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PDBsum entry 1edg

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Cellulose degradation PDB id
1edg
Jmol PyMol
Contents
Protein chain
380 a.a. *
Waters ×375
* Residue conservation analysis
PDB id:
1edg
Name: Cellulose degradation
Title: Single crystal structure determination of the catalytic doma celcca carried out at 15 degreE C
Structure: Endoglucanase a. Chain: a. Fragment: catalytic domain, c terminus truncated. Synonym: endo-(1,4)-beta-glucanase, celcca. Engineered: yes. Other_details: family 5 of glycosyl hydrolases
Source: Clostridium cellulolyticum. Organism_taxid: 394503. Strain: h10. Atcc: 35319. Gene: celcca. Expressed in: escherichia coli. Expression_system_taxid: 562.
Resolution:
1.60Å     R-factor:   0.191     R-free:   0.220
Authors: V.Ducros,M.Czjzek,R.Haser
Key ref:
V.Ducros et al. (1995). Crystal structure of the catalytic domain of a bacterial cellulase belonging to family 5. Structure, 3, 939-949. PubMed id: 8535787 DOI: 10.1016/S0969-2126(01)00228-3
Date:
07-Jul-95     Release date:   17-Aug-96    
PROCHECK
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 Headers
 References

Protein chain
Pfam   ArchSchema ?
P17901  (GUNA_CLOCE) -  Endoglucanase A
Seq:
Struc:
475 a.a.
380 a.a.*
Key:    PfamA domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 5 residue positions (black crosses)

 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     carbohydrate metabolic process   1 term 
  Biochemical function     hydrolase activity, hydrolyzing O-glycosyl compounds     1 term  

 

 
DOI no: 10.1016/S0969-2126(01)00228-3 Structure 3:939-949 (1995)
PubMed id: 8535787  
 
 
Crystal structure of the catalytic domain of a bacterial cellulase belonging to family 5.
V.Ducros, M.Czjzek, A.Belaich, C.Gaudin, H.P.Fierobe, J.P.Belaich, G.J.Davies, R.Haser.
 
  ABSTRACT  
 
BACKGROUND: Cellulases are glycosyl hydrolases--enzymes that hydrolyze glycosidic bonds. They have been widely studied using biochemical and microbiological techniques and have attracted industrial interest because of their potential in biomass conversion and in the paper and textile industries. Glycosyl hydrolases have lately been assigned to specific families on the basis of similarities in their amino acid sequences. The cellulase endoglucanase A produced by Clostridium cellulolyticum (CelCCA) belongs to family 5. RESULTS: We have determined the crystal structure of the catalytic domain of CelCCA at a resolution of 2.4 A and refined it to 1.6 A. The structure was solved by the multiple isomorphous replacement method. The overall structural fold, (alpha/beta)8, belongs to the TIM barrel motif superfamily. The catalytic centre is located at the C-terminal ends of the beta strands; the aromatic residues, forming the substrate-binding site, are arranged along a long cleft on the surface of the globular enzyme. CONCLUSIONS: Strictly conserved residues within family 5 are described with respect to their catalytic function. The proton donor, Glu170, and the nucleophile, Glu307, are localized on beta strands IV and VII, respectively, and are separated by 5.5 A, as expected for enzymes which retain the configuration of the substrate's anomeric carbon. Structure determination of the catalytic domain of CelCCA allows a comparison with related enzymes belonging to glycosyl hydrolase families 2, 10 and 17, which also display an (alpha/beta)8 fold.
 
  Selected figure(s)  
 
