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PDBsum entry 1fce
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Cellulase degradation PDB id
1fce

 

 

 

 

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Contents
Protein chain
629 a.a. *
Ligands
MGL-SGC-BGC-BGC ×2
Metals
_CA
Waters ×1002
* Residue conservation analysis
PDB id:
1fce
Name: Cellulase degradation
Title: Processive endocellulase celf of clostridium cellulolyticum
Structure: Cellulase celf. Chain: a. Fragment: catalytic domain. Engineered: yes
Source: Clostridium cellulolyticum. Organism_taxid: 1521. Atcc: atcc 35319. Collection: atcc 35319. Cellular_location: secreted on cellulosome. Expressed in: escherichia coli bl21(de3). Expression_system_taxid: 469008.
Resolution:
2.00Å     R-factor:   0.165     R-free:   0.210
Authors: G.Parsiegla,M.Juy,R.Haser
Key ref:
G.Parsiegla et al. (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. PubMed id: 9755156 DOI: 10.1093/emboj/17.19.5551
Date:
06-Jul-98     Release date:   22-Jul-99    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
P37698  (GUNF_CLOCE) -  Endoglucanase F from Ruminiclostridium cellulolyticum (strain ATCC 35319 / DSM 5812 / JCM 6584 / H10)
Seq:
Struc: 		 
Seq:
Struc: 		722 a.a.
629 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 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.

 

 
DOI no: 10.1093/emboj/17.19.5551 EMBO J 17:5551-5562 (1998)
PubMed id: 9755156  
 
 
The crystal structure of the processive endocellulase CelF of Clostridium cellulolyticum in complex with a thiooligosaccharide inhibitor at 2.0 A resolution.
G.Parsiegla, M.Juy, C.Reverbel-Leroy, C.Tardif, J.P.Belaïch, H.Driguez, R.Haser.
 
  ABSTRACT  
 
The mesophilic bacterium Clostridium cellulolyticum exports multienzyme complexes called cellulosomes to digest cellulose. One of the three major components of the cellulosome is the processive endocellulase CelF. The crystal structure of the catalytic domain of CelF in complex with two molecules of a thiooligosaccharide inhibitor was determined at 2.0 A resolution. This is the first three-dimensional structure to be solved of a member of the family 48 glycosyl hydrolases. The structure consists of an (alpha alpha)6-helix barrel with long loops on the N-terminal side of the inner helices, which form a tunnel, and an open cleft region covering one side of the barrel. One inhibitor molecule is enclosed in the tunnel, the other exposed in the open cleft. The active centre is located in a depression at the junction of the cleft and tunnel regions. Glu55 is the proposed proton donor in the cleavage reaction, while the corresponding base is proposed to be either Glu44 or Asp230. The orientation of the reducing ends of the inhibitor molecules together with the chain translation through the tunnel in the direction of the active centre indicates that CelF cleaves processively cellobiose from the reducing to the non-reducing end of the cellulose chain.
 
  Selected figure(s)  
 
Figure 1.
Figure 1 Chemical structure of the thiooligosaccharide inhibitor methyl 4-S- -cellobiosyl-4-thio-cellobioside, which is called IG4 in this article. The sugar subunits are labelled from (A) to (D) from the non-reducing to the O-methylated reducing end. 		Figure 7.
Figure 7 The (2F[o]-F[c]) electron density map contoured at the 1 level, following the inhibitor molecules Inh1 (-6 to -4) and Inh2 (+1 to +4) from the tunnel to the end of the open cleft. It shows as well the unexplained density at the gap between the inhibitor molecules.
 
