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PDBsum entry 1b3y

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Family 10 xylanase PDB id
1b3y
Jmol
Contents
Protein chain
302 a.a. *
Ligands
XYP-XYP-XYP
XYS
Waters ×254
* Residue conservation analysis
PDB id:
1b3y
Name: Family 10 xylanase
Title: Xylanase from penicillium simplicissimum, complex with xylotetraose
Structure: Protein (xylanase). Chain: a. Ec: 3.2.1.8
Source: Penicillium simplicissimum. Organism_taxid: 69488. Cellular_location: secreted. Other_details: penicillium simplicissimum (oudem.) Thom.
Resolution:
2.45Å     R-factor:   0.191     R-free:   0.248
Authors: A.Schmidt,C.Kratky
Key ref: A.Schmidt et al. (1999). Xylan binding subsite mapping in the xylanase from Penicillium simplicissimum using xylooligosaccharides as cryo-protectant. Biochemistry, 38, 2403-2412. PubMed id: 10029534 DOI: 10.1021/bi982108l
Date:
15-Dec-98     Release date:   06-Apr-99    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
P56588  (XYNA_PENSI) -  Endo-1,4-beta-xylanase
Seq:
Struc:
302 a.a.
302 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!
  Cellular component     extracellular region   1 term 
  Biological process     metabolic process   4 terms 
  Biochemical function     hydrolase activity     4 terms  

 

 
DOI no: 10.1021/bi982108l Biochemistry 38:2403-2412 (1999)
PubMed id: 10029534  
 
 
Xylan binding subsite mapping in the xylanase from Penicillium simplicissimum using xylooligosaccharides as cryo-protectant.
A.Schmidt, G.M.Gübitz, C.Kratky.
 
  ABSTRACT  
 
Following a recent low-temperature crystal structure analysis of the native xylanase from Penicillium simplicissimum [Schmidt et al. (1998) Protein Sci. 7, 2081-2088], where an array of glycerol molecules, diffused into the crystal during soaking in a cryoprotectant, was observed within the active-site cleft, we utilized monomeric xylose as well as a variety of linear (Xn, n = 2 to 5) and branched xylooligomers at high concentrations (typically 20% w/v) as cryoprotectant for low-temperature crystallographic experiments. Binding of the glycosidic moiety (or its hydrolysis products) to the enzyme's active-site cleft was observed after as little as 30 s soaking of a native enzyme crystal. The use of a substrate or substrate analogue as cryoprotectant therefore suggests itself as a simple and widely applicable alternative to the use of crystallographic flow-cells for substrate-saturation experiments. Short-chain xylooligomers, i.e., xylobiose (X2) and xylotriose (X3), were found to bind to the active-site cleft with its reducing end hydrogen-bonded to the catalytic acid-base catalyst Glu132. Xylotetraose (X4) and -pentaose (X5) had apparently been cleaved during the soaking time into a xylotriose plus a monomeric (X4) or dimeric (X5) sugar. While the trimeric hydrolysis product was always found to bind in the same way as xylotriose, the monomer or dimer yielded only weak and diffuse electron density within the xylan-binding cleft, at the opposite side of the active center. This suggests that the two catalytic residues divide the binding cleft into a "substrate recognition area" (from the active site toward the nonreducing end of a bound xylan chain), with strong and specific xylan binding and a "product release area" with considerably weaker and less specific binding. The size of the substrate recognition area (3-4 subsites for sugar rings) explains enzyme kinetic data, according to which short oligomers (X2 and X3) bind to the enzyme without being hydrolyzed.
 

