PDBsum entry 1e0x

Go to PDB code: 
protein ligands Protein-protein interface(s) links
Hydrolase PDB id
Protein chains
310 a.a. *
GOL ×3
X2F-XYP ×2
Waters ×717
* Residue conservation analysis
PDB id:
Name: Hydrolase
Title: Xylanase 10a from sreptomyces lividans. Xylobiosyl-enzyme intermediate at 1.65 a
Structure: Endo-1,4-beta-xylanase a. Chain: a, b. Fragment: catalytic module, residues 32-450. Synonym: xylanase a, 1,4-beta-d-xylan xylanohydrolase a. Engineered: yes. Other_details: glycosyl enxyme intermediate. Covalent link between glu 236 and the substrate
Source: Streptomyces lividans. Organism_taxid: 1916. Expressed in: streptomyces lividans. Expression_system_taxid: 1916.
1.65Å     R-factor:   0.126     R-free:   0.162
Authors: V.Ducros,S.J.Charnock,U.Derewenda,Z.S.Derewenda,Z.Dauter, C.Dupont,F.Shareck,R.Morosoli,D.Kluepfel,G.J.Davies
Key ref:
V.Ducros et al. (2000). Substrate specificity in glycoside hydrolase family 10. Structural and kinetic analysis of the Streptomyces lividans xylanase 10A. J Biol Chem, 275, 23020-23026. PubMed id: 10930426 DOI: 10.1074/jbc.275.30.23020
10-Apr-00     Release date:   05-Apr-01    
Go to PROCHECK summary

Protein chains
Pfam   ArchSchema ?
P26514  (XYNA_STRLI) -  Endo-1,4-beta-xylanase A
477 a.a.
310 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: 10.1074/jbc.275.30.23020 J Biol Chem 275:23020-23026 (2000)
PubMed id: 10930426  
Substrate specificity in glycoside hydrolase family 10. Structural and kinetic analysis of the Streptomyces lividans xylanase 10A.
V.Ducros, S.J.Charnock, U.Derewenda, Z.S.Derewenda, Z.Dauter, C.Dupont, F.Shareck, R.Morosoli, D.Kluepfel, G.J.Davies.
Endoxylanases are a group of enzymes that hydrolyze the beta-1, 4-linked xylose backbone of xylans. They are predominantly found in two discrete sequence families known as glycoside hydrolase families 10 and 11. The Streptomyces lividans xylanase Xyl10A is a family 10 enzyme, the native structure of which has previously been determined by x-ray crystallography at a 2.6 A resolution (Derewenda, U., Swenson, L., Green, R., Wei, Y., Morosoli, R., Shareck, F., Kluepfel, D., and Derewenda, Z. S. (1994) J. Biol. Chem. 269, 20811-20814). Here, we report the native structure of Xyl10A refined at a resolution of 1.2 A, which reveals many features such as the rare occurrence of a discretely disordered disulfide bond between residues Cys-168 and Cys-201. In order to investigate substrate binding and specificity in glycoside hydrolase family 10, the covalent xylobiosyl enzyme and the covalent cellobiosyl enzyme intermediates of Xyl10A were trapped through the use of appropriate 2-fluoroglycosides. The alpha-linked intermediate with the nucleophile, Glu-236, is in a (4)C(1) chair conformation as previously observed in the family 10 enzyme Cex from Cellulomonas fimi (Notenboom, V., Birsan, C., Warren, R. A. J., Withers, S. G., and Rose, D. R. (1998) Biochemistry 37, 4751-4758). The different interactions of Xyl10A with the xylobiosyl and cellobiosyl moieties, notably conformational changes in the -2 and -1 subsites, together with the observed kinetics on a range of aryl glycosides, shed new light on substrate specificity in glycoside hydrolase family 10.
  Selected figure(s)  
Figure 4.
Fig. 4. Double displacement reaction mechanism as applied to the S. lividans Xyl10A.
Figure 6.
