1I1W

0.89A Ultra high resolution structure of a Thermostable Xylanase from Thermoascus Aurantiacus

Summary for 1I1W

• Entry DOI: 10.2210/pdb1i1w/pdb
• Related: 1I1X 1TUX
• Descriptor: ENDO-1,4-BETA-XYLANASE, UNKNOWN ATOM OR ION, GLYCEROL, ... (6 entities in total)
• Functional Keywords: xylan degradation, hydrolase, glycosidase, enzyme, ultra high resolution, cryo temperature, 1, 4-beta-xylan xylanohydrolase
• Biological source: Thermoascus aurantiacus
• Total number of polymer chains: 1
• Total formula weight: 33571.51

Authors

Natesh, R.,Ramakumar, S.,Viswamitra, M.A. (deposition date: 2001-02-04, release date: 2003-01-07, Last modification date: 2024-10-30)

Primary citation

Natesh, R.,Manikandan, K.,Bhanumoorthy, P.,Viswamitra, M.A.,Ramakumar, S.
Thermostable xylanase from Thermoascus aurantiacus at ultrahigh resolution (0.89 A) at 100 K and atomic resolution (1.11 A) at 293 K refined anisotropically to small-molecule accuracy.
Acta Crystallogr.,Sect.D, 59:105-117, 2003

PubMed Abstract: Thermoascus aurantiacus xylanase is a thermostable enzyme which hydrolyses xylan, a major hemicellulose component of the biosphere. The crystal structure of this F/10 family xylanase, which has a triosephosphate isomerase (TIM) barrel (beta/alpha)(8) fold, has been solved to small-molecule accuracy at atomic resolution (1.11 A) at 293 K (RTUX) and at ultrahigh resolution (0.89 A) at 100 K (CTUX) using X-ray diffraction data sets collected on a synchrotron light source, resulting in R/R(free) values of 9.94/12.36 and 9.00/10.61% (for all data), respectively. Both structures were refined with anisotropic atomic displacement parameters. The 0.89 A structure, with 177 476 observed unique reflections, was refined without any stereochemical restraints during the final stages. The salt bridge between Arg124 and Glu232, which is bidentate in RTUX, is water-mediated in CTUX, suggesting the possibility of plasticity of ion pairs in proteins, with water molecules mediating some of the alternate arrangements. Two buried waters present inside the barrel form hydrogen-bond interactions with residues in strands beta2, beta3, beta4 and beta7 and presumably contribute to structural stability. The availability of accurate structural information at two different temperatures enabled the study of the temperature-dependent deformations of the TIM-barrel fold of the xylanase. Analysis of the deviation of corresponding C(alpha) atoms between RTUX and CTUX suggests that the interior beta-strands are less susceptible to changes as a function of temperature than are the alpha-helices, which are on the outside of the barrel. betaalpha-loops, which are longer and contribute residues to the active-site region, are more flexible than alphabeta-loops. The 0.89 A structure represents one of the highest resolution structures of a protein of such size with one monomer molecule in the asymmetric unit and also represents the highest resolution TIM-barrel fold structure to date. It may provide a useful template for theoretical modelling studies of the structure and dynamics of the ubiquitous TIM-barrel fold.

PubMed: 12499546
DOI: 10.1107/S0907444902020164

Experimental method

X-RAY DIFFRACTION (0.89 Å)