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PDBsum entry 1cec

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Hydrolase (glycosyl) PDB id
1cec
Jmol
Contents
Protein chain
331 a.a. *
Waters ×165
* Residue conservation analysis
PDB id:
1cec
Name: Hydrolase (glycosyl)
Title: A common protein fold and similar active site in two distinct families of beta-glycanases
Structure: Endoglucanase celc. Chain: a. Synonym: egc, cellulase celc, endo-1\,4-beta-glucanase celc. Engineered: yes. Other_details: cellulase family a/5
Source: Clostridium thermocellum. Organism_taxid: 1515. Strain: ncib 10682. Gene: mc1061. Expressed in: escherichia coli. Expression_system_taxid: 562.
Resolution:
2.15Å     R-factor:   0.168     R-free:   0.215
Authors: P.M.Alzari,R.Dominguez
Key ref: R.Dominguez et al. (1995). A common protein fold and similar active site in two distinct families of beta-glycanases. Nat Struct Biol, 2, 569-576. PubMed id: 7664125
Date:
07-Jun-95     Release date:   29-Jan-96    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
P0C2S3  (GUNC_CLOTM) -  Endoglucanase C
Seq:
Struc:
343 a.a.
331 a.a.*
Key:    PfamA domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 1 residue position (black cross)

 Enzyme reactions 
   Enzyme class: E.C.3.2.1.4  - Cellulase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: Endohydrolysis of 1,4-beta-D-glucosidic linkages in cellulose, lichenin and cereal beta-D-glucans.
 Gene Ontology (GO) functional annotation 
  GO annot!
  Biological process     metabolic process   4 terms 
  Biochemical function     hydrolase activity     4 terms  

 

 
Nat Struct Biol 2:569-576 (1995)
PubMed id: 7664125  
 
 
A common protein fold and similar active site in two distinct families of beta-glycanases.
R.Dominguez, H.Souchon, S.Spinelli, Z.Dauter, K.S.Wilson, S.Chauvaux, P.Béguin, P.M.Alzari.
 
  ABSTRACT  
 
The structure of Clostridium thermocellum endoglucanase CelC, a member of the largest cellulase family (family A), has been determined at 2.15 A resolution. The protein folds into an (alpha/beta)8 barrel, with a deep active-site cleft generated by the insertion of a helical subdomain. The structure of the catalytic core of xylanase XynZ, which belongs to xylanase family F, has been determined at 1.4 A resolution. In spite of significant differences in substrate specificity and structure (including the absence of the helical subdomain), the general polypeptide folding pattern, architecture of the active site and catalytic mechanism of XynZ and CelC are similar, suggesting a common evolutionary origin.
 

