PDBsum entry 1r87

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Hydrolase PDB id
Protein chain
371 a.a. *
_ZN ×7
_CL ×2
Waters ×303
* Residue conservation analysis
PDB id:
Name: Hydrolase
Title: Crystal structure of the extracellular xylanase from geobaci stearothermophilus t-6 (xt6, monoclinic form): the complex enzyme with xylopentaose at 1.67a resolution
Structure: Endo-1,4-beta-xylanase. Chain: a. Synonym: xylanase, 1,4-beta-d-xylan xylanohydrolase, xylana engineered: yes
Source: Geobacillus stearothermophilus. Organism_taxid: 1422. Gene: xyna. Expressed in: escherichia coli bl21. Expression_system_taxid: 511693.
1.67Å     R-factor:   0.169     R-free:   0.186
Authors: M.Bar,G.Golan,G.Zolotnitsky,Y.Shoham,G.Shoham
Key ref:
G.Zolotnitsky et al. (2004). Mapping glycoside hydrolase substrate subsites by isothermal titration calorimetry. Proc Natl Acad Sci U S A, 101, 11275-11280. PubMed id: 15277671 DOI: 10.1073/pnas.0404311101
23-Oct-03     Release date:   20-Jul-04    
Go to PROCHECK summary

Protein chain
Pfam   ArchSchema ?
P40943  (XYN1_GEOSE) -  Endo-1,4-beta-xylanase
407 a.a.
371 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!
  Cellular component     extracellular region   1 term 
  Biological process     metabolic process   4 terms 
  Biochemical function     hydrolase activity     4 terms  


