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PDBsum entry 1vbr

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protein ligands Protein-protein interface(s) links
Hydrolase PDB id
1vbr
Jmol
Contents
Protein chains
324 a.a. *
Ligands
XYS-XYP ×2
ACY ×6
Waters ×646
* Residue conservation analysis
PDB id:
1vbr
Name: Hydrolase
Title: Crystal structure of complex xylanase 10b from thermotoga maritima with xylobiose
Structure: Endo-1,4-beta-xylanase b. Chain: a, b. Synonym: xylanase, xylanase 10b. Engineered: yes
Source: Thermotoga maritima. Organism_taxid: 2336. Expressed in: escherichia coli. Expression_system_taxid: 562.
Resolution:
1.80Å     R-factor:   0.181     R-free:   0.215
Authors: Ihsanawati,T.Kumasaka,T.Kaneko,S.Nakamura,N.Tanaka
Key ref:
Ihsanawati et al. (2005). Structural basis of the substrate subsite and the highly thermal stability of xylanase 10B from Thermotoga maritima MSB8. Proteins, 61, 999. PubMed id: 16247799 DOI: 10.1002/prot.20700
Date:
02-Mar-04     Release date:   28-Jun-05    
PROCHECK
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 Headers
 References

Protein chains
Pfam   ArchSchema ?
Q9WXS5  (Q9WXS5_THEMA) -  Endo-1,4-beta-xylanase
Seq:
Struc:
347 a.a.
324 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 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   3 terms 
  Biochemical function     hydrolase activity     4 terms  

 

 
DOI no: 10.1002/prot.20700 Proteins 61:999 (2005)
PubMed id: 16247799  
 
 
Structural basis of the substrate subsite and the highly thermal stability of xylanase 10B from Thermotoga maritima MSB8.
Ihsanawati, T.Kumasaka, T.Kaneko, C.Morokuma, R.Yatsunami, T.Sato, S.Nakamura, N.Tanaka.
 
  ABSTRACT  
 
The crystal structure of xylanase 10B from Thermotoga maritima MSB8 (TmxB), a hyperthermostable xylanase, has been solved in its native form and in complex with xylobiose or xylotriose at 1.8 A resolution. In order to gain insight into the substrate subsite and the molecular features for thermal stability, we compared TmxB with family 10 xylanase structures from nine microorganisms. As expected, TmxB folds into a (beta/alpha)8-barrel structure, which is common among the glycoside hydrolase family 10. The enzyme active site and the environment surrounding the xylooligosaccharide of TmxB are highly similar to those of family 10 xylanases. However, only two xylose moieties were found in its binding pocket from the TmxB-xylotriose complex structure. This finding suggests that TmxB could be a potential biocatalyst for the large-scale production of xylobiose. The result of structural analyses also indicated that TmxB possesses some additional features that account for its thermostability. In particular, clusters of aromatic residues together with a lack of exposed hydrophobic residues are characteristic of the TmxB structure. TmxB has also a significant number of ion pairs on the protein surface that are not found in other thermophilic family 10 xylanases.
 
  Selected figure(s)  
 
Figure 1.
Figure 1. A: Overall structure of TmxB (in stereo) from the top view. Major -helices and -strands are drawn in red and green, respectively, and labeled according to the ideal ( / )[8] barrel structure.[42] The two catalytic residues are labeled and depicted by ball-and-stick facing two xylose moieties. B: Stereo view of superimposition of TmxB-xylotriose (yellow) with Psx-xylotriose (blue) in the catalytic site. Red dash lines indicate hydrogen bonds in the TmxB complex structure, which are also found in Psx. Blue dash lines represent hydrogen bonds, which are only found in Psx.
Figure 4.
Figure 4. Molecular interactions for thermal stability of TmxB. A: Aromatic interactions from the top view showing five distinct clusters drawn in different colors. B: Electrostatic interactions in the C-terminal region consist of a triad salt bridge (Asp780-Asp784-Lys836) and single ones (Lys769-Glu773, Asp798-Lys823 and Lys835-Glu839. C-E: Comparison of aromatic interactions, connecting 1, 2, 1, and 8 in TmxB, Ctx, and Pfx, respectively.
 
  The above figures are reprinted by permission from John Wiley & Sons, Inc.: Proteins (2005, 61, 999-0) copyright 2005.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
20596542 A.Bhardwaj, S.Leelavathi, S.Mazumdar-Leighton, A.Ghosh, S.Ramakumar, and V.S.Reddy (2010).
The critical role of N- and C-terminal contact in protein stability and folding of a family 10 xylanase under extreme conditions.
  PLoS One, 5, e11347.  
18725971 A.Bharadwaj, S.Leelavathi, S.Mazumdar-Leighton, A.Ghosh, S.Ramakumar, and V.S.Reddy (2008).
The critical role of partially exposed N-terminal valine residue in stabilizing GH10 xylanase from Bacillus sp.NG-27 under poly-extreme conditions.
  PLoS ONE, 3, e3063.  
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
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