Fig. 6. Schematic diagram of the protein-ligand interactions for the 2F-xylobiosyl enzyme intermediate of Xyl10A. Distances less than 3.2 Å are indicated.
  The above figures are reprinted by permission from the ASBMB: J Biol Chem (2000, 275, 23020-23026) copyright 2000.  
  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.  
20532756 C.Mirande, P.Mosoni, C.Béra-Maillet, A.Bernalier-Donadille, and E.Forano (2010).
Characterization of Xyn10A, a highly active xylanase from the human gut bacterium Bacteroides xylanisolvens XB1A.
  Appl Microbiol Biotechnol, 87, 2097-2105.  
20382811 P.Shi, J.Tian, T.Yuan, X.Liu, H.Huang, Y.Bai, P.Yang, X.Chen, N.Wu, and B.Yao (2010).
Paenibacillus sp. strain E18 bifunctional xylanase-glucanase with a single catalytic domain.
  Appl Environ Microbiol, 76, 3620-3624.  
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.  
19052739 H.L.Cheng, C.Y.Tsai, H.J.Chen, S.S.Yang, and Y.C.Chen (2009).
The identification, purification, and characterization of STXF10 expressed in Streptomyces thermonitrificans NTU-88.
  Appl Microbiol Biotechnol, 82, 681-689.  
17642511 V.Solomon, A.Teplitsky, S.Shulami, G.Zolotnitsky, Y.Shoham, and G.Shoham (2007).
Structure-specificity relationships of an intracellular xylanase from Geobacillus stearothermophilus.
  Acta Crystallogr D Biol Crystallogr, 63, 845-859.
PDB code: 2q8x
16461639 S.C.Wu, J.E.Halley, C.Luttig, L.M.Fernekes, G.Gutiérrez-Sanchez, A.G.Darvill, and P.Albersheim (2006).
Identification of an endo-beta-1,4-D-xylanase from Magnaporthe grisea by gene knockout analysis, purification, and heterologous expression.
  Appl Environ Microbiol, 72, 986-993.  
15914908 M.Nishimoto, M.Kitaoka, S.Fushinobu, and K.Hayashi (2005).
The role of conserved arginine residue in loop 4 of glycoside hydrolase family 10 xylanases.
  Biosci Biotechnol Biochem, 69, 904-910.  
12876348 A.Canals, M.C.Vega, F.X.Gomis-Rüth, M.Díaz, R.I.Santamaría R, and M.Coll (2003).
Structure of xylanase Xys1delta from Streptomyces halstedii.
  Acta Crystallogr D Biol Crystallogr, 59, 1447-1453.
PDB code: 1nq6
11937059 D.Nurizzo, T.Nagy, H.J.Gilbert, and G.J.Davies (2002).
The structural basis for catalysis and specificity of the Pseudomonas cellulosa alpha-glucuronidase, GlcA67A.
  Structure, 10, 547-556.
PDB codes: 1gqi 1gqj 1gqk 1gql
16233206 Y.Honda, M.Kitaoka, K.Sakka, K.Ohmiya, and K.Hayashi (2002).
An investigation of the pH-activity relationships of Cex, a family 10 xylanase from Cellulomonas fimi: xylan inhibition and the influence of nitro-substituted aryl-beta-D-xylobiosides on xylanase activity.
  J Biosci Bioeng, 93, 313-317.  
11709165 M.Hrmova, J.N.Varghese, R.De Gori, B.J.Smith, H.Driguez, and G.B.Fincher (2001).
Catalytic mechanisms and reaction intermediates along the hydrolytic pathway of a plant beta-D-glucan glucohydrolase.
  Structure, 9, 1005-1016.
PDB codes: 1ieq 1iev 1iew 1iex
11223515 S.Teixeira, L.Lo Leggio, R.Pickersgill, and C.Cardin (2001).
Anisotropic refinement of the structure of Thermoascus aurantiacus xylanase I.
  Acta Crystallogr D Biol Crystallogr, 57, 385-392.
PDB code: 1fxm
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.