Literature references that cite this PDB file's key reference

  PubMed id Reference
  20944220 P.J.Turnbaugh, B.Henrissat, and J.I.Gordon (2010).
Viewing the human microbiome through three-dimensional glasses: integrating structural and functional studies to better define the properties of myriad carbohydrate-active enzymes.
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19666559 A.Dorléans, B.Gigant, R.B.Ravelli, P.Mailliet, V.Mikol, and M.Knossow (2009).
Variations in the colchicine-binding domain provide insight into the structural switch of tubulin.
  Proc Natl Acad Sci U S A, 106, 13775-13779.
PDB codes: 3hkb 3hkc 3hkd 3hke
  19255469 B.Zheng, W.Yang, Y.Wang, Y.Feng, and Z.Lou (2009).
Crystallization and preliminary crystallographic analysis of thermophilic cellulase from Fervidobacterium nodosum Rt17-B1.
  Acta Crystallogr Sect F Struct Biol Cryst Commun, 65, 219-222.  
  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.  
16428847 B.Al Balaa, J.Wouters, S.Dogne, C.Rossini, J.M.Schaus, E.Depiereux, J.Vandenhaute, and I.Housen (2006).
Identification, cloning, and expression of the Scytalidium acidophilum XYL1 gene encoding for an acidophilic xylanase.
  Biosci Biotechnol Biochem, 70, 269-272.  
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.  
15659364 F.De Lemos Esteves, T.Gouders, J.Lamotte-Brasseur, S.Rigali, and J.M.Frère (2005).
Improving the alkalophilic performances of the Xyl1 xylanase from Streptomyces sp. S38: structural comparison and mutational analysis.
  Protein Sci, 14, 292-302.  
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.  
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
15340924 K.B.Murray, W.R.Taylor, and J.M.Thornton (2004).
Toward the detection and validation of repeats in protein structure.
  Proteins, 57, 365-380.  
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
12475991 F.Van Petegem, T.Collins, M.A.Meuwis, C.Gerday, G.Feller, and J.Van Beeumen (2003).
The structure of a cold-adapted family 8 xylanase at 1.3 A resolution. Structural adaptations to cold and investgation of the active site.
  J Biol Chem, 278, 7531-7539.
PDB codes: 1h12 1h13 1h14
12089151 T.Collins, M.A.Meuwis, I.Stals, M.Claeyssens, G.Feller, and C.Gerday (2002).
A novel family 8 xylanase, functional and physicochemical characterization.
  J Biol Chem, 277, 35133-35139.  
10671457 D.L.Blum, I.A.Kataeva, X.L.Li, and L.G.Ljungdahl (2000).
Feruloyl esterase activity of the Clostridium thermocellum cellulosome can be attributed to previously unknown domains of XynY and XynZ.
  J Bacteriol, 182, 1346-1351.  
  10752608 J.Georis, F.de Lemos Esteves, J.Lamotte-Brasseur, V.Bougnet, B.Devreese, F.Giannotta, B.Granier, and J.M.Frère (2000).
An additional aromatic interaction improves the thermostability and thermophilicity of a mesophilic family 11 xylanase: structural basis and molecular study.
  Protein Sci, 9, 466-475.  
11210125 J.X.Feng, S.Karita, E.Fujino, T.Fujino, T.Kimura, K.Sakka, and K.Ohmiya (2000).
Cloning, sequencing, and expression of the gene encoding a cell-bound multi-domain xylanase from Clostridium josui, and characterization of the translated product.
  Biosci Biotechnol Biochem, 64, 2614-2624.  
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
  10211841 A.Marina, P.M.Alzari, J.Bravo, M.Uriarte, B.Barcelona, I.Fita, and V.Rubio (1999).
Carbamate kinase: New structural machinery for making carbamoyl phosphate, the common precursor of pyrimidines and arginine.
  Protein Sci, 8, 934-940.
PDB codes: 1b7b 2we4 2we5
  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.  
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.  
10029988 P.F.Esteban, C.R.Vazquez de Aldana, and F.del Rey (1999).
Cloning and characterization of 1,3-beta-glucanase-encoding genes from non-conventional yeasts.
  Yeast, 15, 91.  
10391926 S.Kawaminami, H.Takahashi, S.Ito, Y.Arata, and I.Shimada (1999).
A multinuclear NMR study of the active site of an endoglucanase from a strain of Bacillus. Use of Trp residues as structural probes.
  J Biol Chem, 274, 19823-19828.  
  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.  
  9521098 S.Jones, M.Stewart, A.Michie, M.B.Swindells, C.Orengo, and J.M.Thornton (1998).
Domain assignment for protein structures using a consensus approach: characterization and analysis.
  Protein Sci, 7, 233-242.  
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
9208940 B.Gigant, J.B.Charbonnier, B.Golinelli-Pimpaneau, R.R.Zemel, Z.Eshhar, B.S.Green, and M.Knossow (1997).
Mechanism of inactivation of a catalytic antibody by p-nitrophenyl esters.
  Eur J Biochem, 246, 471-476.  
  9385643 G.Pujadas, and J.Palau (1997).
Anatomy of a conformational transition of beta-strand 6 in soybean beta-amylase caused by substrate (or inhibitor) binding to the catalytical site.
  Protein Sci, 6, 2409-2417.  
  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.  
9013549 L.F.Mackenzie, G.S.Brooke, J.F.Cutfield, P.A.Sullivan, and S.G.Withers (1997).
Identification of Glu-330 as the catalytic nucleophile of Candida albicans exo-beta-(1,3)-glucanase.
  J Biol Chem, 272, 3161-3167.  
18576090 M.E.Himmel, P.A.Karplus, J.Sakon, W.S.Adney, J.O.Baker, and S.R.Thomas (1997).
Polysaccharide hydrolase folds diversity of structure and convergence of function.
  Appl Biochem Biotechnol, 63, 315-325.  
14538158 M.K.Bhat, and S.Bhat (1997).
Cellulose degrading enzymes and their potential industrial applications.
  Biotechnol Adv, 15, 583-620.  
9291571 P.Christakopoulos, W.Nerinckx, D.Kekos, B.Macris, and M.Claeyssens (1997).
The alkaline xylanase III from Fusarium oxysporum F3 belongs to family F/10.
  Carbohydr Res, 302, 191-195.  
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
8913681 J.P.Turkenburg, and E.J.Dodson (1996).
Modern developments in molecular replacement.
  Curr Opin Struct Biol, 6, 604-610.  
8914532 M.Banik, T.P.Garrett, and G.B.Fincher (1996).
Molecular cloning of cDNAs encoding (1-->4)-beta-xylan endohydrolases from the aleurone layer of germinated barley (Hordeum vulgare).
  Plant Mol Biol, 31, 1163-1172.  
  8817076 P.Béguin, and M.Lemaire (1996).
The cellulosome: an exocellular, multiprotein complex specialized in cellulose degradation.
  Crit Rev Biochem Mol Biol, 31, 201-236.  
8805535 P.M.Alzari, H.Souchon, and R.Dominguez (1996).
The crystal structure of endoglucanase CelA, a family 8 glycosyl hydrolase from Clostridium thermocellum.
  Structure, 4, 265-275.
PDB code: 1cem
8905079 R.A.Warren (1996).
Microbial hydrolysis of polysaccharides.
  Annu Rev Microbiol, 50, 183-212.  
  8762144 S.Janecek (1996).
Invariant glycines and prolines flanking in loops the strand beta 2 of various (alpha/beta)8-barrel enzymes: a hidden homology?
  Protein Sci, 5, 1136-1143.  
8785441 T.W.Jeffries (1996).
Biochemistry and genetics of microbial xylanases.
  Curr Opin Biotechnol, 7, 337-342.  
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