PDBsum entry 1m4w

Go to PDB code: 
protein ligands links
Hydrolase PDB id
Protein chain
197 a.a. *
Waters ×183
* Residue conservation analysis
PDB id:
Name: Hydrolase
Title: Thermophilic b-1,4-xylanase from nonomuraea flexuosa
Structure: Endoxylanase. Chain: a. Engineered: yes
Source: Thermopolyspora flexuosa. Organism_taxid: 103836. Expressed in: hypocrea jecorina. Expression_system_taxid: 51453
2.10Å     R-factor:   0.146     R-free:   0.209
Authors: N.Hakulinen,O Turunen,J.Janis,M.Leisola,J.Rouvinen
Key ref:
N.Hakulinen et al. (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. PubMed id: 12653995 DOI: 10.1046/j.1432-1033.2003.03496.x
05-Jul-02     Release date:   08-Jul-03    
Go to PROCHECK summary

Protein chain
Pfam   ArchSchema ?
Q8GMV7  (Q8GMV7_9ACTO) -  Endo-1,4-beta-xylanase
344 a.a.
197 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Enzyme reactions 
   Enzyme class: E.C.  - 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     carbohydrate metabolic process   1 term 
  Biochemical function     hydrolase activity, hydrolyzing O-glycosyl compounds     1 term  


DOI no: 10.1046/j.1432-1033.2003.03496.x Eur J Biochem 270:1399-1412 (2003)
PubMed id: 12653995  
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.
N.Hakulinen, O.Turunen, J.Jänis, M.Leisola, J.Rouvinen.
The crystal structures of thermophilic xylanases from Chaetomium thermophilum and Nonomuraea flexuosa were determined at 1.75 and 2.1 A resolution, respectively. Both enzymes have the overall fold typical to family 11 xylanases with two highly twisted beta-sheets forming a large cleft. The comparison of 12 crystal structures of family 11 xylanases from both mesophilic and thermophilic organisms showed that the structures of different xylanases are very similar. The sequence identity differences correlated well with the structural differences. Several minor modifications appeared to be responsible for the increased thermal stability of family 11 xylanases: (a) higher Thr : Ser ratio (b) increased number of charged residues, especially Arg, resulting in enhanced polar interactions, and (c) improved stabilization of secondary structures involved the higher number of residues in the beta-strands and stabilization of the alpha-helix region. Some members of family 11 xylanases have a unique strategy to improve their stability, such as a higher number of ion pairs or aromatic residues on protein surface, a more compact structure, a tighter packing, and insertions at some regions resulting in enhanced interactions.
  Selected figure(s)  
Figure 1.
Fig. 1. CTX. (A) The overall structure of CTX. Glycerol and catalytic glutamates are shown in the active site. (B) A tetrameric assembly with sulfate ions. Molecules A and B are shown in white and symmetry molecules C and D in blue.
Figure 2.
Fig. 2. NFX. (A) The overall structure of NFX with a glycerol molecule in the active site. Carbohydrates attached to Asn7 are shown in gray sticks. (B) The representative 2F[o] –F[c] electron density map from the final model of NFX. The figure shows the density of carbohydrates, contoured at a level of 1.5 .
  The above figures are reprinted by permission from the Federation of European Biochemical Societies: Eur J Biochem (2003, 270, 1399-1412) copyright 2003.  
  Figures were selected by the author.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
21349882 A.Morin, K.W.Kaufmann, C.Fortenberry, J.M.Harp, L.S.Mizoue, and J.Meiler (2011).
Computational design of an endo-1,4-{beta}-xylanase ligand binding site.
  Protein Eng Des Sel, 24, 503-516.
PDB codes: 3mf6 3mf9 3mfa 3mfc
19680819 A.Knob, and E.C.Carmona (2010).
Purification and characterization of two extracellular xylanases from Penicillium sclerotiorum: a novel acidophilic xylanase.
  Appl Biochem Biotechnol, 162, 429-443.  
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.  
19854928 S.Anbarasan, J.Jänis, M.Paloheimo, M.Laitaoja, M.Vuolanto, J.Karimäki, P.Vainiotalo, M.Leisola, and O.Turunen (2010).
Effect of glycosylation and additional domains on the thermostability of a family 10 xylanase produced by Thermopolyspora flexuosa.
  Appl Environ Microbiol, 76, 356-360.  
18500584 S.G.Nair, R.Sindhu, and S.Shashidhar (2008).
Purification and biochemical characterization of two xylanases from Aspergillus sydowii SBS 45.
  Appl Biochem Biotechnol, 149, 229-243.  
17549471 A.Mäntylä, M.Paloheimo, S.Hakola, E.Lindberg, S.Leskinen, J.Kallio, J.Vehmaanperä, R.Lantto, and P.Suominen (2007).
Production in Trichoderma reesei of three xylanases from Chaetomium thermophilum: a recombinant thermoxylanase for biobleaching of kraft pulp.
  Appl Microbiol Biotechnol, 76, 377-386.  
17139507 H.M.Yang, B.Yao, K.Meng, Y.R.Wang, Y.G.Bai, and N.F.Wu (2007).
Introduction of a disulfide bridge enhances the thermostability of a Streptomyces olivaceoviridis xylanase mutant.
  J Ind Microbiol Biotechnol, 34, 213-218.  
17404726 M.Leisola, and O.Turunen (2007).
Protein engineering: opportunities and challenges.
  Appl Microbiol Biotechnol, 75, 1225-1232.  
16652352 M.Kozak (2006).
Solution scattering studies of conformation stability of xylanase XYNII from Trichoderma longibrachiatum.
  Biopolymers, 83, 95.  
16404950 N.Brito, J.J.Espino, and C.González (2006).
The endo-beta-1,4-xylanase xyn11A is required for virulence in Botrytis cinerea.
  Mol Plant Microbe Interact, 19, 25-32.  
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.  
16247799 Ihsanawati, T.Kumasaka, T.Kaneko, C.Morokuma, R.Yatsunami, T.Sato, S.Nakamura, and N.Tanaka (2005).
Structural basis of the substrate subsite and the highly thermal stability of xylanase 10B from Thermotoga maritima MSB8.
  Proteins, 61, 999.
PDB codes: 1vbr 1vbu
15853815 J.Jänis, J.Hakanpää, N.Hakulinen, F.M.Ibatullin, A.Hoxha, P.J.Derrick, J.Rouvinen, and P.Vainiotalo (2005).
Determination of thioxylo-oligosaccharide binding to family 11 xylanases using electrospray ionization Fourier transform ion cyclotron resonance mass spectrometry and X-ray crystallography.
  FEBS J, 272, 2317-2333.
PDB code: 1xnk
15944805 M.L.Polizeli, A.C.Rizzatti, R.Monti, H.F.Terenzi, J.A.Jorge, and D.S.Amorim (2005).
Xylanases from fungi: properties and industrial applications.
  Appl Microbiol Biotechnol, 67, 577-591.  
15650852 S.Leskinen, A.Mäntylä, R.Fagerström, J.Vehmaanperä, R.Lantto, M.Paloheimo, and P.Suominen (2005).
Thermostable xylanases, Xyn10A and Xyn11A, from the actinomycete Nonomuraea flexuosa: isolation of the genes and characterization of recombinant Xyn11A polypeptides produced in Trichoderma reesei.
  Appl Microbiol Biotechnol, 67, 495-505.  
15652973 T.Collins, C.Gerday, and G.Feller (2005).
Xylanases, xylanase families and extremophilic xylanases.
  FEMS Microbiol Rev, 29, 3.  
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.  
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.