Figure 2.
Figure 2. The eightfold α/β barrel of the catalytic domain of the endoglucanase A from C. cellulolyticum. (a) Ribbon representation, viewed from the side, of the barrel showing the cleft formed by the loops at the C-terminal extremity of the barrel. β strands are shown as green arrows and the α helices as violet spirals. One additional α helix is located at the N-terminal extremity and this is coloured red. (Figure generated using TURBO-FRODO [50].) (b) Stereo Cα trace of CelCCA viewed along the barrel axis. Figure 2. The eightfold α/β barrel of the catalytic domain of the endoglucanase A from C. cellulolyticum. (a) Ribbon representation, viewed from the side, of the barrel showing the cleft formed by the loops at the C-terminal extremity of the barrel. β strands are shown as green arrows and the α helices as violet spirals. One additional α helix is located at the N-terminal extremity and this is coloured red. (Figure generated using TURBO-FRODO [[4]50].) (b) Stereo Cα trace of CelCCA viewed along the barrel axis.
Figure 5.
Figure 5. Top view of the groove running along the surface of the (α/β)[8] barrel showing the distribution of the aromatic residues (purple), which form the substrate-binding site, on alternate sides of the groove. The two catalytic glutamates are shown in blue. Figure 5. Top view of the groove running along the surface of the (α/β)[8] barrel showing the distribution of the aromatic residues (purple), which form the substrate-binding site, on alternate sides of the groove. The two catalytic glutamates are shown in blue.
 
