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PDBsum entry 1gkk

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protein ligands metals Protein-protein interface(s) links
Hydrolase PDB id
1gkk
Jmol
Contents
Protein chains
283 a.a. *
Ligands
GOL
Metals
_CD ×10
Waters ×752
* Residue conservation analysis
PDB id:
1gkk
Name: Hydrolase
Title: Feruloyl esterase domain of xyny from clostridium thermocellum
Structure: Endo-1,4-beta-xylanase y. Chain: a, b. Fragment: feruloyl esterase domain residues 792-1077. Synonym: cbm22-2,xylanase y, xyly, 1,4-beta-d-xylan xylanohydrolase y. Engineered: yes
Source: Clostridium thermocellum. Organism_taxid: 1515. Strain: ys. Expressed in: escherichia coli. Expression_system_taxid: 469008.
Biol. unit: Monomer (from PDB file)
Resolution:
1.60Å     R-factor:   0.155     R-free:   0.173
Authors: J.A.M.Prates,N.Tarbouriech,S.J.Charnock,C.M.G.A.Fontes, L.M.A.Ferreira,G.J.Davies
Key ref:
J.A.Prates et al. (2001). The structure of the feruloyl esterase module of xylanase 10B from Clostridium thermocellum provides insights into substrate recognition. Structure, 9, 1183-1190. PubMed id: 11738044 DOI: 10.1016/S0969-2126(01)00684-0
Date:
15-Aug-01     Release date:   13-Dec-01    
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 2 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: 10.1016/S0969-2126(01)00684-0 Structure 9:1183-1190 (2001)
PubMed id: 11738044  
 
 
The structure of the feruloyl esterase module of xylanase 10B from Clostridium thermocellum provides insights into substrate recognition.
J.A.Prates, N.Tarbouriech, S.J.Charnock, C.M.Fontes, L.M.Ferreira, G.J.Davies.
 
  ABSTRACT  
 
BACKGROUND: Degradation of the plant cell wall requires the synergistic action of a consortium of predominantly modular enzymes. In Clostridiae, these biocatalysts are organized into a supramolecular assembly termed a "cellulosome." This multienzyme complex possesses, in addition to its well-described cellulolytic activity, an apparatus specific for xylan degradation. Cinnamic acid esterases hydrolyze the ferulate groups involved in the crosslinking of arabinoxylans to lignin and thus play a key role in the degradation of the plant cell wall in addition to having promising industrial and medical applications. RESULTS: We have cloned and overexpressed the feruloyl esterase module from a 5 domain xylanase, Xyn10B from Clostridium thermocellum. The native structure at 1.6 A resolution has been solved with selenomethionine multiple wavelength anomalous dispersion and refined to a final R(free) of 17.8%. The structure of a hydrolytically inactive mutant, S954A, in complex with the reaction product ferulic acid has been refined at a resolution of 1.4 A with an R(free) of 16.0%. CONCLUSIONS: The C. thermocellum Xyn10B ferulic acid esterase displays the alpha/beta-hydrolase fold and possesses a classical Ser-His-Asp catalytic triad. Ferulate esterases are characterized by their specificity, and the active center reveals the binding site for ferulic acid and related compounds. Ferulate binds in a small surface depression that possesses specificity determinants for both the methoxy and hydroxyl ring substituents of the substrate. There appears to be a lack of specificity for the xylan backbone, which may reflect the intrinsic chemical heterogeneity of the natural substrate.
 
  Selected figure(s)  
 
Figure 4.
Figure 4. Observed Electron Density for the Modified Active Center of FAEThe electron density shown is a maximum-likelihood/s[A]-weighted 2F[obs] - F[calc] synthesis contoured at approximately 0.4 electrons/3 in divergent stereo. The catalytic triad is formed by residues Ser954, Asp1018, and His 1058. The posttranslation modification may be modeled as either a phosphate or a sulfate adduct. This figure was prepared with MOLSCRIPT [35] and BOBSCRIPT [36].
 
