Dehaloperoxidase (DHP) is a multifunctional hemeprotein
with a
functional switch generally regulated by the chemical class of the
substrate. Its two isoforms, DHP-A and DHP-B, differ by only five
amino acids and have an almost identical protein fold. However, the
catalytic efficiency of DHP-B for oxidation by a peroxidase mechanism
ranges from 2- to 6-fold greater than that of DHP-A depending on the
conditions. X-ray crystallography has shown that many substrates and
ligands have nearly identical binding in the two isoenzymes, suggesting
that the difference in catalytic efficiency could be due to differences
in the conformational dynamics. We compared the backbone dynamics
of the DHP isoenzymes at pH 7 through heteronuclear relaxation dynamics
at 11.75, 16.45, and 19.97 T in combination with four 300 ns MD simulations.
While the overall dynamics of the isoenzymes are similar, there are
specific local differences in functional regions of each protein.
In DHP-A, Phe35 undergoes a slow chemical exchange between two conformational
states likely coupled to a swinging motion of Tyr34. Moreover, Asn37
undergoes fast chemical exchange in DHP-A. Given that Phe35 and Asn37
are adjacent to Tyr34 and Tyr38, it is possible that their dynamics
modulate the formation and migration of the active tyrosyl radicals
in DHP-A at pH 7. Another significant difference is that both distal
and proximal histidines have a 15–18% smaller S
2 value in DHP-B, thus their greater flexibility could
account for the higher catalytic activity. The distal histidine grants
substrate access to the distal pocket. The greater flexibility of
the proximal histidine could also accelerate H2O2 activation at the heme Fe by increased coupling of an amino acid
charge relay to stabilize the ferryl Fe(IV) oxidation state in a Poulos-Kraut
“push–pull”-type peroxidase mechanism.