DOI no: 10.1073/pnas.0404311101 Proc Natl Acad Sci U S A 101:11275-11280 (2004)
PubMed id: 15277671  
Mapping glycoside hydrolase substrate subsites by isothermal titration calorimetry.
G.Zolotnitsky, U.Cogan, N.Adir, V.Solomon, G.Shoham, Y.Shoham.
Relating thermodynamic parameters to structural and biochemical data allows a better understanding of substrate binding and its contribution to catalysis. The analysis of the binding of carbohydrates to proteins or enzymes is a special challenge because of the multiple interactions and forces involved. Isothermal titration calorimetry (ITC) provides a direct measure of binding enthalpy (DeltaHa) and allows the determination of the binding constant (free energy), entropy, and stoichiometry. In this study, we used ITC to elucidate the binding thermodynamics of xylosaccharides for two xylanases of family 10 isolated from Geobacillus stearothermophilus T-6. The change in the heat capacity of binding (DeltaCp = DeltaH/DeltaT) for xylosaccharides differing in one sugar unit was determined by using ITC measurements at different temperatures. Because hydrophobic stacking interactions are associated with negative DeltaCp, the data allow us to predict the substrate binding preference in the binding subsites based on the crystal structure of the enzyme. The proposed positional binding preference was consistent with mutants lacking aromatic binding residues at different subsites and was also supported by tryptophan fluorescence analysis.
  Selected figure(s)  
Figure 3.
Fig. 3. Substrate positional binding in XT6. (A) Schematic representation of the hydrogen bonding network and stacking interactions in the XT6 binding site. (B) Structure of XT6 in complex with X[3] and X[2] (cleaved X[5]), showing only the aromatic amino acids and the sugars. Tyr-203 and Trp-273 form stacking interactions with the sugar rings at subsites +1 and +2, respectively. (C) The suggested positional binding of xylosaccharides to the binding subsites of XT6, obtained by combining the C[p] with the structural data.
Figure 5.
Fig. 5. Enthalpy-entropy compensation plot for the binding of X[2], X[3], X[4], X[5], X[6], beech wood xylan (Be), birch wood xylan (Bi), and oat spelts xylan (Oat) to IXT6 ( ) and to XT6 ( ) at 303 K. The dashed lines are the theoretical range of G[a], where the binding constants vary by three orders of magnitude.
  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.  
19505290 A.Alhassid, A.Ben-David, O.Tabachnikov, D.Libster, E.Naveh, G.Zolotnitsky, Y.Shoham, and G.Shoham (2009).
Crystal structure of an inverting GH 43 1,5-alpha-L-arabinanase from Geobacillus stearothermophilus complexed with its substrate.
  Biochem J, 422, 73-82.
PDB codes: 3cu9 3d5y 3d5z 3d60 3d61
19352037 P.Jommuengbout, S.Pinitglang, K.L.Kyu, and K.Ratanakhanokchai (2009).
Substrate-binding site of family 11 xylanase from Bacillus firmus K-1 by molecular docking.
  Biosci Biotechnol Biochem, 73, 833-839.  
19270338 X.Zhai, M.L.Malakhova, H.M.Pike, L.M.Benson, H.R.Bergen, I.P.Sugár, L.Malinina, D.J.Patel, and R.E.Brown (2009).
Glycolipid acquisition by human glycolipid transfer protein dramatically alters intrinsic tryptophan fluorescence: insights into glycolipid binding affinity.
  J Biol Chem, 284, 13620-13628.  
18952792 Y.Nataf, S.Yaron, F.Stahl, R.Lamed, E.A.Bayer, T.H.Scheper, A.L.Sonenshein, and Y.Shoham (2009).
Cellodextrin and laminaribiose ABC transporters in Clostridium thermocellum.
  J Bacteriol, 191, 203-209.  
19767466 d.o. .Y.Kim, M.K.Han, D.S.Park, J.S.Lee, H.W.Oh, D.H.Shin, T.S.Jeong, S.U.Kim, K.S.Bae, K.H.Son, and H.Y.Park (2009).
Novel GH10 xylanase, with a fibronectin type 3 domain, from Cellulosimicrobium sp. strain HY-13, a bacterium in the gut of Eisenia fetida.
  Appl Environ Microbiol, 75, 7275-7279.  
17955483 A.Ben-David, T.Bravman, Y.S.Balazs, M.Czjzek, D.Schomburg, G.Shoham, and Y.Shoham (2007).
Glycosynthase activity of Geobacillus stearothermophilus GH52 beta-xylosidase: efficient synthesis of xylooligosaccharides from alpha-D-xylopyranosyl fluoride through a conjugated reaction.
  Chembiochem, 8, 2145-2151.  
17705310 J.Kondo, M.Hainrichson, I.Nudelman, D.Shallom-Shezifi, C.M.Barbieri, D.S.Pilch, E.Westhof, and T.Baasov (2007).
Differential selectivity of natural and synthetic aminoglycosides towards the eukaryotic and prokaryotic decoding A sites.
  Chembiochem, 8, 1700-1709.
PDB codes: 2o3v 2o3w 2o3x 2o3y
17142383 S.Shulami, G.Zaide, G.Zolotnitsky, Y.Langut, G.Feld, A.L.Sonenshein, and Y.Shoham (2007).
A two-component system regulates the expression of an ABC transporter for xylo-oligosaccharides in Geobacillus stearothermophilus.
  Appl Environ Microbiol, 73, 874-884.  
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
16220545 A.Ababou, and J.E.Ladbury (2006).
Survey of the year 2004: literature on applications of isothermal titration calorimetry.
  J Mol Recognit, 19, 79-89.  
16823036 K.Manikandan, A.Bhardwaj, N.Gupta, N.K.Lokanath, A.Ghosh, V.S.Reddy, and S.Ramakumar (2006).
Crystal structures of native and xylosaccharide-bound alkali thermostable xylanase from an alkalophilic Bacillus sp. NG-27: structural insights into alkalophilicity and implications for adaptation to polyextreme conditions.
  Protein Sci, 15, 1951-1960.
PDB codes: 2f8q 2fgl
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
16607570 V.Spiwok, P.Lipovová, T.Skálová, E.Vondrácková, J.Dohnálek, J.Hasek, and B.Králová (2005).
Modelling of carbohydrate-aromatic interactions: ab initio energetics and force field performance.
  J Comput Aided Mol Des, 19, 887-901.  
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.