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PDBsum entry 1yna

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protein links
Hydrolase PDB id
1yna
Jmol
Contents
Protein chain
194 a.a. *
Waters ×138
* Residue conservation analysis
PDB id:
1yna
Name: Hydrolase
Title: Endo-1,4-beta-xylanase, room temperature, ph 4.0
Structure: Endo-1,4-beta-xylanase. Chain: a. Synonym: xyna. Ec: 3.2.1.8
Source: Thermomyces lanuginosus. Organism_taxid: 5541. Strain: tsiklinsky. Atcc: dsm 5826
Resolution:
1.55Å     R-factor:   0.193    
Authors: K.Gruber,C.Kratky
Key ref:
K.Gruber et al. (1998). Thermophilic xylanase from Thermomyces lanuginosus: high-resolution X-ray structure and modeling studies. Biochemistry, 37, 13475-13485. PubMed id: 9753433 DOI: 10.1021/bi980864l
Date:
22-Aug-96     Release date:   12-Feb-97    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
O43097  (XYNA_THELA) -  Endo-1,4-beta-xylanase
Seq:
Struc:
225 a.a.
194 a.a.*
Key:    PfamA domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 1 residue position (black cross)

 Enzyme reactions 
   Enzyme class: E.C.3.2.1.8  - Endo-1,4-beta-xylanase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: Endohydrolysis of 1,4-beta-D-xylosidic linkages in xylans.
 Gene Ontology (GO) functional annotation 
  GO annot!
  Biological process     metabolic process   4 terms 
  Biochemical function     hydrolase activity     4 terms  

 

 
DOI no: 10.1021/bi980864l Biochemistry 37:13475-13485 (1998)
PubMed id: 9753433  
 
 
Thermophilic xylanase from Thermomyces lanuginosus: high-resolution X-ray structure and modeling studies.
K.Gruber, G.Klintschar, M.Hayn, A.Schlacher, W.Steiner, C.Kratky.
 
  ABSTRACT  
 
The crystal structure of the thermostable xylanase from Thermomyces lanuginosus was determined by single-crystal X-ray diffraction. The protein crystallizes in space group P21, a = 40.96(4) A, b = 52. 57(5) A, c = 50.47 (5) A, beta = 100.43(5) degrees, Z = 2. Diffraction data were collected at room temperature for a resolution range of 25-1.55 A, and the structure was solved by molecular replacement with the coordinates of xylanase II from Trichoderma reesei as a search model and refined to a crystallographic R-factor of 0.155 for all observed reflections. The enzyme belongs to the family 11 of glycosyl hydrolases [Henrissat, B., and Bairoch, A. (1993) Biochem. J. 293, 781-788]. pKa calculations were performed to assess the protonation state of residues relevant for catalysis and enzyme stability, and a heptaxylan was fitted into the active-site groove by homology modeling, using the published crystal structure of a complex between the Bacillus circulans xylanase and a xylotetraose. Molecular dynamics indicated the central three sugar rings to be tightly bound, whereas the peripheral ones can assume different orientations and conformations, suggesting that the enzyme might also accept xylan chains which are branched at these positions. The reasons for the thermostability of the T. lanuginosus xylanase were analyzed by comparing its crystal structure with known structures of mesophilic family 11 xylanases. It appears that the thermostability is due to the presence of an extra disulfide bridge, as well as to an increase in the density of charged residues throughout the protein.
 

