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PDBsum entry 2xyl

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Hydrolase PDB id
2xyl
Jmol
Contents
Protein chain
312 a.a. *
Ligands
XYP-X2F
Waters ×122
* Residue conservation analysis
PDB id:
2xyl
Name: Hydrolase
Title: Cellulomonas fimi xylanase/cellulase complexed with 2-deoxy- 2-fluoro-xylobiose
Structure: Beta-1,4-glycanase. Chain: a. Fragment: catalytic domain. Synonym: cex, 1,4-beta-cellobiohydrolase. Engineered: yes
Source: Cellulomonas fimi. Organism_taxid: 1708. Expressed in: escherichia coli. Expression_system_taxid: 562
Resolution:
1.90Å     R-factor:   0.212     R-free:   0.260
Authors: V.Monem,C.Birsan,R.A.J.Warren,S.G.Withers,D.R.Rose
Key ref: V.Notenboom et al. (1998). Exploring the cellulose/xylan specificity of the beta-1,4-glycanase cex from Cellulomonas fimi through crystallography and mutation. Biochemistry, 37, 4751-4758. PubMed id: 9537990 DOI: 10.1021/bi9729211
Date:
20-Nov-97     Release date:   18-Mar-98    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
P07986  (GUX_CELFI) -  Exoglucanase/xylanase
Seq:
Struc:
484 a.a.
312 a.a.*
Key:    PfamA domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 3 residue positions (black crosses)

 Enzyme reactions 
   Enzyme class 1: 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.
   Enzyme class 2: E.C.3.2.1.91  - Cellulose 1,4-beta-cellobiosidase (non-reducing end).
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: Hydrolysis of 1,4-beta-D-glucosidic linkages in cellulose and cellotetraose, releasing cellobiose from the non-reducing ends of the chains.
Note, where more than one E.C. class is given (as above), each may correspond to a different protein domain or, in the case of polyprotein precursors, to a different mature protein.
 Gene Ontology (GO) functional annotation 
  GO annot!
  Biological process     carbohydrate metabolic process   1 term 
  Biochemical function     hydrolase activity, hydrolyzing O-glycosyl compounds     1 term  

 

 
DOI no: 10.1021/bi9729211 Biochemistry 37:4751-4758 (1998)
PubMed id: 9537990  
 
 
Exploring the cellulose/xylan specificity of the beta-1,4-glycanase cex from Cellulomonas fimi through crystallography and mutation.
V.Notenboom, C.Birsan, R.A.Warren, S.G.Withers, D.R.Rose.
 
  ABSTRACT  
 
The retaining beta-1,4-glycanase Cex from Cellulomonas fimi, a family 10 glycosyl hydrolase, hydrolyzes xylan 40-fold more efficiently than cellulose. To gain insight into the nature of its preference for xylan, we determined the crystal structure of the Cex catalytic domain (Cex-cd) trapped as its covalent 2-deoxy-2-fluoroxylobiosyl-enzyme intermediate to 1.9 A resolution. Together with the crystal structure of unliganded Cex-cd [White, A., et al. (1994) Biochemistry 33, 12546-12552] and the previously determined crystal structure of the covalent 2-deoxy-2-fluorocellobiosyl-Cex-cd intermediate [White, A., et al. (1996) Nat. Struct. Biol. 3, 149-154], this structure provides a convincing rationale for the observed substrate specificity in Cex. Two active site residues, Gln87 and Trp281, are found to sterically hinder the binding of glucosides and must rearrange to accommodate these substrates. Such rearrangements are not necessary for the binding of xylobiosides. The importance of this observation was tested by examining the catalytic behavior of the enzyme with Gln87 mutated to Met. This mutation had no measurable effect on substrate affinity or turnover number relative to the wild type enzyme, indicating that the Met side chain could accommodate the glucoside moiety as effectively as the wild type Gln residue. Subsequent mutagenesis studies will address the role of entropic versus enthalpic contributions to binding by introducing side chains that might be more rigid in the unliganded enzyme.
 