  The above figures are reprinted by permission from Cell Press: Structure (1995, 3, 939-949) copyright 1995.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
20039037 D.D.Wong, V.J.Chan, A.A.McCormack, and S.B.Batt (2010).
A novel xyloglucan-specific endo-beta-1,4-glucanase: biochemical properties and inhibition studies.
  Appl Microbiol Biotechnol, 86, 1463-1471.  
19617364 B.J.Watson, H.Zhang, A.G.Longmire, Y.H.Moon, and S.W.Hutcheson (2009).
Processive endoglucanases mediate degradation of cellulose by Saccharophagus degradans.
  J Bacteriol, 191, 5697-5705.  
  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.  
19050861 L.Lin, X.Meng, P.Liu, Y.Hong, G.Wu, X.Huang, C.Li, J.Dong, L.Xiao, and Z.Liu (2009).
Improved catalytic efficiency of endo-beta-1,4-glucanase from Bacillus subtilis BME-15 by directed evolution.
  Appl Microbiol Biotechnol, 82, 671-679.  
18330853 H.Tao, P.Peralta-Yahya, J.Decatur, and V.W.Cornish (2008).
Characterization of a new glycosynthase cloned by using chemical complementation.
  Chembiochem, 9, 681-684.  
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.  
17597061 S.Ravaud, X.Robert, H.Watzlawick, R.Haser, R.Mattes, and N.Aghajari (2007).
Trehalulose synthase native and carbohydrate complexed structures provide insights into sucrose isomerization.
  J Biol Chem, 282, 28126-28136.
PDB codes: 1zja 2pwd 2pwe 2pwf 2pwg 2pwh
17376777 T.M.Gloster, F.M.Ibatullin, K.Macauley, J.M.Eklöf, S.Roberts, J.P.Turkenburg, M.E.Bjørnvad, P.L.Jørgensen, S.Danielsen, K.S.Johansen, T.V.Borchert, K.S.Wilson, H.Brumer, and G.J.Davies (2007).
Characterization and three-dimensional structures of two distinct bacterial xyloglucanases from families GH5 and GH12.
  J Biol Chem, 282, 19177-19189.
PDB codes: 2jem 2jen 2jep 2jeq
17022659 M.Desvaux (2006).
Unravelling carbon metabolism in anaerobic cellulolytic bacteria.
  Biotechnol Prog, 22, 1229-1238.  
16102601 M.Desvaux (2005).
Clostridium cellulolyticum: model organism of mesophilic cellulolytic clostridia.
  FEMS Microbiol Rev, 29, 741-764.  
15724214 Y.Sakamoto, T.Irie, and T.Sato (2005).
Isolation and characterization of a fruiting body-specific exo-beta-1,3-glucanase-encoding gene, exg1, from Lentinula edodes.
  Curr Genet, 47, 244-252.  
14756796 H.Maamar, O.Valette, H.P.Fierobe, A.Bélaich, J.P.Bélaich, and C.Tardif (2004).
Cellulolysis is severely affected in Clostridium cellulolyticum strain cipCMut1.
  Mol Microbiol, 51, 589-598.  
12220178 G.Parsiegla, A.Belaïch, J.P.Belaïch, and R.Haser (2002).
Crystal structure of the cellulase Cel9M enlightens structure/function relationships of the variable catalytic modules in glycoside hydrolases.
  Biochemistry, 41, 11134-11142.
PDB codes: 1ia6 1ia7
12139610 K.Murashima, A.Kosugi, and R.H.Doi (2002).
Thermostabilization of cellulosomal endoglucanase EngB from Clostridium cellulovorans by in vitro DNA recombination with non-cellulosomal endoglucanase EngD.
  Mol Microbiol, 45, 617-626.  
11134925 M.Hilge, A.Perrakis, J.P.Abrahams, K.Winterhalter, K.Piontek, and S.M.Gloor (2001).
Structure elucidation of beta-mannanase: from the electron-density map to the DNA sequence.
  Acta Crystallogr D Biol Crystallogr, 57, 37-43.  
11166997 Y.Hakamada, Y.Hatada, T.Ozawa, K.Ozaki, T.Kobayashi, and S.Ito (2001).
Identification of thermostabilizing residues in a Bacillus alkaline cellulase by construction of chimeras from mesophilic and thermostable enzymes and site-directed mutagenesis.
  FEMS Microbiol Lett, 195, 67-72.  
10666621 E.Sabini, H.Schubert, G.Murshudov, K.S.Wilson, M.Siika-Aho, and M.Penttilä (2000).
The three-dimensional structure of a Trichoderma reesei beta-mannanase from glycoside hydrolase family 5.
  Acta Crystallogr D Biol Crystallogr, 56, 3.
PDB codes: 1qno 1qnp 1qnq 1qnr 1qns
10875331 H.Jahr, J.Dreier, D.Meletzus, R.Bahro, and R.Eichenlaub (2000).
The endo-beta-1,4-glucanase CelA of Clavibacter michiganensis subsp. michiganensis is a pathogenicity determinant required for induction of bacterial wilt of tomato.
  Mol Plant Microbe Interact, 13, 703-714.  
10705451 H.Ohara, J.Noguchi, S.Karita, T.Kimura, K.Sakka, and K.Ohmiya (2000).
Sequence of egV and properties of EgV, a Ruminococcus albus endoglucanase containing a dockerin domain.
  Biosci Biotechnol Biochem, 64, 80-88.  
10824094 S.Zhang, D.C.Irwin, and D.B.Wilson (2000).
Site-directed mutation of noncatalytic residues of Thermobifida fusca exocellulase Cel6B.
  Eur J Biochem, 267, 3101-3115.  
11018131 T.Y.Wong, L.A.Preston, and N.L.Schiller (2000).
ALGINATE LYASE: review of major sources and enzyme characteristics, structure-function analysis, biological roles, and applications.
  Annu Rev Microbiol, 54, 289-340.  