Literature references that cite this PDB file's key reference

  PubMed id Reference
20225927 A.Pollet, J.A.Delcour, and C.M.Courtin (2010).
Structural determinants of the substrate specificities of xylanases from different glycoside hydrolase families.
  Crit Rev Biotechnol, 30, 176-191.  
20722923 E.Gogou, P.Katapodis, and P.S.Taoukis (2010).
High pressure inactivation kinetics of a Thermomyces lanuginosus xylanase evaluated as a process indicator.
  J Food Sci, 75, E379-E386.  
20607149 J.Jia, W.Chen, H.Ma, K.Wang, and C.Zhao (2010).
Use of a rhodamine-based bifunctional probe in N-terminal specific labeling of Thermomyces lanuginosus xylanase.
  Mol Biosyst, 6, 1829-1833.  
19422059 A.Pollet, E.Vandermarliere, J.Lammertyn, S.V.Strelkov, J.A.Delcour, and C.M.Courtin (2009).
Crystallographic and activity-based evidence for thumb flexibility and its relevance in glycoside hydrolase family 11 xylanases.
  Proteins, 77, 395-403.
PDB code: 3exu
19769747 A.Pollet, S.Sansen, G.Raedschelders, K.Gebruers, A.Rabijns, J.A.Delcour, and C.M.Courtin (2009).
Identification of structural determinants for inhibition strength and specificity of wheat xylanase inhibitors TAXI-IA and TAXI-IIA.
  FEBS J, 276, 3916-3927.
PDB codes: 2b42 3hd8
18292971 Q.Wang, and T.Xia (2008).
Enhancement of the activity and alkaline pH stability of Thermobifida fusca xylanase A by directed evolution.
  Biotechnol Lett, 30, 937-944.  
19111067 R.R.Thangudu, M.Manoharan, N.Srinivasan, F.Cadet, R.Sowdhamini, and B.Offmann (2008).
Analysis on conservation of disulphide bonds and their structural features in homologous protein domain families.
  BMC Struct Biol, 8, 55.  
18391461 S.Watanabe, D.N.Viet, J.Kaneko, Y.Kamio, and S.Yoshida (2008).
Cloning, expression, and transglycosylation reaction of Paenibacillus sp. strain W-61 xylanase 1.
  Biosci Biotechnol Biochem, 72, 951-958.  
17487548 B.C.Salles, V.S.Te'o, M.D.Gibbs, P.L.Bergquist, E.X.Filho, E.A.Ximenes, and K.M.Nevalainen (2007).
Identification of two novel xylanase-encoding genes (xyn5 and xyn6) from Acrophialophora nainiana and heterologous expression of xyn6 in Trichoderma reesei.
  Biotechnol Lett, 29, 1195-1201.  
16652352 M.Kozak (2006).
Solution scattering studies of conformation stability of xylanase XYNII from Trichoderma longibrachiatum.
  Biopolymers, 83, 95.  
  16510999 M.T.Murakami, R.Ruller, R.J.Ward, and R.K.Arni (2005).
Crystallization and preliminary X-ray crystallographic studies of the mesophilic xylanase A from Bacillus subtilis 1A1.
  Acta Crystallogr Sect F Struct Biol Cryst Commun, 61, 219-220.  
15652973 T.Collins, C.Gerday, and G.Feller (2005).
Xylanases, xylanase families and extremophilic xylanases.
  FEMS Microbiol Rev, 29, 3.  
15096627 F.de Lemos Esteves, V.Ruelle, J.Lamotte-Brasseur, B.Quinting, and J.M.Frère (2004).
Acidophilic adaptation of family 11 endo-beta-1,4-xylanases: modeling and mutational analysis.
  Protein Sci, 13, 1209-1218.  
15278768 H.Xiong, F.Fenel, M.Leisola, and O.Turunen (2004).
Engineering the thermostability of Trichoderma reesei endo-1,4-beta-xylanase II by combination of disulphide bridges.
  Extremophiles, 8, 393-400.  
15213390 N.Moiseeva, and M.Allaire (2004).
Crystals of family 11 xylanase II from Trichoderma longibrachiatum that diffract to atomic resolution.
  Acta Crystallogr D Biol Crystallogr, 60, 1275-1277.  
14718652 N.Palackal, Y.Brennan, W.N.Callen, P.Dupree, G.Frey, F.Goubet, G.P.Hazlewood, S.Healey, Y.E.Kang, K.A.Kretz, E.Lee, X.Tan, G.L.Tomlinson, J.Verruto, V.W.Wong, E.J.Mathur, J.M.Short, D.E.Robertson, and B.A.Steer (2004).
An evolutionary route to xylanase process fitness.
  Protein Sci, 13, 494-503.  
15184164 Y.Brennan, W.N.Callen, L.Christoffersen, P.Dupree, F.Goubet, S.Healey, M.Hernández, M.Keller, K.Li, N.Palackal, A.Sittenfeld, G.Tamayo, S.Wells, G.P.Hazlewood, E.J.Mathur, J.M.Short, D.E.Robertson, and B.A.Steer (2004).
Unusual microbial xylanases from insect guts.
  Appl Environ Microbiol, 70, 3609-3617.  
