2BIE

Radiation damage of the Schiff base in phosphoserine aminotransferase (structure H)

Summary for 2BIE

• Entry DOI: 10.2210/pdb2bie/pdb
• Related: 1W23 2BHX 2BI1 2BI2 2BI3 2BI5 2BI9 2BIA 2BIG
• Descriptor: PHOSPHOSERINE AMINOTRANSFERASE, PYRIDOXAL-5'-PHOSPHATE, MAGNESIUM ION, ... (7 entities in total)
• Functional Keywords: transferase, aminotransferase, pyridoxal-5'-phosphate, radiation damage
• Biological source: BACILLUS ALCALOPHILUS
• Total number of polymer chains: 2
• Total formula weight: 81869.54

Authors

Dubnovitsky, A.P.,Ravelli, R.B.G.,Popov, A.N.,Papageorgiou, A.C. (deposition date: 2005-01-21, release date: 2005-05-19, Last modification date: 2019-07-24)

Primary citation

Dubnovitsky, A.P.,Ravelli, R.B.G.,Popov, A.N.,Papageorgiou, A.C.
Strain Relief at the Active Site of Phosphoserine Aminotransferase Induced by Radiation Damage.
Protein Sci., 14:1498-, 2005

PubMed Abstract: The X-ray susceptibility of the lysine-pyridoxal-5'-phosphate Schiff base in Bacillus alcalophilus phosphoserine aminotransferase has been investigated using crystallographic data collected at 100 K to 1.3 A resolution, complemented by on-line spectroscopic studies. X-rays induce deprotonation of the internal aldimine, changes in the Schiff base conformation, displacement of the cofactor molecule, and disruption of the Schiff base linkage between pyridoxal-5'-phosphate and the Lys residue. Analysis of the "undamaged" structure reveals a significant chemical strain on the internal aldimine bond that leads to a pronounced geometrical distortion of the cofactor. However, upon crystal exposure to the X-rays, the strain and distortion are relaxed and eventually diminished when the total absorbed dose has exceeded 4.7 x 10(6) Ggamma. Our data provide new insights into the enzymatic activation of pyridoxal-5'-phosphate and suggest that special care should be taken while using macromolecular crystallography to study details in strained active sites.

PubMed: 15883191
DOI: 10.1110/PS.051397905

Experimental method

X-RAY DIFFRACTION (1.3 Å)