Literature references that cite this PDB file's key reference Google scholar

  PubMed id Reference
21261814 S.Cuyvers, E.Dornez, M.N.Rezaei, A.Pollet, J.A.Delcour, and C.M.Courtin (2011).
Secondary substrate binding strongly affects activity and binding affinity of Bacillus subtilis and Aspergillus niger GH11 xylanases.
  FEBS J, 278, 1098-1111.  
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.  
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.  
16717424 M.Sugimura, M.Nishimoto, and M.Kitaoka (2006).
Characterization of glycosynthase mutants derived from glycoside hydrolase family 10 xylanases.
  Biosci Biotechnol Biochem, 70, 1210-1217.  
16972282 Z.Zhou, M.Bates, and J.D.Madura (2006).
Structure modeling, ligand binding, and binding affinity calculation (LR-MM-PBSA) of human heparanase for inhibition and drug design.
  Proteins, 65, 580-592.  
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
15981260 X.H.Ma, C.H.Li, L.Z.Shen, X.Q.Gong, W.Z.Chen, and C.X.Wang (2005).
Biologically enhanced sampling geometric docking and backbone flexibility treatment with multiconformational superposition.
  Proteins, 60, 319-323.  
  16511010 Z.Fujimoto, K.Usui, Y.Kondo, K.Yasui, K.Kawai, and T.Suzuki (2005).
Crystallization and preliminary X-ray crystallographic studies of XynX, a family 10 xylanase from Aeromonas punctata ME-1.
  Acta Crystallogr Sect F Struct Biol Cryst Commun, 61, 255-257.  
15181003 F.Payan, P.Leone, S.Porciero, C.Furniss, T.Tahir, G.Williamson, A.Durand, P.Manzanares, H.J.Gilbert, N.Juge, and A.Roussel (2004).
The dual nature of the wheat xylanase protein inhibitor XIP-I: structural basis for the inhibition of family 10 and family 11 xylanases.
  J Biol Chem, 279, 36029-36037.
PDB codes: 1ta3 1te1
14668328 G.Pell, E.J.Taylor, T.M.Gloster, J.P.Turkenburg, C.M.Fontes, L.M.Ferreira, T.Nagy, S.J.Clark, G.J.Davies, and H.J.Gilbert (2004).
The mechanisms by which family 10 glycoside hydrolases bind decorated substrates.
  J Biol Chem, 279, 9597-9605.
PDB codes: 1uqy 1uqz 1ur1 1ur2
15078885 S.Kaneko, H.Ichinose, Z.Fujimoto, A.Kuno, K.Yura, M.Go, H.Mizuno, I.Kusakabe, and H.Kobayashi (2004).
Structure and function of a family 10 beta-xylanase chimera of Streptomyces olivaceoviridis E-86 FXYN and Cellulomonas fimi Cex.
  J Biol Chem, 279, 26619-26626.
PDB code: 1v6y
14670957 Z.Fujimoto, S.Kaneko, A.Kuno, H.Kobayashi, I.Kusakabe, and H.Mizuno (2004).
Crystal structures of decorated xylooligosaccharides bound to a family 10 xylanase from Streptomyces olivaceoviridis E-86.
  J Biol Chem, 279, 9606-9614.
PDB codes: 1v6u 1v6v 1v6w 1v6x
14662385 G.M.Gübitz, and A.C.Paulo (2003).
New substrates for reliable enzymes: enzymatic modification of polymers.
  Curr Opin Biotechnol, 14, 577-582.  
12654910 T.Nagy, D.Nurizzo, G.J.Davies, P.Biely, J.H.Lakey, D.N.Bolam, and H.J.Gilbert (2003).
The alpha-glucuronidase, GlcA67A, of Cellvibrio japonicus utilizes the carboxylate and methyl groups of aldobiouronic acid as important substrate recognition determinants.
  J Biol Chem, 278, 20286-20292.
PDB code: 1h41
12005440 S.C.Garman, L.Hannick, A.Zhu, and D.N.Garboczi (2002).
The 1.9 A structure of alpha-N-acetylgalactosaminidase: molecular basis of glycosidase deficiency diseases.
  Structure, 10, 425-434.
PDB codes: 1ktb 1ktc
11327856 W.Huang, L.Boju, L.Tkalec, H.Su, H.O.Yang, N.S.Gunay, R.J.Linhardt, Y.S.Kim, A.Matte, and M.Cygler (2001).
Active site of chondroitin AC lyase revealed by the structure of enzyme-oligosaccharide complexes and mutagenesis.
  Biochemistry, 40, 2359-2372.
PDB codes: 1hm2 1hm3 1hmu 1hmw
11025547 L.L.Leggio, J.Jenkins, G.W.Harris, and R.W.Pickersgill (2000).
X-ray crystallographic study of xylopentaose binding to Pseudomonas fluorescens xylanase A.
  Proteins, 41, 362-373.
PDB code: 1e5n
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 codes are shown on the right.