11193393 Y.Hakamada, Y.Hatada, K.Koike, T.Yoshimatsu, S.Kawai, T.Kobayashi, and S.Ito (2000).
Deduced amino acid sequence and possible catalytic residues of a thermostable, alkaline cellulase from an Alkaliphilic bacillus strain.
  Biosci Biotechnol Biochem, 64, 2281-2289.  
  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.  
10216305 E.Sabini, A.M.Brzozowski, M.Dauter, G.J.Davies, K.S.Wilson, M.Paloheimo, P.Suominen, M.Siika-Aho, and M.Penttilä (1999).
Crystallization and preliminary X-ray crystallographic analysis of a Trichoderma reesei beta-mannanase from glycoside hydrolase family 5.
  Acta Crystallogr D Biol Crystallogr, 55, 1058-1060.  
  10548053 N.Nagano, E.G.Hutchinson, and J.M.Thornton (1999).
Barrel structures in proteins: automatic identification and classification including a sequence analysis of TIM barrels.
  Protein Sci, 8, 2072-2084.  
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.  
9761829 C.Reverbel-Leroy, G.Parsiegla, V.Moreau, M.Juy, C.Tardif, H.Driguez, J.P.Bélaich, and R.Haser (1998).
Crystallization of the catalytic domain of Clostridium cellulolyticum CeLF cellulase in the presence of a newly synthesized cellulase inhibitor.
  Acta Crystallogr D Biol Crystallogr, 54, 114-118.  
9485319 G.J.Davies, M.Dauter, A.M.Brzozowski, M.E.Bjørnvad, K.V.Andersen, and M.Schülein (1998).
Structure of the Bacillus agaradherans family 5 endoglucanase at 1.6 A and its cellobiose complex at 2.0 A resolution.
  Biochemistry, 37, 1926-1932.
PDB codes: 1a3h 2a3h
9755156 G.Parsiegla, M.Juy, C.Reverbel-Leroy, C.Tardif, J.P.Belaïch, H.Driguez, and R.Haser (1998).
The crystal structure of the processive endocellulase CelF of Clostridium cellulolyticum in complex with a thiooligosaccharide inhibitor at 2.0 A resolution.
  EMBO J, 17, 5551-5562.
PDB code: 1fce
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
9761834 M.Scott, R.W.Pickersgill, G.P.Hazlewood, D.Bolam, H.J.Gilbert, and G.W.Harris (1998).
Crystallization and preliminary X-ray diffraction studies of a family 26 endo-beta-1,4 mannanase (ManA) from Pseudomonas fluorescens subspecies cellulosa.
  Acta Crystallogr D Biol Crystallogr, 54, 129-131.  
  8981979 C.Reverbel-Leroy, S.Pages, A.Belaich, J.P.Belaich, and C.Tardif (1997).
The processive endocellulase CelF, a major component of the Clostridium cellulolyticum cellulosome: purification and characterization of the recombinant form.
  J Bacteriol, 179, 46-52.  
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.  
  9055408 L.Gal, S.Pages, C.Gaudin, A.Belaich, C.Reverbel-Leroy, C.Tardif, and J.P.Belaich (1997).
Characterization of the cellulolytic complex (cellulosome) produced by Clostridium cellulolyticum.
  Appl Environ Microbiol, 63, 903-909.  
14538158 M.K.Bhat, and S.Bhat (1997).
Cellulose degrading enzymes and their potential industrial applications.
  Biotechnol Adv, 15, 583-620.  
9370370 M.Saloheimo, T.Nakari-Setälä, M.Tenkanen, and M.Penttilä (1997).
cDNA cloning of a Trichoderma reesei cellulase and demonstration of endoglucanase activity by expression in yeast.
  Eur J Biochem, 249, 584-591.  
  9139893 S.Pagès, L.Gal, A.Bélaïch, C.Gaudin, C.Tardif, and J.P.Bélaïch (1997).
Role of scaffolding protein CipC of Clostridium cellulolyticum in cellulose degradation.
  J Bacteriol, 179, 2810-2816.  
8805552 A.C.Pike, K.Brew, and K.R.Acharya (1996).
Crystal structures of guinea-pig, goat and bovine alpha-lactalbumin highlight the enhanced conformational flexibility of regions that are significant for its action in lactose synthase.
  Structure, 4, 691-703.
PDB codes: 1hfx 1hfy 1hfz
8973192 D.N.Bolam, N.Hughes, R.Virden, J.H.Lakey, G.P.Hazlewood, B.Henrissat, K.L.Braithwaite, and H.J.Gilbert (1996).
Mannanase A from Pseudomonas fluorescens ssp. cellulosa is a retaining glycosyl hydrolase in which E212 and E320 are the putative catalytic residues.
  Biochemistry, 35, 16195-16204.  
8718854 J.Sakon, W.S.Adney, M.E.Himmel, S.R.Thomas, and P.A.Karplus (1996).
Crystal structure of thermostable family 5 endocellulase E1 from Acidothermus cellulolyticus in complex with cellotetraose.
  Biochemistry, 35, 10648-10660.
PDB code: 1ece
  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.  
  8636029 S.Pagès, A.Belaich, C.Tardif, C.Reverbel-Leroy, C.Gaudin, and J.P.Belaich (1996).
Interaction between the endoglucanase CelA and the scaffolding protein CipC of the Clostridium cellulolyticum cellulosome.
  J Bacteriol, 178, 2279-2286.  
8535779 G.Davies, and B.Henrissat (1995).
Structures and mechanisms of glycosyl hydrolases.
  Structure, 3, 853-859.  
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.

 

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