12657781 A.J.Oakley, T.Heinrich, C.A.Thompson, and M.C.Wilce (2003).
Characterization of a family 11 xylanase from Bacillus subtillis B230 used for paper bleaching.
  Acta Crystallogr D Biol Crystallogr, 59, 627-636.
PDB code: 1igo
14532063 M.C.Damaso, M.S.Almeida, E.Kurtenbach, O.B.Martins, N.Pereira, C.M.Andrade, and R.M.Albano (2003).
Optimized expression of a thermostable xylanase from Thermomyces lanuginosus in Pichia pastoris.
  Appl Environ Microbiol, 69, 6064-6072.  
12653995 N.Hakulinen, O.Turunen, J.Jänis, M.Leisola, and J.Rouvinen (2003).
Three-dimensional structures of thermophilic beta-1,4-xylanases from Chaetomium thermophilum and Nonomuraea flexuosa. Comparison of twelve xylanases in relation to their thermal stability.
  Eur J Biochem, 270, 1399-1412.
PDB codes: 1h1a 1m4w
12697339 S.Singh, A.M.Madlala, and B.A.Prior (2003).
Thermomyces lanuginosus: properties of strains and their hemicellulases.
  FEMS Microbiol Rev, 27, 3.  
12207016 T.A.Tahir, J.G.Berrin, R.Flatman, A.Roussel, P.Roepstorff, G.Williamson, and N.Juge (2002).
Specific characterization of substrate and inhibitor binding sites of a glycosyl hydrolase family 11 xylanase from Aspergillus niger.
  J Biol Chem, 277, 44035-44043.  
11717493 J.Wouters, J.Georis, D.Engher, J.Vandenhaute, J.Dusart, J.M.Frere, E.Depiereux, and P.Charlier (2001).
Crystallographic analysis of family 11 endo-beta-1,4-xylanase Xyl1 from Streptomyces sp. S38.
  Acta Crystallogr D Biol Crystallogr, 57, 1813-1819.
PDB code: 1hix
11053833 A.A.McCarthy, D.D.Morris, P.L.Bergquist, and E.N.Baker (2000).
Structure of XynB, a highly thermostable beta-1,4-xylanase from Dictyoglomus thermophilum Rt46B.1, at 1.8 A resolution.
  Acta Crystallogr D Biol Crystallogr, 56, 1367-1375.
PDB code: 1f5j
  10752608 J.Georis, F.de Lemos Esteves, J.Lamotte-Brasseur, V.Bougnet, B.Devreese, F.Giannotta, B.Granier, and J.M.Frère (2000).
An additional aromatic interaction improves the thermostability and thermophilicity of a mesophilic family 11 xylanase: structural basis and molecular study.
  Protein Sci, 9, 466-475.  
10974122 R.Maheshwari, G.Bharadwaj, and M.K.Bhat (2000).
Thermophilic fungi: their physiology and enzymes.
  Microbiol Mol Biol Rev, 64, 461-488.  
10029534 A.Schmidt, G.M.Gübitz, and C.Kratky (1999).
Xylan binding subsite mapping in the xylanase from Penicillium simplicissimum using xylooligosaccharides as cryo-protectant.
  Biochemistry, 38, 2403-2412.
PDB codes: 1b30 1b31 1b3v 1b3w 1b3x 1b3y 1b3z
10381409 E.Sabini, G.Sulzenbacher, M.Dauter, Z.Dauter, P.L.Jørgensen, M.Schülein, C.Dupont, G.J.Davies, and K.S.Wilson (1999).
Catalysis and specificity in enzymatic glycoside hydrolysis: a 2,5B conformation for the glycosyl-enzyme intermediate revealed by the structure of the Bacillus agaradhaerens family 11 xylanase.
  Chem Biol, 6, 483-492.
PDB codes: 1h4g 1h4h 1qh6 1qh7
10200171 G.Sulzenbacher, L.F.Mackenzie, K.S.Wilson, S.G.Withers, C.Dupont, and G.J.Davies (1999).
The crystal structure of a 2-fluorocellotriosyl complex of the Streptomyces lividans endoglucanase CelB2 at 1.2 A resolution.
  Biochemistry, 38, 4826-4833.
PDB code: 2nlr
10508763 J.Jiménez-Barbero, J.L.Asensio, F.J.Cañada, and A.Poveda (1999).
Free and protein-bound carbohydrate structures.
  Curr Opin Struct Biol, 9, 549-555.  
  10548044 J.Zuegg, K.Gruber, M.Gugganig, U.G.Wagner, and C.Kratky (1999).
Three-dimensional structures of enzyme-substrate complexes of the hydroxynitrile lyase from Hevea brasiliensis.
  Protein Sci, 8, 1990-2000.
PDB codes: 2yas 3yas 4yas 5yas 6yas 7yas
The most recent references are shown first. Citation data come partly from CiteXplore and partly from an automated harvesting procedure. Note that this is likely to be only a partial list as not all journals are covered by either method. However, we are continually building up the citation data so more and more references will be included with time. Where a reference describes a PDB structure, the PDB code is shown on the right.