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PDBsum entry 2exo

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Hydrolase (o-glycosyl) PDB id
2exo
Jmol
Contents
Protein chain
312 a.a. *
Waters ×65
* Residue conservation analysis
PDB id:
2exo
Name: Hydrolase (o-glycosyl)
Title: Crystal structure of the catalytic domain of the beta-1,4- glycanase cex from cellulomonas fimi
Structure: Exo-1,4-beta-d-glycanase. Chain: a. Engineered: yes
Source: Cellulomonas fimi. Organism_taxid: 1708
Resolution:
1.80Å     R-factor:   0.213     R-free:   0.266
Authors: A.White,S.G.Withers,N.R.Gilkes,D.R.Rose
Key ref:
A.White et al. (1994). Crystal structure of the catalytic domain of the beta-1,4-glycanase cex from Cellulomonas fimi. Biochemistry, 33, 12546-12552. PubMed id: 7918478 DOI: 10.1021/bi00208a003
Date:
11-Jul-94     Release date:   07-Feb-95    
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/bi00208a003 Biochemistry 33:12546-12552 (1994)
PubMed id: 7918478  
 
 
Crystal structure of the catalytic domain of the beta-1,4-glycanase cex from Cellulomonas fimi.
A.White, S.G.Withers, N.R.Gilkes, D.R.Rose.
 
  ABSTRACT  
 
beta-1,4-Glycanases, principally cellulases and xylanases, are responsible for the hydrolysis of plant biomass. The bifunctional beta-1,4-xylanase/glucanase Cex from the bacterium Cellulomonas fimi, one of a large family of cellulases/xylanases, depolymerizes oligosaccharides and releases a disaccharide unit from the substrate nonreducing end. Hydrolysis occurs with net retention of the anomeric configuration of the sugar through a double-displacement mechanism involving a covalent glycosyl-enzyme intermediate. The active site nucleophile, Glu233, has been unambiguously identified by trapping of such an intermediate [Tull et al. (1991) J. Biol. Chem. 266, 15621-15625] and the acid/base catalyst, Glu127, by detailed kinetic analysis of mutants [MacLeod et al. (1994) Biochemistry 33, 6371-6376]. However, little is known about the enzyme's overall folding and its active site architecture. We report here the high-resolution crystal structure of the catalytic domain of Cex. The atomic structure refinement results in a model that includes 2400 protein atoms and 45 water molecules, with an R-factor of 0.217 for data extending to 1.8-A resolution. The protein forms an eight-parallel-stranded alpha/beta-barrel, which is a novel folding pattern for a microbial beta-glycanase. The active site, inferred from the location of Glu233, Glu127, and other conserved residues, is an open cleft on the carboxy-terminal end of the alpha/beta-barrel. An extensive hydrogen-bonding network stabilizes the ionization states of the key residues; in particular, the Asp235-His205-Glu233 hydrogen-bonding network may play a role in modulating the ionization state of Glu233 and in controlling local charge balance during the reaction.
 

Literature references that cite this PDB file's key reference

  PubMed id Reference
18379842 O.Pérez-Avalos, L.M.Sánchez-Herrera, L.M.Salgado, and T.Ponce-Noyola (2008).
A bifunctional endoglucanase/endoxylanase from Cellulomonas flavigena with potential use in industrial processes at different pH.
  Curr Microbiol, 57, 39-44.  
17121820 D.K.Poon, S.G.Withers, and L.P.McIntosh (2007).
Direct demonstration of the flexibility of the glycosylated proline-threonine linker in the Cellulomonas fimi Xylanase Cex through NMR spectroscopic analysis.
  J Biol Chem, 282, 2091-2100.  
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.  
17642511 V.Solomon, A.Teplitsky, S.Shulami, G.Zolotnitsky, Y.Shoham, and G.Shoham (2007).
Structure-specificity relationships of an intracellular xylanase from Geobacillus stearothermophilus.