  The above figures are reprinted from an Open Access publication published by Macmillan Publishers Ltd: EMBO J (1998, 17, 5551-5562) copyright 1998.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
20373916 C.M.Fontes, and H.J.Gilbert (2010).
Cellulosomes: highly efficient nanomachines designed to deconstruct plant cell wall complex carbohydrates.
  Annu Rev Biochem, 79, 655-681.  
20382819 J.A.Izquierdo, M.V.Sizova, and L.R.Lynd (2010).
Diversity of bacteria and glycosyl hydrolase family 48 genes in cellulolytic consortia enriched from thermophilic biocompost.
  Appl Environ Microbiol, 76, 3545-3553.  
20967294 M.Saharay, H.Guo, and J.C.Smith (2010).
Catalytic mechanism of cellulose degradation by a cellobiohydrolase, CelS.
  PLoS One, 5, e12947.  
19830421 X.Z.Zhang, Z.Zhang, Z.Zhu, N.Sathitsuksanoh, Y.Yang, and Y.H.Zhang (2010).
The noncellulosomal family 48 cellobiohydrolase from Clostridium phytofermentans ISDg: heterologous expression, characterization, and processivity.
  Appl Microbiol Biotechnol, 86, 525-533.  
19234687 H.Rakotoarivonina, C.Terrie, C.Chambon, E.Forano, and P.Mosoni (2009).
Proteomic identification of CBM37-containing cellulases produced by the rumen cellulolytic bacterium Ruminococcus albus 20 and their putative involvement in bacterial adhesion to cellulose.
  Arch Microbiol, 191, 379-388.  
19622857 J.H.Pereira, R.Sapra, J.V.Volponi, C.L.Kozina, B.Simmons, and P.D.Adams (2009).
Structure of endoglucanase Cel9A from the thermoacidophilic Alicyclobacillus acidocaldarius.
  Acta Crystallogr D Biol Crystallogr, 65, 744-750.
PDB code: 3ez8
19193645 T.Ishida, S.Fushinobu, R.Kawai, M.Kitaoka, K.Igarashi, and M.Samejima (2009).
Crystal structure of glycoside hydrolase family 55 {beta}-1,3-glucanase from the basidiomycete Phanerochaete chrysosporium.
  J Biol Chem, 284, 10100-10109.
PDB codes: 3eqn 3eqo
18378599 D.B.Wilson (2008).
Three microbial strategies for plant cell wall degradation.
  Ann N Y Acad Sci, 1125, 289-297.  
18292875 V.A.Money, A.Cartmell, C.I.Guerreiro, V.M.Ducros, C.M.Fontes, H.J.Gilbert, and G.J.Davies (2008).
Probing the beta-1,3:1,4 glucanase, CtLic26A, with a thio-oligosaccharide and enzyme variants.
  Org Biomol Chem, 6, 851-853.
PDB code: 2vi0
17459873 M.Nagae, A.Tsuchiya, T.Katayama, K.Yamamoto, S.Wakatsuki, and R.Kato (2007).
Structural basis of the catalytic reaction mechanism of novel 1,2-alpha-L-fucosidase from Bifidobacterium bifidum.
  J Biol Chem, 282, 18497-18509.
PDB codes: 2eab 2eac 2ead 2eae
16550377 G.Michel, P.Nyval-Collen, T.Barbeyron, M.Czjzek, and W.Helbert (2006).
Bioconversion of red seaweed galactans: a focus on bacterial agarases and carrageenases.
  Appl Microbiol Biotechnol, 71, 23-33.  
15755956 A.L.Demain, M.Newcomb, and J.H.Wu (2005).
Cellulase, clostridia, and ethanol.
  Microbiol Mol Biol Rev, 69, 124-154.  
16102601 M.Desvaux (2005).
Clostridium cellulolyticum: model organism of mesophilic cellulolytic clostridia.
  FEMS Microbiol Rev, 29, 741-764.  
15718242 S.Fushinobu, M.Hidaka, Y.Honda, T.Wakagi, H.Shoun, and M.Kitaoka (2005).
Structural basis for the specificity of the reducing end xylose-releasing exo-oligoxylanase from Bacillus halodurans C-125.
  J Biol Chem, 280, 17180-17186.
PDB codes: 1wu4 1wu5 1wu6
15652973 T.Collins, C.Gerday, and G.Feller (2005).
Xylanases, xylanase families and extremophilic xylanases.
  FEMS Microbiol Rev, 29, 3.  
15502162 M.Hammel, H.P.Fierobe, M.Czjzek, S.Finet, and V.Receveur-Bréchot (2004).
Structural insights into the mechanism of formation of cellulosomes probed by small angle X-ray scattering.
  J Biol Chem, 279, 55985-55994.  
15236244 M.M.Sánchez, D.C.Irwin, F.I.Pastor, D.B.Wilson, and P.Diaz (2004).
Synergistic activity of Paenibacillus sp. BP-23 cellobiohydrolase Cel48C in association with the contiguous endoglucanase Cel9B and with endo- or exo-acting glucanases from Thermobifida fusca.
