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PDBsum entry 1wb4

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protein ligands metals Protein-protein interface(s) links
Hydrolase PDB id
1wb4
Jmol
Contents
Protein chains
283 a.a. *
Ligands
SXX ×2
GOL ×6
ACY ×2
Metals
_CD ×18
Waters ×750
* Residue conservation analysis
PDB id:
1wb4
Name: Hydrolase
Title: S954a mutant of the feruloyl esterase module from clostridium thermocellum complexed with sinapinate
Structure: Endo-1,4-beta-xylanase y. Chain: a, b. Fragment: feruloyl esterase domain, residues 792-1077. Synonym: xylanase y, xyly, 1,4-beta-d-xylan xylanohydrolase y, xylanase xyn10b. Engineered: yes. Mutation: yes
Source: Clostridium thermocellum. Organism_taxid: 1515. Expressed in: escherichia coli. Expression_system_taxid: 469008.
Biol. unit: Monomer (from PDB file)
Resolution:
1.4Å     R-factor:   0.113     R-free:   0.134
Authors: N.Tarbouriech,J.A.Prates,C.Fontes,G.J.Davies
Key ref:
N.Tarbouriech et al. (2005). Molecular determinants of substrate specificity in the feruloyl esterase module of xylanase 10B from Clostridium thermocellum. Acta Crystallogr D Biol Crystallogr, 61, 194-197. PubMed id: 15681871 DOI: 10.1107/S0907444904029695
Date:
30-Oct-04     Release date:   02-Feb-05    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chains
Pfam   ArchSchema ?
P51584  (XYNY_CLOTM) -  Endo-1,4-beta-xylanase Y
Seq:
Struc:
 
Seq:
Struc:
 
Seq:
Struc:
1077 a.a.
283 a.a.*
Key:    PfamA domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 3 residue positions (black crosses)

 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.

 

 
DOI no: 10.1107/S0907444904029695 Acta Crystallogr D Biol Crystallogr 61:194-197 (2005)
PubMed id: 15681871  
 
 
Molecular determinants of substrate specificity in the feruloyl esterase module of xylanase 10B from Clostridium thermocellum.
N.Tarbouriech, J.A.Prates, C.M.Fontes, G.J.Davies.
 
  ABSTRACT  
 
Feruloyl esterases play a key role in the degradation of the intricate structure of the plant cell wall by hydrolysing the ferulate ester groups involved in the cross-linking between hemicelluloses and between hemicellulose and lignin. The structure of the feruloyl esterase module of Clostridium thermocellum cellulosomal xylanase 10B has been reported previously. It displays the alpha/beta hydrolase fold with a classical Ser-His-Asp catalytic triad. Here, the structures of a Ser-Ala mutant of this feruloyl esterase in complexes with methyl syringate, methyl sinapinate and methyl vanillate are described. Substrate binding is accompanied by subtle conformational changes at amino acids Trp982, Met955, Asn1023 and Ile1019 in the ligand-binding cavity. The structural determinants, particularly the m-methoxy substituent, governing the substrate specificity of Xyn10B feruloyl esterase are rationalized.
 
  Selected figure(s)  
 
Figure 3.
Figure 3 Superimposition of the active-site environment and substrates. Residues involved in movements are labelled as well as the catalytic triad. The methyl sinapinate complex is in orange, methyl vanillate in pink, methyl syringate in blue and the native uncomplexed structure in white. The figure was prepared using PyMOL (DeLano Scientific).
 
  The above figure is reprinted by permission from the IUCr: Acta Crystallogr D Biol Crystallogr (2005, 61, 194-197) copyright 2005.  
  Figure was selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
20724792 J.Gabadinho, A.Beteva, M.Guijarro, V.Rey-Bakaikoa, D.Spruce, M.W.Bowler, S.Brockhauser, D.Flot, E.J.Gordon, D.R.Hall, B.Lavault, A.A.McCarthy, J.McCarthy, E.Mitchell, S.Monaco, C.Mueller-Dieckmann, D.Nurizzo, R.B.Ravelli, X.Thibault, M.A.Walsh, G.A.Leonard, and S.M.McSweeney (2010).
MxCuBE: a synchrotron beamline control environment customized for macromolecular crystallography experiments.
  J Synchrotron Radiat, 17, 700-707.  
  18678939 S.Najmudin, B.A.Pinheiro, M.J.Romão, J.A.Prates, and C.M.Fontes (2008).
Purification, crystallization and crystallographic analysis of Clostridium thermocellum endo-1,4-beta-D-xylanase 10B in complex with xylohexaose.
  Acta Crystallogr Sect F Struct Biol Cryst Commun, 64, 715-718.  
17989872 A.E.Fazary, and Y.H.Ju (2007).
Feruloyl esterases as biotechnological tools: current and future perspectives.
  Acta Biochim Biophys Sin (Shanghai), 39, 811-828.  
16431911 E.J.Taylor, T.M.Gloster, J.P.Turkenburg, F.Vincent, A.M.Brzozowski, C.Dupont, F.Shareck, M.S.Centeno, J.A.Prates, V.Puchart, L.M.Ferreira, C.M.Fontes, P.Biely, and G.J.Davies (2006).
Structure and activity of two metal ion-dependent acetylxylan esterases involved in plant cell wall degradation reveals a close similarity to peptidoglycan deacetylases.
  J Biol Chem, 281, 10968-10975.
PDB codes: 2c71 2c79 2cc0
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