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PDBsum entry 1exp

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protein ligands links
Hydrolase PDB id
1exp
Jmol
Contents
Protein chain
312 a.a. *
Ligands
BGC-G2F
Waters ×189
* Residue conservation analysis
PDB id:
1exp
Name: Hydrolase
Title: Beta-1,4-glycanase cex-cd
Structure: Beta-1,4-d-glycanase cex-cd. Chain: a. Fragment: catalytically active domain. Synonym: cellobiohydrolase/xylanase b. Engineered: yes
Source: Cellulomonas fimi. Organism_taxid: 1708. Atcc: atcc 484. Expressed in: escherichia coli. Expression_system_taxid: 562.
Resolution:
1.80Å     R-factor:   0.208     R-free:   0.283
Authors: A.White,D.Tull,K.L.Johns,S.G.Withers,D.R.Rose
Key ref: A.White et al. (1996). Crystallographic observation of a covalent catalytic intermediate in a beta-glycosidase. Nat Struct Biol, 3, 149-154. PubMed id: 8564541
Date:
11-Jan-96     Release date:   27-Jan-97    
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  

 

 
Nat Struct Biol 3:149-154 (1996)
PubMed id: 8564541  
 
 
Crystallographic observation of a covalent catalytic intermediate in a beta-glycosidase.
A.White, D.Tull, K.Johns, S.G.Withers, D.R.Rose.
 
  ABSTRACT  
 
The three-dimensional structure of a catalytically competent glycosyl-enzyme intermediate of a retaining beta-1,4-glycanase has been determined at a resolution of 1.8 A by X-ray diffraction. A fluorinated slow substrate forms an alpha-D-glycopyranosyl linkage to one of the two invariant carboxylates, Glu 233, as supported in solution by 19F-NMR studies. The resulting ester linkage is coplanar with the cyclic oxygen of the proximal saccharide and is inferred to form a strong hydrogen bond with the 2-hydroxyl of that saccharide unit in natural substrates. The active-site architecture of this covalent intermediate gives insights into both the classical double-displacement catalytic mechanism and the basis for the enzyme's specificity.
 