  Biotechnol Bioeng, 87, 161-169.  
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
12966571 H.Jung, D.B.Wilson, and L.P.Walker (2003).
Binding and reversibility of Thermobifida fusca Cel5A, Cel6B, and Cel48A and their respective catalytic domains to bacterial microcrystalline cellulose.
  Biotechnol Bioeng, 84, 151-159.  
12823562 M.M.Sánchez, F.I.Pastor, and P.Diaz (2003).
Exo-mode of action of cellobiohydrolase Cel48C from Paenibacillus sp. BP-23. A unique type of cellulase among Bacillales.
  Eur J Biochem, 270, 2913-2919.  
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
12193625 K.Murashima, A.Kosugi, and R.H.Doi (2002).
Synergistic effects on crystalline cellulose degradation between cellulosomal cellulases from Clostridium cellulovorans.
  J Bacteriol, 184, 5088-5095.  
12209002 L.R.Lynd, P.J.Weimer, W.H.van Zyl, and I.S.Pretorius (2002).
Microbial cellulose utilization: fundamentals and biotechnology.
  Microbiol Mol Biol Rev, 66, 506.  
11980476 M.Abou-Hachem, E.N.Karlsson, P.J.Simpson, S.Linse, P.Sellers, M.P.Williamson, S.J.Jamieson, H.J.Gilbert, D.N.Bolam, and O.Holst (2002).
Calcium binding and thermostability of carbohydrate binding module CBM4-2 of Xyn10A from Rhodothermus marinus.
  Biochemistry, 41, 5720-5729.  
11914490 S.Khademi, L.A.Guarino, H.Watanabe, G.Tokuda, and E.F.Meyer (2002).
Structure of an endoglucanase from termite, Nasutitermes takasagoensis.
  Acta Crystallogr D Biol Crystallogr, 58, 653-659.
PDB codes: 1ks8 1ksc 1ksd
11921222 V.Boyer, S.Fort, T.P.Frandsen, M.Schülein, S.Cottaz, and H.Driguez (2002).
Chemoenzymatic synthesis of a bifunctionalized cellohexaoside as a specific substrate for the sensitive assay of cellulase by fluorescence quenching.
  Chemistry, 8, 1389-1394.  
11435116 G.Michel, L.Chantalat, E.Duee, T.Barbeyron, B.Henrissat, B.Kloareg, and O.Dideberg (2001).
The kappa-carrageenase of P. carrageenovora features a tunnel-shaped active site: a novel insight in the evolution of Clan-B glycoside hydrolases.
  Structure, 9, 513-525.
PDB code: 1dyp
11514661 W.A.Breyer, and B.W.Matthews (2001).
A structural basis for processivity.
  Protein Sci, 10, 1699-1711.  
11327856 W.Huang, L.Boju, L.Tkalec, H.Su, H.O.Yang, N.S.Gunay, R.J.Linhardt, Y.S.Kim, A.Matte, and M.Cygler (2001).
Active site of chondroitin AC lyase revealed by the structure of enzyme-oligosaccharide complexes and mutagenesis.
  Biochemistry, 40, 2359-2372.
PDB codes: 1hm2 1hm3 1hmu 1hmw
11006547 C.S.Rye, and S.G.Withers (2000).
Glycosidase mechanisms.
  Curr Opin Chem Biol, 4, 573-580.  
10931180 D.C.Irwin, S.Zhang, and D.B.Wilson (2000).
Cloning, expression and characterization of a family 48 exocellulase, Cel48A, from Thermobifida fusca.
  Eur J Biochem, 267, 4988-4997.  
10675327 F.Vallée, F.Lipari, P.Yip, B.Sleno, A.Herscovics, and P.L.Howell (2000).
Crystal structure of a class I alpha1,2-mannosidase involved in N-glycan processing and endoplasmic reticulum quality control.
  EMBO J, 19, 581-588.
PDB code: 1dl2
10985769 G.Parsiegla, C.Reverbel-Leroy, C.Tardif, J.P.Belaich, H.Driguez, and R.Haser (2000).
Crystal structures of the cellulase Cel48F in complex with inhibitors and substrates give insights into its processive action.
  Biochemistry, 39, 11238-11246.
PDB codes: 1f9d 1f9o 1fae 1fbo 1fbw
10390637 Y.Shoham, R.Lamed, and E.A.Bayer (1999).
The cellulosome concept as an efficient microbial strategy for the degradation of insoluble polysaccharides.
  Trends Microbiol, 7, 275-281.  
9818257 E.A.Bayer, H.Chanzy, R.Lamed, and Y.Shoham (1998).
Cellulose, cellulases and cellulosomes.
  Curr Opin Struct Biol, 8, 548-557.  
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.

 

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