  The above figure is reprinted by permission from Cell Press: Structure (2001, 9, 1183-1190) copyright 2001.  
  Figure was selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
22868763 S.Brockhauser, O.Svensson, M.W.Bowler, M.Nanao, E.Gordon, R.M.Leal, A.Popov, M.Gerring, A.A.McCarthy, and A.Gotz (2012).
The use of workflows in the design and implementation of complex experiments in macromolecular crystallography.
  Acta Crystallogr D Biol Crystallogr, 68, 975-984.  
21525645 D.de Sanctis, P.A.Tucker, and S.Panjikar (2011).
Additional phase information from UV damage of selenomethionine labelled proteins.
  J Synchrotron Radiat, 18, 374-380.  
21525646 R.M.Leal, G.P.Bourenkov, O.Svensson, D.Spruce, M.Guijarro, and A.N.Popov (2011).
Experimental procedure for the characterization of radiation damage in macromolecular crystals.
  J Synchrotron Radiat, 18, 381-386.  
20382994 G.P.Bourenkov, and A.N.Popov (2010).
Optimization of data collection taking radiation damage into account.
  Acta Crystallogr D Biol Crystallogr, 66, 409-419.  
21049050 J.M.Otero, M.A.Papadakis, D.B.Udatha, J.Nielsen, and G.Panagiotou (2010).
Yeast biological networks unfold the interplay of antioxidants, genome and phenotype, and reveal a novel regulator of the oxidative stress response.
  PLoS One, 5, e13606.  
20562876 M.Funabashi, Z.Yang, K.Nonaka, M.Hosobuchi, Y.Fujita, T.Shibata, X.Chi, and S.G.Van Lanen (2010).
An ATP-independent strategy for amide bond formation in antibiotic biosynthesis.
  Nat Chem Biol, 6, 581-586.  
19644688 T.Koseki, S.Fushinobu, Ardiansyah, H.Shirakawa, and M.Komai (2009).
Occurrence, properties, and applications of feruloyl esterases.
  Appl Microbiol Biotechnol, 84, 803-810.  
18378601 L.G.Ljungdahl (2008).
The cellulase/hemicellulase system of the anaerobic fungus Orpinomyces PC-2 and aspects of its applied use.
  Ann N Y Acad Sci, 1125, 308-321.  
  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.  
17103163 N.Palackal, C.S.Lyon, S.Zaidi, P.Luginbühl, P.Dupree, F.Goubet, J.L.Macomber, J.M.Short, G.P.Hazlewood, D.E.Robertson, and B.A.Steer (2007).
A multifunctional hybrid glycosyl hydrolase discovered in an uncultured microbial consortium from ruminant gut.
  Appl Microbiol Biotechnol, 74, 113-124.  
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
16128806 C.B.Faulds, R.Molina, R.Gonzalez, F.Husband, N.Juge, J.Sanz-Aparicio, and J.A.Hermoso (2005).
Probing the determinants of substrate specificity of a feruloyl esterase, AnFaeA, from Aspergillus niger.
  FEBS J, 272, 4362-4371.
PDB code: 2bjh
15681871 N.Tarbouriech, J.A.Prates, C.M.Fontes, and G.J.Davies (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.
PDB codes: 1wb4 1wb5 1wb6
14557261 F.Vincent, D.Yates, E.Garman, G.J.Davies, and J.A.Brannigan (2004).
The three-dimensional structure of the N-acetylglucosamine-6-phosphate deacetylase, NagA, from Bacillus subtilis: a member of the urease superfamily.
  J Biol Chem, 279, 2809-2816.
PDB codes: 1un7 2vhl
15103133 K.E.McAuley, A.Svendsen, S.A.Patkar, and K.S.Wilson (2004).
Structure of a feruloyl esterase from Aspergillus niger.
  Acta Crystallogr D Biol Crystallogr, 60, 878-887.
PDB codes: 1uwc 1uza
12831897 D.Shallom, and Y.Shoham (2003).
Microbial hemicellulases.
  Curr Opin Microbiol, 6, 219-228.  
12957952 K.Rumbold, P.Biely, M.Mastihubová, M.Gudelj, G.Gübitz, K.H.Robra, and B.A.Prior (2003).
Purification and properties of a feruloyl esterase involved in lignocellulose degradation by Aureobasidium pullulans.
  Appl Environ Microbiol, 69, 5622-5626.  
12716882 Y.Chen, and P.A.Rice (2003).
The role of the conserved Trp330 in Flp-mediated recombination. Functional and structural analysis.
  J Biol Chem, 278, 24800-24807.
PDB code: 1p4e
11937059 D.Nurizzo, T.Nagy, H.J.Gilbert, and G.J.Davies (2002).
The structural basis for catalysis and specificity of the Pseudomonas cellulosa alpha-glucuronidase, GlcA67A.
  Structure, 10, 547-556.
PDB codes: 1gqi 1gqj 1gqk 1gql
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.