Literature references that cite this PDB file's key reference

  PubMed id Reference
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.  
20921614 W.Zhang, A.G.Oliver, and A.S.Serianni (2010).
4-Deoxy-4-fluoro-β-D-glucopyranose.
  Acta Crystallogr C, 66, o496-o498.  
19279191 R.Suzuki, Z.Fujimoto, S.Ito, S.Kawahara, S.Kaneko, K.Taira, T.Hasegawa, and A.Kuno (2009).
Crystallographic snapshots of an entire reaction cycle for a retaining xylanase from Streptomyces olivaceoviridis E-86.
  J Biochem, 146, 61-70.
PDB codes: 2d1z 2d20 2d22 2d23 2d24
  19727327 D.B.Berkowitz, K.R.Karukurichi, R.de la Salud-Bea, D.L.Nelson, and C.D.McCune (2008).
Use of Fluorinated Functionality in Enzyme Inhibitor Development: Mechanistic and Analytical Advantages.
  J Fluor Chem, 129, 731-742.  
17274025 A.Babakhani, A.A.Gorfe, J.Gullingsrud, J.E.Kim, and J.Andrew McCammon (2007).
Peptide insertion, positioning, and stabilization in a membrane: insight from an all-atom molecular dynamics simulation.
  Biopolymers, 85, 490-497.  
17887954 B.Sterner, R.Singh, and B.Berger (2007).
Predicting and annotating catalytic residues: an information theoretic approach.
  J Comput Biol, 14, 1058-1073.  
16539386 J.Yu, and R.P.Mason (2006).
Synthesis and characterization of novel lacZ gene reporter molecules: detection of beta-galactosidase activity by 19F nuclear magnetic resonance of polyglycosylated fluorinated vitamin B6.
  J Med Chem, 49, 1991-1999.  
16972282 Z.Zhou, M.Bates, and J.D.Madura (2006).
Structure modeling, ligand binding, and binding affinity calculation (LR-MM-PBSA) of human heparanase for inhibition and drug design.
  Proteins, 65, 580-592.  
16247799 Ihsanawati, T.Kumasaka, T.Kaneko, C.Morokuma, R.Yatsunami, T.Sato, S.Nakamura, and N.Tanaka (2005).
Structural basis of the substrate subsite and the highly thermal stability of xylanase 10B from Thermotoga maritima MSB8.
  Proteins, 61, 999.
PDB codes: 1vbr 1vbu
14668328 G.Pell, E.J.Taylor, T.M.Gloster, J.P.Turkenburg, C.M.Fontes, L.M.Ferreira, T.Nagy, S.J.Clark, G.J.Davies, and H.J.Gilbert (2004).
The mechanisms by which family 10 glycoside hydrolases bind decorated substrates.
  J Biol Chem, 279, 9597-9605.
PDB codes: 1uqy 1uqz 1ur1 1ur2
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
15062085 J.Allouch, W.Helbert, B.Henrissat, and M.Czjzek (2004).
Parallel substrate binding sites in a beta-agarase suggest a novel mode of action on double-helical agarose.
  Structure, 12, 623-632.
PDB code: 1urx
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
15317808 V.Vathipadiekal, and M.Rao (2004).
Inhibition of 1,4-beta-D-xylan xylanohydrolase by the specific aspartic protease inhibitor pepstatin: probing the two-step inhibition mechanism.
  J Biol Chem, 279, 47024-47033.  
15252054 Y.W.Kim, S.S.Lee, R.A.Warren, and S.G.Withers (2004).
Directed evolution of a glycosynthase from Agrobacterium sp. increases its catalytic activity dramatically and expands its substrate repertoire.
  J Biol Chem, 279, 42787-42793.  
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
11844793 C.Dash, V.Vathipadiekal, S.P.George, and M.Rao (2002).
Slow-tight binding inhibition of xylanase by an aspartic protease inhibitor: kinetic parameters and conformational changes that determine the affinity and selectivity of the bifunctional nature of the inhibitor.
  J Biol Chem, 277, 17978-17986.  
12146939 D.J.Vocadlo, J.Wicki, K.Rupitz, and S.G.Withers (2002).
A case for reverse protonation: identification of Glu160 as an acid/base catalyst in Thermoanaerobacterium saccharolyticum beta-xylosidase and detailed kinetic analysis of a site-directed mutant.
  Biochemistry, 41, 9736-9746.  
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
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.  
11522797 B.L.Mark, D.J.Vocadlo, D.Zhao, S.Knapp, S.G.Withers, and M.N.James (2001).
Biochemical and structural assessment of the 1-N-azasugar GalNAc-isofagomine as a potent family 20 beta-N-acetylhexosaminidase inhibitor.
  J Biol Chem, 276, 42131-42137.
PDB code: 1jak
11358691 C.Mayer, D.L.Jakeman, M.Mah, G.Karjala, L.Gal, R.A.Warren, and S.G.Withers (2001).
Directed evolution of new glycosynthases from Agrobacterium beta-glucosidase: a general screen to detect enzymes for oligosaccharide synthesis.
  Chem Biol, 8, 437-443.  
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
11006547 C.S.Rye, and S.G.Withers (2000).
Glycosidase mechanisms.
  Curr Opin Chem Biol, 4, 573-580.  
10679381 G.A.Petsko, and D.Ringe (2000).
Observation of unstable species in enzyme-catalyzed transformations using protein crystallography.
  Curr Opin Chem Biol, 4, 89-94.  
  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.  
11106409 J.C.Arribas, A.G.Herrero, M.Martín-Lomas, F.J.Cañada, S.He, and S.G.Withers (2000).
Differential mechanism-based labeling and unequivocal activity assignment of the two active sites of intestinal lactase/phlorizin hydrolase.
  Eur J Biochem, 267, 6996-7005.  
11025547 L.L.Leggio, J.Jenkins, G.W.Harris, and R.W.Pickersgill (2000).
X-ray crystallographic study of xylopentaose binding to Pseudomonas fluorescens xylanase A.
  Proteins, 41, 362-373.
PDB code: 1e5n
11003139 M.D.Burkart, S.P.Vincent, A.Düffels, B.W.Murray, S.V.Ley, and C.H.Wong (2000).
Chemo-enzymatic synthesis of fluorinated sugar nucleotide: useful mechanistic probes for glycosyltransferases.
  Bioorg Med Chem, 8, 1937-1946.  
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
10872458 H.D.Ly, and S.G.Withers (1999).
Mutagenesis of glycosidases.
  Annu Rev Biochem, 68, 487-522.  
10446364 I.Connerton, N.Cummings, G.W.Harris, P.Debeire, and C.Breton (1999).
A single domain thermophilic xylanase can bind insoluble xylan: evidence for surface aromatic clusters.
  Biochim Biophys Acta, 1433, 110-121.  
10570988 Y.Sato, Y.Niimura, K.Yura, and M.Go (1999).
Module-intron correlation and intron sliding in family F/10 xylanase genes.
  Gene, 238, 93.  
  9792094 A.Schmidt, A.Schlacher, W.Steiner, H.Schwab, and C.Kratky (1998).
Structure of the xylanase from Penicillium simplicissimum.
  Protein Sci, 7, 2081-2088.
PDB code: 1bg4
9817845 M.Hilge, S.M.Gloor, W.Rypniewski, O.Sauer, T.D.Heightman, W.Zimmermann, K.Winterhalter, and K.Piontek (1998).
High-resolution native and complex structures of thermostable beta-mannanase from Thermomonospora fusca - substrate specificity in glycosyl hydrolase family 5.
  Structure, 6, 1433-1444.
PDB codes: 1bqc 2man 3man
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
9345622 A.White, and D.R.Rose (1997).
Mechanism of catalysis by retaining beta-glycosyl hydrolases.
  Curr Opin Struct Biol, 7, 645-651.  
9345621 B.Henrissat, and G.Davies (1997).
Structural and sequence-based classification of glycoside hydrolases.
  Curr Opin Struct Biol, 7, 637-644.  
9242666 R.Kuroki, Y.Ito, Y.Kato, and T.Imoto (1997).
A covalent enzyme-substrate adduct in a mutant hen egg white lysozyme (D52E).
  J Biol Chem, 272, 19976-19981.  
9312086 S.He, and S.G.Withers (1997).
Assignment of sweet almond beta-glucosidase as a family 1 glycosidase and identification of its active site nucleophile.
  J Biol Chem, 272, 24864-24867.  
9195886 W.P.Burmeister, S.Cottaz, H.Driguez, R.Iori, S.Palmieri, and B.Henrissat (1997).
The crystal structures of Sinapis alba myrosinase and a covalent glycosyl-enzyme intermediate provide insights into the substrate recognition and active-site machinery of an S-glycosidase.
  Structure, 5, 663-675.
PDB codes: 1myr 2myr
8564531 A.J.Kirby (1996).
Illuminating the ancient retainer.
  Nat Struct Biol, 3, 107-108.  
8662946 A.Reddy, and F.Maley (1996).
Studies on identifying the catalytic role of Glu-204 in the active site of yeast invertase.
  J Biol Chem, 271, 13953-13957.  
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.