Literature references that cite this PDB file's key reference

  PubMed id Reference
17005414 M.Tesić, J.Wicki, D.K.Poon, S.G.Withers, and D.J.Douglas (2007).
Gas phase noncovalent protein complexes that retain solution binding properties: Binding of xylobiose inhibitors to the beta-1, 4 exoglucanase from cellulomonas fimi.
  J Am Soc Mass Spectrom, 18, 64-73.  
16397879 S.J.Williams, O.Hekmat, and S.G.Withers (2006).
Synthesis and testing of mechanism-based protein-profiling probes for retaining endo-glycosidases.
  Chembiochem, 7, 116-124.  
16688347 Y.W.Kim, D.T.Fox, O.Hekmat, T.Kantner, L.P.McIntosh, R.A.Warren, and S.G.Withers (2006).
Glycosynthase-based synthesis of xylo-oligosaccharides using an engineered retaining xylanase from Cellulomonas fimi.
  Org Biomol Chem, 4, 2025-2032.  
16085650 O.Hekmat, Y.W.Kim, S.J.Williams, S.He, and S.G.Withers (2005).
Active-site peptide "fingerprinting" of glycosidases in complex mixtures by mass spectrometry. Discovery of a novel retaining beta-1,4-glycanase in Cellulomonas fimi.
  J Biol Chem, 280, 35126-35135.  
14670951 G.Pell, L.Szabo, S.J.Charnock, H.Xie, T.M.Gloster, G.J.Davies, and H.J.Gilbert (2004).
Structural and biochemical analysis of Cellvibrio japonicus xylanase 10C: how variation in substrate-binding cleft influences the catalytic profile of family GH-10 xylanases.
  J Biol Chem, 279, 11777-11788.
PDB codes: 1us2 1us3
14597633 M.Hrmova, R.De Gori, B.J.Smith, A.Vasella, J.N.Varghese, and G.B.Fincher (2004).
Three-dimensional structure of the barley beta-D-glucan glucohydrolase in complex with a transition state mimic.
  J Biol Chem, 279, 4970-4980.
PDB code: 1lq2
15078885 S.Kaneko, H.Ichinose, Z.Fujimoto, A.Kuno, K.Yura, M.Go, H.Mizuno, I.Kusakabe, and H.Kobayashi (2004).
Structure and function of a family 10 beta-xylanase chimera of Streptomyces olivaceoviridis E-86 FXYN and Cellulomonas fimi Cex.
  J Biol Chem, 279, 26619-26626.
PDB code: 1v6y
12925805 Ihsanawati, T.Kumasaka, T.Kaneko, C.Morokuma, S.Nakamura, and N.Tanaka (2003).
Crystallization and preliminary X-ray studies of xylanase 10B from Thermotoga maritima.
  Acta Crystallogr D Biol Crystallogr, 59, 1659-1661.  
14517232 K.Hövel, D.Shallom, K.Niefind, V.Belakhov, G.Shoham, T.Baasov, Y.Shoham, and D.Schomburg (2003).
Crystal structure and snapshots along the reaction pathway of a family 51 alpha-L-arabinofuranosidase.
  EMBO J, 22, 4922-4932.
PDB codes: 1pz2 1pz3 1qw8 1qw9
12039744 K.C.Raj, L.A.Talarico, L.O.Ingram, and J.A.Maupin-Furlow (2002).
Cloning and characterization of the Zymobacter palmae pyruvate decarboxylase gene (pdc) and comparison to bacterial homologues.
  Appl Environ Microbiol, 68, 2869-2876.  
16233206 Y.Honda, M.Kitaoka, K.Sakka, K.Ohmiya, and K.Hayashi (2002).
An investigation of the pH-activity relationships of Cex, a family 10 xylanase from Cellulomonas fimi: xylan inhibition and the influence of nitro-substituted aryl-beta-D-xylobiosides on xylanase activity.
  J Biosci Bioeng, 93, 313-317.  
11709165 M.Hrmova, J.N.Varghese, R.De Gori, B.J.Smith, H.Driguez, and G.B.Fincher (2001).
Catalytic mechanisms and reaction intermediates along the hydrolytic pathway of a plant beta-D-glucan glucohydrolase.
