes for a protein of unknown function. Sequence analysis showed moderate homology to several vitamin B(6) dependent enzymes, suggesting that it may bind pyridoxal-5'-phosphate. The structure analysis of YbdL to 2.35 A resolution by protein crystallography verifies that it is a PLP dependent enzyme of fold type I, the typical aspartate aminotransferase fold. The active site contains a bound pyridoxal-5'-phosphate, covalently attached to the conserved active site lysine residue Lys236. The pattern of conserved amino acids in the putative substrate binding pocket of the enzyme reveals that it is most closely related to a hyperthermophilic aromatic residue aminotransferase from the archeon Pyrococcus horikoshii. Activity tests with 10 amino acids as amino-donors reveal, however, a preference for Met, followed by His and Phe, results which can be rationalized by modelization studies.

PubMed: 15280032
DOI: 10.1016/j.febslet.2004.06.075

Experimental method

X-RAY DIFFRACTION (2.35 Å)