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PDBsum entry 1hix
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Hydrolase PDB id
1hix

 

 

 

 

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Contents
Protein chains
185 a.a. *
Waters ×219
* Residue conservation analysis
PDB id:
1hix
Name: Hydrolase
Title: Crystallographic analyses of family 11 endo-beta-1,4-xylanase xyl1 from streptomyces sp. S38
Structure: Endo-1,4-beta-xylanase. Chain: a, b. Engineered: yes
Source: Streptomyces sp. S38. Organism_taxid: 181109. Gene: xyl1. Expressed in: streptomyces lividans. Expression_system_taxid: 1916. Other_details: streptomyces sp. S38 was isolated by bio-argos from forest soil (liege, belgium)
Biol. unit: Trimer (from PDB file)
Resolution:
2.00Å     R-factor:   0.204     R-free:   0.309
Authors: J.Wouters,J.Georis,J.Dusart,J.M.Frere,E.Depiereux,P.Charlier
Key ref:
J.Wouters et al. (2001). Crystallographic analysis of family 11 endo-beta-1,4-xylanase Xyl1 from Streptomyces sp. S38. Acta Crystallogr D Biol Crystallogr, 57, 1813-1819. PubMed id: 11717493 DOI: 10.1107/S0907444901015153
Date:
05-Jan-01     Release date:   30-Nov-01    
PROCHECK
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 Headers
 References

Protein chains
Pfam   ArchSchema ?
Q59962  (Q59962_9ACTN) -  Endo-1,4-beta-xylanase from Streptomyces sp. S38
Seq:
Struc: 		228 a.a.
185 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 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.

 

 
DOI no: 10.1107/S0907444901015153 Acta Crystallogr D Biol Crystallogr 57:1813-1819 (2001)
PubMed id: 11717493  
 
 
Crystallographic analysis of family 11 endo-beta-1,4-xylanase Xyl1 from Streptomyces sp. S38.
J.Wouters, J.Georis, D.Engher, J.Vandenhaute, J.Dusart, J.M.Frere, E.Depiereux, P.Charlier.
 
  ABSTRACT  
 
Family 11 endo-beta-1,4-xylanases degrade xylan, the main constituent of plant hemicelluloses, and have many potential uses in biotechnology. The structure of Xyl1, a family 11 endo-xylanase from Streptomyces sp. S38, has been solved. The protein crystallized from ammonium sulfate in the trigonal space group P321, with unit-cell parameters a = b = 71.49, c = 130.30 A, gamma = 120.0 degrees. The structure was solved at 2.0 A by X-ray crystallography using the molecular-replacement method and refined to a final R factor of 18.5% (R(free) = 26.9%). Xyl1 has the overall fold characteristic of family 11 xylanases, with two highly twisted beta-sheets defining a long cleft containing the two catalytic residues Glu87 and Glu177.
 
  Selected figure(s)  
 
Figure 4.
Figure 4 (a) Topologies of family 11 endo-xylanases allowing the separation of those enzymes into two groups. Exs 11 type I: endo-xylanases from T. reseei XYNI ([220]1xyn ), A. niger ([221]1ukr ), A. kawachii ([222]1bk1 ), B. circulans ([223]1bcx ). Exs 11 type II: endo-xylanases from T. reseei XYNII ([224]1xyp ), T. lanuginosa ([225]1yna ), T. harzianum ([226]1xnd ), P. varioti ([227]1pvx ), B. agaradhaerens ([228]1qh6 ), D. thermophilum XynB ([229]1f5j ). An enlargement of the arrangement of the secondary elements around the N-terminal region of Exs 11 is presented in (b). 		Figure 5.
Figure 5 Stereoview of the active site of Xyl1 from Streptomyces sp. S38.
 
  The above figures are reprinted by permission from the IUCr: Acta Crystallogr D Biol Crystallogr (2001, 57, 1813-1819) copyright 2001.  
  Figures were selected by an automated process.  

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.  
20393704 G.Wang, Y.Wang, P.Yang, H.Luo, H.Huang, P.Shi, K.Meng, and B.Yao (2010).
Molecular detection and diversity of xylanase genes in alpine tundra soil.
  Appl Microbiol Biotechnol, 87, 1383-1393.  
18384043 G.André-Leroux, J.G.Berrin, J.Georis, F.Arnaut, and N.Juge (2008).
Structure-based mutagenesis of Penicillium griseofulvum xylanase using computational design.
  Proteins, 72, 1298-1307.  
17646981 Y.Cao, J.Qiao, Y.Li, and W.Lu (2007).
De novo synthesis, constitutive expression of Aspergillus sulphureus beta-xylanase gene in Pichia pastoris and partial enzymic characterization.
  Appl Microbiol Biotechnol, 76, 579-585.  
16652352 M.Kozak (2006).
Solution scattering studies of conformation stability of xylanase XYNII from Trichoderma longibrachiatum.
  Biopolymers, 83, 95.  
15981268 E.Ben-Zeev, N.Kowalsman, A.Ben-Shimon, D.Segal, T.Atarot, O.Noivirt, T.Shay, and M.Eisenstein (2005).
Docking to single-domain and multiple-domain proteins: old and new challenges.
  Proteins, 60, 195-201.  
15659364 F.De Lemos Esteves, T.Gouders, J.Lamotte-Brasseur, S.Rigali, and J.M.Frère (2005).
Improving the alkalophilic performances of the Xyl1 xylanase from Streptomyces sp. S38: structural comparison and mutational analysis.
  Protein Sci, 14, 292-302.  
  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.  
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
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.  
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 codes are shown on the right.

 

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