1U08: Crystal Structure And Reactivity Of Ybdl From Escherichia Coli Identify A Methionine Aminotransferase Function

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.
PDB ID: 1U08Download
MMDB ID: 28742
PDB Deposition Date: 2004/7/13
Updated in MMDB: 2012/11
Experimental Method:
x-ray diffraction
Resolution: 2.35  Å
Source Organism:
Similar Structures:
Biological Unit for 1U08: dimeric; determined by author and by software (PISA)
Molecular Components in 1U08
Label Count Molecule
Proteins (2 molecules)
Hypothetical Aminotransferase Ybdl(Gene symbol: ybdL)
Molecule annotation
Chemicals (2 molecules)
* Click molecule labels to explore molecular sequence information.

Citing MMDB