3NIY

Crystal structure of native xylanase 10B from Thermotoga petrophila RKU-1

Summary for 3NIY

• Entry DOI: 10.2210/pdb3niy/pdb
• Related: 3NJ3
• Descriptor: Endo-1,4-beta-xylanase, SULFATE ION, ACETATE ION, ... (4 entities in total)
• Functional Keywords: tim-barrel, xylanase, hydrolase
• Biological source: Thermotoga petrophila RKU-1
• Total number of polymer chains: 2
• Total formula weight: 81622.98

Authors

Santos, C.R.,Meza, A.N.,Trindade, D.M.,Ruller, R.,Squina, F.M.,Prade, R.A.,Murakami, M.T. (deposition date: 2010-06-16, release date: 2011-05-04, Last modification date: 2024-02-21)

Primary citation

Santos, C.R.,Meza, A.N.,Hoffmam, Z.B.,Silva, J.C.,Alvarez, T.M.,Ruller, R.,Giesel, G.M.,Verli, H.,Squina, F.M.,Prade, R.A.,Murakami, M.T.
Thermal-induced conformational changes in the product release area drive the enzymatic activity of xylanases 10B: Crystal structure, conformational stability and functional characterization of the xylanase 10B from Thermotoga petrophila RKU-1.
Biochem.Biophys.Res.Commun., 403:214-219, 2010

PubMed Abstract: Endo-xylanases play a key role in the depolymerization of xylan and recently, they have attracted much attention owing to their potential applications on biofuels and paper industries. In this work, we have investigated the molecular basis for the action mode of xylanases 10B at high temperatures using biochemical, biophysical and crystallographic methods. The crystal structure of xylanase 10B from hyperthermophilic bacterium Thermotoga petrophila RKU-1 (TpXyl10B) has been solved in the native state and in complex with xylobiose. The complex crystal structure showed a classical binding mode shared among other xylanases, which encompasses the -1 and -2 subsites. Interestingly, TpXyl10B displayed a temperature-dependent action mode producing xylobiose and xylotriose at 20°C, and exclusively xylobiose at 90°C as assessed by capillary zone electrophoresis. Moreover, circular dichroism spectroscopy suggested a coupling effect of temperature-induced structural changes with this particular enzymatic behavior. Molecular dynamics simulations supported the CD analysis suggesting that an open conformational state adopted by the catalytic loop (Trp297-Lys326) provokes significant modifications in the product release area (+1,+2 and +3 subsites), which drives the enzymatic activity to the specific release of xylobiose at high temperatures.

PubMed: 21070746
DOI: 10.1016/j.bbrc.2010.11.010

Experimental method

X-RAY DIFFRACTION (1.58 Å)