  Acta Crystallogr D Biol Crystallogr, 63, 845-859.
PDB code: 2q8x
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
16717424 M.Sugimura, M.Nishimoto, and M.Kitaoka (2006).
Characterization of glycosynthase mutants derived from glycoside hydrolase family 10 xylanases.
  Biosci Biotechnol Biochem, 70, 1210-1217.  
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
  16511146 K.Manikandan, A.Bhardwaj, A.Ghosh, V.S.Reddy, and S.Ramakumar (2005).
Crystallization and preliminary X-ray study of a family 10 alkali-thermostable xylanase from alkalophilic Bacillus sp. strain NG-27.
  Acta Crystallogr Sect F Struct Biol Cryst Commun, 61, 747-749.  
15914908 M.Nishimoto, M.Kitaoka, S.Fushinobu, and K.Hayashi (2005).
The role of conserved arginine residue in loop 4 of glycoside hydrolase family 10 xylanases.
  Biosci Biotechnol Biochem, 69, 904-910.  
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.  
15652973 T.Collins, C.Gerday, and G.Feller (2005).
Xylanases, xylanase families and extremophilic xylanases.
  FEMS Microbiol Rev, 29, 3.  
  16511010 Z.Fujimoto, K.Usui, Y.Kondo, K.Yasui, K.Kawai, and T.Suzuki (2005).
Crystallization and preliminary X-ray crystallographic studies of XynX, a family 10 xylanase from Aeromonas punctata ME-1.
  Acta Crystallogr Sect F Struct Biol Cryst Commun, 61, 255-257.  
15103129 A.Teplitsky, A.Mechaly, V.Stojanoff, G.Sainz, G.Golan, H.Feinberg, R.Gilboa, V.Reiland, G.Zolotnitsky, D.Shallom, A.Thompson, Y.Shoham, and G.Shoham (2004).
Structure determination of the extracellular xylanase from Geobacillus stearothermophilus by selenomethionyl MAD phasing.
  Acta Crystallogr D Biol Crystallogr, 60, 836-848.
PDB code: 1hiz
15277671 G.Zolotnitsky, U.Cogan, N.Adir, V.Solomon, G.Shoham, and Y.Shoham (2004).
Mapping glycoside hydrolase substrate subsites by isothermal titration calorimetry.
  Proc Natl Acad Sci U S A, 101, 11275-11280.
PDB codes: 1r85 1r87
14993688 M.Bar, G.Golan, M.Nechama, G.Zolotnitsky, Y.Shoham, and G.Shoham (2004).
A new crystal form of XT6 enables a significant improvement of its diffraction quality and resolution.
  Acta Crystallogr D Biol Crystallogr, 60, 545-549.  
14747719 M.Nishimoto, S.Fushinobu, A.Miyanaga, T.Wakagi, H.Shoun, K.Sakka, K.Ohmiya, S.Nirasawa, M.Kitaoka, and K.Hayashi (2004).
Crystallization and preliminary X-ray analysis of xylanase B from Clostridium stercorarium.
  Acta Crystallogr D Biol Crystallogr, 60, 342-343.  
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
15576784 S.O.Han, H.Yukawa, M.Inui, and R.H.Doi (2004).
Isolation and expression of the xynB gene and its product, XynB, a consistent component of the Clostridium cellulovorans cellulosome.
  J Bacteriol, 186, 8347-8355.  
15166216 S.Sansen, C.J.De Ranter, K.Gebruers, K.Brijs, C.M.Courtin, J.A.Delcour, and A.Rabijns (2004).
Structural basis for inhibition of Aspergillus niger xylanase by triticum aestivum xylanase inhibitor-I.
  J Biol Chem, 279, 36022-36028.
PDB codes: 1t6e 1t6g
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.  
14670957 Z.Fujimoto, S.Kaneko, A.Kuno, H.Kobayashi, I.Kusakabe, and H.Mizuno (2004).
Crystal structures of decorated xylooligosaccharides bound to a family 10 xylanase from Streptomyces olivaceoviridis E-86.
