H.Taberman,C.S.Bury,M.J.Van Der Woerd,E.H.Snell,E.F.Garman
Key ref:
H.Taberman
et al.
(2019).
Structural knowledge or X-ray damage? A case study on xylose isomerase illustrating both.
J Synchrotron Radiat,
26,
931-944.
PubMed id: 31274415
DOI: 10.1107/S1600577519005599
Date:
19-Feb-19
Release date:
17-Jul-19
PROCHECK
Headers
References
Protein chain
P24300 (XYLA_STRRU) -
Xylose isomerase from Streptomyces rubiginosus
Seq: Struc:
388 a.a.
387 a.a.*
Key:
Secondary structure
*
PDB and UniProt seqs differ
at 3 residue positions (black
crosses)
Structural knowledge or X-ray damage? A case study on xylose isomerase illustrating both.
H.Taberman,
C.S.Bury,
M.J.van der Woerd,
E.H.Snell,
E.F.Garman.
ABSTRACT
Xylose isomerase (XI) is an industrially important metalloprotein studied for
decades. Its reaction mechanism has been postulated to involve movement of the
catalytic metal cofactor to several different conformations. Here, a
dose-dependent approach was used to investigate the radiation damage effects on
XI and their potential influence on the reaction mechanism interpreted from the
X-ray derived structures. Radiation damage is still one of the major challenges
for X-ray diffraction experiments and causes both global and site-specific
damage. In this study, consecutive high-resolution data sets from a single XI
crystal from the same wedge were collected at 100 K and the progression of
radiation damage was tracked over increasing dose (0.13-3.88 MGy). The
catalytic metal and its surrounding amino acid environment experience a build-up
of free radicals, and the results show radiation-damage-induced structural
perturbations ranging from an absolute metal positional shift to specific
residue motions in the active site. The apparent metal movement is an artefact
of global damage and the resulting unit-cell expansion, but residue motion
appears to be driven by the dose. Understanding and identifying
radiation-induced damage is an important factor in accurately interpreting the
biological conclusions being drawn.
Links
