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Conformational transitions driven by pyridoxal‐5′‐phosphate uptake in the psychrophilic serine hydroxymethyltransferase from P sychromonas ingrahamii
Author(s) -
Angelaccio Sebastiana,
Dworkowski Florian,
Bello Angela,
Milano Teresa,
Capitani Guido,
Pascarella Stefano
Publication year - 2014
Publication title -
proteins: structure, function, and bioinformatics
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 1.699
H-Index - 191
eISSN - 1097-0134
pISSN - 0887-3585
DOI - 10.1002/prot.24646
Subject(s) - serine hydroxymethyltransferase , psychrophile , cofactor , chemistry , pyridoxal phosphate , serine , biochemistry , enzyme , stereochemistry , protein structure , active site
Serine hydroxymethyltransferase (SHMT) is a pyridoxal‐5′‐phosphate (PLP)‐dependent enzyme belonging to the fold type I superfamily, which catalyzes in vivo the reversible conversion of l ‐serine and tetrahydropteroylglutamate (H 4 PteGlu) to glycine and 5,10‐methylenetetrahydropteroylglutamate (5,10‐CH 2 ‐H 4 PteGlu). The SHMT from the psychrophilic bacterium Psychromonas ingrahamii ( pi SHMT) had been recently purified and characterized. This enzyme was shown to display catalytic and stability properties typical of psychrophilic enzymes, namely high catalytic activity at low temperature and thermolability. To gain deeper insights into the structure–function relationship of pi SHMT, the three‐dimensional structure of its apo form was determined by X‐ray crystallography. Homology modeling techniques were applied to build a model of the pi SHMT holo form. Comparison of the two forms unraveled the conformation modifications that take place when the apo enzyme binds its cofactor. Our results show that the apo form is in an “open” conformation and possesses four (or five, in chain A) disordered loops whose electron density is not visible by X‐ray crystallography. These loops contain residues that interact with the PLP cofactor and three of them are localized in the major domain that, along with the small domain, constitutes the single subunit of the SHMT homodimer. Cofactor binding triggers a rearrangement of the small domain that moves toward the large domain and screens the PLP binding site at the solvent side. Comparison to the mesophilic apo SHMT from Salmonella typhimurium suggests that the backbone conformational changes are wider in psychrophilic SHMT. Proteins 2014; 82:2831–2841. © 2014 Wiley Periodicals, Inc.