2dcy
From Proteopedia
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|PDB= 2dcy |SIZE=350|CAPTION= <scene name='initialview01'>2dcy</scene>, resolution 1.40Å | |PDB= 2dcy |SIZE=350|CAPTION= <scene name='initialview01'>2dcy</scene>, resolution 1.40Å | ||
|SITE= | |SITE= | ||
| - | |LIGAND= <scene name='pdbligand= | + | |LIGAND= <scene name='pdbligand=DIO:1,4-DIETHYLENE+DIOXIDE'>DIO</scene>, <scene name='pdbligand=TAR:D(-)-TARTARIC+ACID'>TAR</scene> |
| - | |ACTIVITY= [http://en.wikipedia.org/wiki/Endo-1,4-beta-xylanase Endo-1,4-beta-xylanase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.2.1.8 3.2.1.8] | + | |ACTIVITY= <span class='plainlinks'>[http://en.wikipedia.org/wiki/Endo-1,4-beta-xylanase Endo-1,4-beta-xylanase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.2.1.8 3.2.1.8] </span> |
|GENE= xynA ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1423 Bacillus subtilis]) | |GENE= xynA ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1423 Bacillus subtilis]) | ||
| + | |DOMAIN= | ||
| + | |RELATEDENTRY=[[2dcz|2DCZ]] | ||
| + | |RESOURCES=<span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2dcy FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2dcy OCA], [http://www.ebi.ac.uk/pdbsum/2dcy PDBsum], [http://www.rcsb.org/pdb/explore.do?structureId=2dcy RCSB]</span> | ||
}} | }} | ||
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[[Category: Takenouchi, M.]] | [[Category: Takenouchi, M.]] | ||
[[Category: Tsuda, S.]] | [[Category: Tsuda, S.]] | ||
| - | [[Category: DIO]] | ||
| - | [[Category: TAR]] | ||
[[Category: all beta]] | [[Category: all beta]] | ||
| - | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on | + | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Mon Mar 31 02:33:05 2008'' |
Revision as of 23:33, 30 March 2008
| |||||||
| , resolution 1.40Å | |||||||
|---|---|---|---|---|---|---|---|
| Ligands: | , | ||||||
| Gene: | xynA (Bacillus subtilis) | ||||||
| Activity: | Endo-1,4-beta-xylanase, with EC number 3.2.1.8 | ||||||
| Related: | 2DCZ
| ||||||
| Resources: | FirstGlance, OCA, PDBsum, RCSB | ||||||
| Coordinates: | save as pdb, mmCIF, xml | ||||||
Crystal structure of Bacillus subtilis family-11 xylanase
Overview
We used directed evolution to enhance the thermostability of glycosyl hydrolase family-11 xylanase from Bacillus subtilis. By combining random point mutagenesis, saturation mutagenesis, and DNA shuffling, a thermostable variant, Xyl(st), was identified which contained three amino acid substitutions: Q7H, N8F, and S179C. The half-inactivation temperature (the midpoint of the melting curves) for the Xyl(st) variant compared with the wild-type enzyme after incubation for 10 min was elevated from 58 to 68 degrees C. At 60 degrees C the wild-type enzyme was inactivated within 5 min, but Xyl(st) retained full activity for at least 2 h. The stabilization was accompanied by evidence of thermophilicity; that is, an increase in the optimal reaction temperature from 55 to 65 degrees C and lower activity at low temperatures and higher activity at higher temperatures relative to wild type. To elucidate the mechanism of thermal stabilization, three-dimensional structures were determined for the wild-type and Xyl(st) enzymes. A cavity was identified around Gln-7/Asn-8 in wild type that was filled with bulky, hydrophobic residues in Xyl(st). This site was not identified by previous approaches, but directed evolution identified the region as a weak point. Formation of an intermolecular disulfide bridge via Cys-179 was observed between monomers in Xyl(st). However, the stability was essentially the same in the presence and absence of a reducing agent, indicating that the increased hydrophobicity around the Cys-179 accounted for the stability.
About this Structure
2DCY is a Single protein structure of sequence from Bacillus subtilis. Full crystallographic information is available from OCA.
Reference
Thermal stabilization of Bacillus subtilis family-11 xylanase by directed evolution., Miyazaki K, Takenouchi M, Kondo H, Noro N, Suzuki M, Tsuda S, J Biol Chem. 2006 Apr 14;281(15):10236-42. Epub 2006 Feb 8. PMID:16467302
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