  J Biol Chem, 279, 9606-9614.
PDB codes: 1v6u 1v6v 1v6w 1v6x
12876348 A.Canals, M.C.Vega, F.X.Gomis-Rüth, M.Díaz, R.I.Santamaría R, and M.Coll (2003).
Structure of xylanase Xys1delta from Streptomyces halstedii.
  Acta Crystallogr D Biol Crystallogr, 59, 1447-1453.
PDB code: 1nq6
12486727 M.Roberge, R.N.Lewis, F.Shareck, R.Morosoli, D.Kluepfel, C.Dupont, and R.N.McElhaney (2003).
Differential scanning calorimetric, circular dichroism, and Fourier transform infrared spectroscopic characterization of the thermal unfolding of xylanase A from Streptomyces lividans.
  Proteins, 50, 341-354.  
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.  
  16233324 M.Nishimoto, M.Kitaoka, and K.Hayashi (2002).
Employing chimeric xylanases to identify regions of an alkaline xylanase participating in enzyme activity at basic pH.
  J Biosci Bioeng, 94, 395-400.  
11958335 S.Subramaniyan, and P.Prema (2002).
Biotechnology of microbial xylanases: enzymology, molecular biology, and application.
  Crit Rev Biotechnol, 22, 33-64.  
11526340 E.Sabini, K.S.Wilson, S.Danielsen, M.Schülein, and G.J.Davies (2001).
Oligosaccharide binding to family 11 xylanases: both covalent intermediate and mutant product complexes display (2,5)B conformations at the active centre.
  Acta Crystallogr D Biol Crystallogr, 57, 1344-1347.
PDB codes: 1h4g 1h4h
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.  
11358504 S.P.George, and M.B.Rao (2001).
Conformation and polarity of the active site of xylanase I from Thermomonospora sp. as deduced by fluorescent chemoaffinity labeling. Site and significance of a histidine residue.
  Eur J Biochem, 268, 2881-2888.  
11223515 S.Teixeira, L.Lo Leggio, R.Pickersgill, and C.Cardin (2001).
Anisotropic refinement of the structure of Thermoascus aurantiacus xylanase I.
  Acta Crystallogr D Biol Crystallogr, 57, 385-392.
PDB code: 1fxm
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
11087953 N.Panasik, J.E.Brenchley, and G.K.Farber (2000).
Distributions of structural features contributing to thermostability in mesophilic and thermophilic alpha/beta barrel glycosyl hydrolases.
  Biochim Biophys Acta, 1543, 189-201.  
10617668 S.Armand, M.J.Wagemaker, P.Sánchez-Torres, H.C.Kester, Y.van Santen, B.W.Dijkstra, J.Visser, and J.A.Benen (2000).
The active site topology of Aspergillus niger endopolygalacturonase II as studied by site-directed mutagenesis.
  J Biol Chem, 275, 691-696.  
  10210191 D.H.Juers, R.E.Huber, and B.W.Matthews (1999).
Structural comparisons of TIM barrel proteins suggest functional and evolutionary relationships between beta-galactosidase and other glycohydrolases.
  Protein Sci, 8, 122-136.  
10409823 L.Lo Leggio, S.Kalogiannis, M.K.Bhat, and R.W.Pickersgill (1999).
High resolution structure and sequence of T. aurantiacus xylanase I: implications for the evolution of thermostability in family 10 xylanases and enzymes with (beta)alpha-barrel architecture.
  Proteins, 36, 295-306.
PDB codes: 1tax 1tix
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
9692186 K.Inagaki, K.Nakahira, K.Mukai, T.Tamura, and H.Tanaka (1998).
Gene cloning and characterization of an acidic xylanase from Acidobacterium capsulatum.
  Biosci Biotechnol Biochem, 62, 1061-1067.  
