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PDBsum entry 2b4f

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protein ligands links
Hydrolase PDB id
2b4f
Jmol
Contents
Protein chain
404 a.a. *
Ligands
XYP-XYP-XYP-XYP-
XYP
×2
Waters ×448
* Residue conservation analysis
PDB id:
2b4f
Name: Hydrolase
Title: Structure of a cold-adapted family 8 xylanase in complex with substrate
Structure: Endo-1,4-beta-xylanase. Chain: a. Engineered: yes. Mutation: yes
Source: Pseudoalteromonas haloplanktis. Organism_taxid: 228. Expressed in: escherichia coli. Expression_system_taxid: 562
Resolution:
1.95Å     R-factor:   0.148     R-free:   0.178
Authors: D.De Vos,T.Collins,S.N.Savvides,G.Feller,J.J.Van Beeumen
Key ref:
D.De Vos et al. (2006). Oligosaccharide binding in family 8 glycosidases: crystal structures of active-site mutants of the beta-1,4-xylanase pXyl from Pseudoaltermonas haloplanktis TAH3a in complex with substrate and product. Biochemistry, 45, 4797-4807. PubMed id: 16605248 DOI: 10.1021/bi052193e
Date:
23-Sep-05     Release date:   05-Sep-06    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
Q8RJN8  (Q8RJN8_PSEHA) -  Endo-1,4-beta-xylanase
Seq:
Struc:
426 a.a.
404 a.a.*
Key:    PfamA domain  PfamB 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   3 terms 
  Biochemical function     catalytic activity     5 terms  

 

 
DOI no: 10.1021/bi052193e Biochemistry 45:4797-4807 (2006)
PubMed id: 16605248  
 
 
Oligosaccharide binding in family 8 glycosidases: crystal structures of active-site mutants of the beta-1,4-xylanase pXyl from Pseudoaltermonas haloplanktis TAH3a in complex with substrate and product.
D.De Vos, T.Collins, W.Nerinckx, S.N.Savvides, M.Claeyssens, C.Gerday, G.Feller, J.Van Beeumen.
 
  ABSTRACT  
 
The structures of inactive mutants D144A and E78Q of the glycoside hydrolase family 8 (GH-8) endo-beta-1,4-d-xylanase (pXyl) from the Antarctic bacterium Pseudoalteromonas haloplanktis TAH3a in complex with its substrate xylopentaose (at 1.95 A resolution) and product xylotriose (at 1.9 A resolution) have been determined by X-ray crystallography. A detailed comparative analysis of these with the apo-enzyme and with other GH-8 structures indicates an induced fit mechanism upon ligand binding whereby a number of conformational changes and, in particular, a repositioning of the proton donor into a more catalytically competent position occurs. This has also allowed for the description of protein-ligand interactions in this enzyme and for the demarcation of subsites -3 to +3. An in-depth analysis of each of these subsites gives an insight into the structure-function relationship of this enzyme and the basis of xylose/glucose discrimination in family 8 glycoside hydrolases. Furthermore, the structure of the -1/+1 subsite spanning complex reveals that the substrate is distorted from its ground state conformation. Indeed, structural analysis and in silico docking studies indicate that substrate hydrolysis in GH-8 members is preceded by a conformational change, away from the substrate ground-state chair conformation, to a pretransition state local minimum (2)S(O) conformation.
 

Literature references that cite this PDB file's key reference

  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.  
20552357 A.Pollet, J.Schoepe, E.Dornez, S.V.Strelkov, J.A.Delcour, and C.M.Courtin (2010).
Functional analysis of glycoside hydrolase family 8 xylanases shows narrow but distinct substrate specificities and biotechnological potential.
  Appl Microbiol Biotechnol, 87, 2125-2135.  
19819900 M.Hidaka, S.Fushinobu, Y.Honda, T.Wakagi, H.Shoun, and M.Kitaoka (2010).
Structural explanation for the acquisition of glycosynthase activity.
  J Biochem, 147, 237-244.
PDB codes: 2dro 2drq 2drr 2drs 3a3v
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.  
19458918 Y.M.Park, and S.Y.Ghim (2009).
Enhancement of the activity and pH-performance of chitosanase from Bacillus cereus strains by DNA shuffling.
  Biotechnol Lett, 31, 1463-1467.  
18320143 J.G.Berrin, and N.Juge (2008).
Factors affecting xylanase functionality in the degradation of arabinoxylans.
  Biotechnol Lett, 30, 1139-1150.  
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
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.