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PDBsum entry 1red

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protein ligands Protein-protein interface(s) links
Hydrolase PDB id
1red
Jmol
Contents
Protein chains
190 a.a. *
Ligands
C5X
BEZ
Waters ×290
* Residue conservation analysis
PDB id:
1red
Name: Hydrolase
Title: Endo-1,4-beta-xylanase ii complex with 4,5-epoxypentyl-beta- d-xyloside
Structure: Endo-1,4-beta-xylanase ii. Chain: a, b. Synonym: xynii. Ec: 3.2.1.8
Source: Hypocrea jecorina. Organism_taxid: 51453. Strain: trichoderma reesei rut-c30
Resolution:
1.60Å     R-factor:   0.180     R-free:   0.222
Authors: J.Rouvinen,R.Havukainen,A.Torronen
Key ref:
R.Havukainen et al. (1996). Covalent binding of three epoxyalkyl xylosides to the active site of endo-1,4-xylanase II from Trichoderma reesei. Biochemistry, 35, 9617-9624. PubMed id: 8755744 DOI: 10.1021/bi953052n
Date:
21-Dec-95     Release date:   11-Jan-97    
PROCHECK
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 Headers
 References

Protein chains
Pfam   ArchSchema ?
P36217  (XYN2_HYPJE) -  Endo-1,4-beta-xylanase 2
Seq:
Struc:
222 a.a.
190 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/bi953052n Biochemistry 35:9617-9624 (1996)
PubMed id: 8755744  
 
 
Covalent binding of three epoxyalkyl xylosides to the active site of endo-1,4-xylanase II from Trichoderma reesei.
R.Havukainen, A.Törrönen, T.Laitinen, J.Rouvinen.
 
  ABSTRACT  
 
The three-dimensional structures of endo-1,4-xylanase II (XYNII) from Trichoderma reesei complexed with 4,5-epoxypentyl beta-D-xyloside (X-O-C5),3,4-epoxybutyl beta-D-xyloside (X-O-C4), and 2,3-epoxypropyl beta-D-xyloside (X-O-C3) were determined by X-ray crystallography. High-resolution measurement revealed clear electron densities for each ligand. Both X-O-C5 and X-O-C3 were found to form a covalent bond with the putative nucleophile Glu86. Unexpectedly, X-O-C4 was found to bind to the putative acid/base catalyst Glu177. In all three complexes, clear conformational changes were found in XYNII compared to the native structure. These changes were largest in the X-O-C3 complex structure.
 

Literature references that cite this PDB file's key reference

  PubMed id Reference
21085740 M.Rejzek, C.E.Stevenson, A.M.Southard, D.Stanley, K.Denyer, A.M.Smith, M.J.Naldrett, D.M.Lawson, and R.A.Field (2011).
Chemical genetics and cereal starch metabolism: structural basis of the non-covalent and covalent inhibition of barley β-amylase.
  Mol Biosyst, 7, 718-730.
PDB codes: 2xff 2xfr 2xfy 2xg9 2xgb 2xgi
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.  
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
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.  
16790934 N.Watanabe, T.Akiba, R.Kanai, and K.Harata (2006).
Structure of an orthorhombic form of xylanase II from Trichoderma reesei and analysis of thermal displacement.
  Acta Crystallogr D Biol Crystallogr, 62, 784-792.
PDB codes: 2dfb 2dfc
16524900 R.Rauscher, E.Würleitner, C.Wacenovsky, N.Aro, A.R.Stricker, S.Zeilinger, C.P.Kubicek, M.Penttilä, and R.L.Mach (2006).
Transcriptional regulation of xyn1, encoding xylanase I, in Hypocrea jecorina.
  Eukaryot Cell, 5, 447-456.  
15965663 J.Beaugrand, G.Paës, D.Reis, M.Takahashi, P.Debeire, M.O'donohue, and B.Chabbert (2005).
Probing the cell wall heterogeneity of micro-dissected wheat caryopsis using both active and inactive forms of a GH11 xylanase.
  Planta, 222, 246-257.  
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
12582132 E.Würleitner, L.Pera, C.Wacenovsky, A.Cziferszky, S.Zeilinger, C.P.Kubicek, and R.L.Mach (2003).
Transcriptional regulation of xyn2 in Hypocrea jecorina.
  Eukaryot Cell, 2, 150-158.  
12720276 M.Muraki, and K.Harata (2003).
X-ray structural analysis of the ligand-recognition mechanism in the dual-affinity labeling of c-type lysozyme with 2',3'-epoxypropyl beta-glycoside of N-acetyllactosamine.
  J Mol Recognit, 16, 72-82.
PDB codes: 1ubz 1uc0
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
12146939 D.J.Vocadlo, J.Wicki, K.Rupitz, and S.G.Withers (2002).
A case for reverse protonation: identification of Glu160 as an acid/base catalyst in Thermoanaerobacterium saccharolyticum beta-xylosidase and detailed kinetic analysis of a site-directed mutant.
  Biochemistry, 41, 9736-9746.  
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.  
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
10220321 G.Sidhu, S.G.Withers, N.T.Nguyen, L.P.McIntosh, L.Ziser, and G.D.Brayer (1999).
Sugar ring distortion in the glycosyl-enzyme intermediate of a family G/11 xylanase.
  Biochemistry, 38, 5346-5354.
PDB codes: 1bvv 2bvv
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
9888793 M.Muraki, K.Harata, N.Sugita, and K.Sato (1999).
Dual affinity labeling of the active site of human lysozyme with an N-acetyllactosamine derivative: first ligand assisted recognition of the second ligand.
  Biochemistry, 38, 540-548.
PDB code: 1re2
9698381 J.L.Viladot, E.de Ramon, O.Durany, and A.Planas (1998).
Probing the mechanism of Bacillus 1,3-1,4-beta-D-glucan 4-glucanohydrolases by chemical rescue of inactive mutants at catalytically essential residues.
  Biochemistry, 37, 11332-11342.  
9345622 A.White, and D.R.Rose (1997).
Mechanism of catalysis by retaining beta-glycosyl hydrolases.
  Curr Opin Struct Biol, 7, 645-651.  
9345621 B.Henrissat, and G.Davies (1997).
Structural and sequence-based classification of glycoside hydrolases.
  Curr Opin Struct Biol, 7, 637-644.  
9153432 G.Sulzenbacher, M.Schülein, and G.J.Davies (1997).
Structure of the endoglucanase I from Fusarium oxysporum: native, cellobiose, and 3,4-epoxybutyl beta-D-cellobioside-inhibited forms, at 2.3 A resolution.
  Biochemistry, 36, 5902-5911.
PDB codes: 2ovw 3ovw 4ovw
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.