  Structure, 9, 1005-1016.
PDB codes: 1ieq 1iev 1iew 1iex
11118593 M.M.Ahsan, S.Kaneko, Q.Wang, K.Yura, M.Go, and K.Hayash (2001).
Capacity of thermomonospora alba XylA to impart thermostability in family F/10 chimeric xylanases.
  Enzyme Microb Technol, 28, 8.  
  10752613 G.P.Connelly, S.G.Withers, and L.P.McIntosh (2000).
Analysis of the dynamic properties of Bacillus circulans xylanase upon formation of a covalent glycosyl-enzyme intermediate.
  Protein Sci, 9, 512-524.  
11042447 U.M.Unligil, and J.M.Rini (2000).
Glycosyltransferase structure and mechanism.
  Curr Opin Struct Biol, 10, 510-517.  
11032794 U.M.Unligil, S.Zhou, S.Yuwaraj, M.Sarkar, H.Schachter, and J.M.Rini (2000).
X-ray crystal structure of rabbit N-acetylglucosaminyltransferase I: catalytic mechanism and a new protein superfamily.
  EMBO J, 19, 5269-5280.
PDB codes: 1fo8 1fo9 1foa
10995222 V.Notenboom, S.J.Williams, R.Hoos, S.G.Withers, and D.R.Rose (2000).
Detailed structural analysis of glycosidase/inhibitor interactions: complexes of Cex from Cellulomonas fimi with xylobiose-derived aza-sugars.
  Biochemistry, 39, 11553-11563.
PDB codes: 1fh7 1fh8 1fh9 1fhd
10381409 E.Sabini, G.Sulzenbacher, M.Dauter, Z.Dauter, P.L.Jørgensen, M.Schülein, C.Dupont, G.J.Davies, and K.S.Wilson (1999).
Catalysis and specificity in enzymatic glycoside hydrolysis: a 2,5B conformation for the glycosyl-enzyme intermediate revealed by the structure of the Bacillus agaradhaerens family 11 xylanase.
  Chem Biol, 6, 483-492.
PDB codes: 1h4g 1h4h 1qh6 1qh7
10220321 G.Sidhu, S.G.Withers, N.T.Nguyen, L.P.McIntosh, L.Ziser, and G.D.Brayer (1999).
Sugar ring distortion in the glycosyl-enzyme intermediate of a family G/11 xylanase.
  Biochemistry, 38, 5346-5354.
PDB codes: 1bvv 2bvv
10200171 G.Sulzenbacher, L.F.Mackenzie, K.S.Wilson, S.G.Withers, C.Dupont, and G.J.Davies (1999).
The crystal structure of a 2-fluorocellotriosyl complex of the Streptomyces lividans endoglucanase CelB2 at 1.2 A resolution.
  Biochemistry, 38, 4826-4833.
PDB code: 2nlr
10872458 H.D.Ly, and S.G.Withers (1999).
Mutagenesis of glycosidases.
  Annu Rev Biochem, 68, 487-522.  
9818257 E.A.Bayer, H.Chanzy, R.Lamed, and Y.Shoham (1998).
Cellulose, cellulases and cellulosomes.
  Curr Opin Struct Biol, 8, 548-557.  
9718293 G.J.Davies, L.Mackenzie, A.Varrot, M.Dauter, A.M.Brzozowski, M.Schülein, and S.G.Withers (1998).
Snapshots along an enzymatic reaction coordinate: analysis of a retaining beta-glycoside hydrolase.
  Biochemistry, 37, 11707-11713.
PDB codes: 3a3h 4a3h 5a3h 6a3h 7a3h
9822697 S.J.Charnock, T.D.Spurway, H.Xie, M.H.Beylot, R.Virden, R.A.Warren, G.P.Hazlewood, and H.J.Gilbert (1998).
The topology of the substrate binding clefts of glycosyl hydrolase family 10 xylanases are not conserved.
  J Biol Chem, 273, 32187-32199.  
9731776 V.Notenboom, C.Birsan, M.Nitz, D.R.Rose, R.A.Warren, and S.G.Withers (1998).
Insights into transition state stabilization of the beta-1,4-glycosidase Cex by covalent intermediate accumulation in active site mutants.
  Nat Struct Biol, 5, 812-818.
PDB code: 2his
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.