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
  9251186 A.Ruiz-Arribas, P.Sánchez, J.J.Calvete, M.Raida, J.M.Fernández-Abalos, and R.I.Santamaría (1997).
Analysis of xysA, a gene from Streptomyces halstedii JM8 that encodes a 45-kilodalton modular xylanase, Xys1.
  Appl Environ Microbiol, 63, 2983-2988.  
9345622 A.White, and D.R.Rose (1997).
Mechanism of catalysis by retaining beta-glycosyl hydrolases.
  Curr Opin Struct Biol, 7, 645-651.  
  9209040 H.Hayashi, K.I.Takagi, M.Fukumura, T.Kimura, S.Karita, K.Sakka, and K.Ohmiya (1997).
Sequence of xynC and properties of XynC, a major component of the Clostridium thermocellum cellulosome.
  J Bacteriol, 179, 4246-4253.  
14538158 M.K.Bhat, and S.Bhat (1997).
Cellulose degrading enzymes and their potential industrial applications.
  Biotechnol Adv, 15, 583-620.  
14538714 P.Chaudhary, N.N.Kumar, and D.N.Deobagkar (1997).
The glucanases of Cellulomonas.
  Biotechnol Adv, 15, 315-331.  
9006940 S.J.Charnock, J.H.Lakey, R.Virden, N.Hughes, M.L.Sinnott, G.P.Hazlewood, R.Pickersgill, and H.J.Gilbert (1997).
Key residues in subsite F play a critical role in the activity of Pseudomonas fluorescens subspecies cellulosa xylanase A against xylooligosaccharides but not against highly polymeric substrates such as xylan.
  J Biol Chem, 272, 2942-2951.  
9211898 T.D.Spurway, C.Morland, A.Cooper, I.Sumner, G.P.Hazlewood, A.G.O'Donnell, R.W.Pickersgill, and H.J.Gilbert (1997).
Calcium protects a mesophilic xylanase from proteinase inactivation and thermal unfolding.
  J Biol Chem, 272, 17523-17530.  
8564541 A.White, D.Tull, K.Johns, S.G.Withers, and D.R.Rose (1996).
Crystallographic observation of a covalent catalytic intermediate in a beta-glycosidase.
  Nat Struct Biol, 3, 149-154.
PDB code: 1exp
8785441 T.W.Jeffries (1996).
Biochemistry and genetics of microbial xylanases.
  Curr Opin Biotechnol, 7, 337-342.  
7624375 B.Henrissat, I.Callebaut, S.Fabrega, P.Lehn, J.P.Mornon, and G.Davies (1995).
Conserved catalytic machinery and the prediction of a common fold for several families of glycosyl hydrolases.
  Proc Natl Acad Sci U S A, 92, 7090-7094.  
8535789 C.Wiesmann, G.Beste, W.Hengstenberg, and G.E.Schulz (1995).
The three-dimensional structure of 6-phospho-beta-galactosidase from Lactococcus lactis.
  Structure, 3, 961-968.
PDB code: 1pbg
7664125 R.Dominguez, H.Souchon, S.Spinelli, Z.Dauter, K.S.Wilson, S.Chauvaux, P.Béguin, and P.M.Alzari (1995).
A common protein fold and similar active site in two distinct families of beta-glycanases.
  Nat Struct Biol, 2, 569-576.
PDB codes: 1cec 1xyz
  7795519 S.G.Withers, and R.Aebersold (1995).
Approaches to labeling and identification of active site residues in glycosidases.
  Protein Sci, 4, 361-372.  
8535787 V.Ducros, M.Czjzek, A.Belaich, C.Gaudin, H.P.Fierobe, J.P.Belaich, G.J.Davies, and R.Haser (1995).
Crystal structure of the catalytic domain of a bacterial cellulase belonging to family 5.
  Structure, 3, 939-949.
PDB code: 1edg
7712292 J.D.McCarter, and S.G.Withers (1994).
Mechanisms of enzymatic glycoside hydrolysis.
  Curr Opin Struct Biol, 4, 885-892.  
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 code is shown on the right.