PDBsum entry 1f9o

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Hydrolase/hydrolase inhibitor PDB id
Protein chain
629 a.a. *
PIH ×2
Waters ×218
* Residue conservation analysis
PDB id:
Name: Hydrolase/hydrolase inhibitor
Title: Crystal structure of the cellulase cel48f from c. Cellulolyticum with the thiooligosaccharide inhibitor pips- ig3
Structure: Endo-1,4-beta-glucanase f. Chain: a. Fragment: catalytic module. Synonym: cellulase cel48f. Engineered: yes
Source: Clostridium cellulolyticum. Organism_taxid: 1521. Expressed in: escherichia coli bl21(de3). Expression_system_taxid: 469008.
2.50Å     R-factor:   0.179     R-free:   0.243
Authors: G.Parsiegla,C.Reverbel-Leroy,C.Tardif,J.P.Belaich,H.Driguez, R.Haser
Key ref:
G.Parsiegla et al. (2000). Crystal structures of the cellulase Cel48F in complex with inhibitors and substrates give insights into its processive action. Biochemistry, 39, 11238-11246. PubMed id: 10985769 DOI: 10.1021/bi001139p
11-Jul-00     Release date:   02-Aug-00    
Go to PROCHECK summary

Protein chain
Pfam   ArchSchema ?
P37698  (GUNF_CLOCE) -  Endoglucanase F
722 a.a.
629 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Enzyme reactions 
   Enzyme class: E.C.  - 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     catalytic activity     5 terms  


DOI no: 10.1021/bi001139p Biochemistry 39:11238-11246 (2000)
PubMed id: 10985769  
Crystal structures of the cellulase Cel48F in complex with inhibitors and substrates give insights into its processive action.
G.Parsiegla, C.Reverbel-Leroy, C.Tardif, J.P.Belaich, H.Driguez, R.Haser.
Cellulase Cel48F from Clostridium cellulolyticum was described as a processive endo-cellulase. The active site is composed of a 25 A long tunnel which is followed by an open cleft. During the processive action, the cellulose substrate has to slide through the tunnel to continuously supply the leaving group site with sugar residues after the catalytic cleavage. To study this processive action in the tunnel, the native catalytic module of Cel48F and the inactive mutant E55Q, have been cocrystallized with cellobiitol, two thio-oligosaccharide inhibitors (PIPS-IG3 and IG4) and the cello-oligosaccharides cellobiose, -tetraose and -hexaose. Seven sub-sites in the tunnel section of the active center could be identified and three of the four previously reported sub-sites in the open cleft section were reconfirmed. The sub-sites observed for the thio-oligosaccharide inhibitors and oligosaccharides, respectively, were located at two different positions in the tunnel corresponding to a shift in the chain direction of about a half sugar subunit. These two positions have different patterns of stacking interactions with aromatic residues present in the tunnel. Multiple patterns are not observed in nonprocessive endo-cellulases, where only one sugar position is favored by aromatic stacking. It is therefore proposed that the aromatic residues serve as lubricating agents to reduce the sliding barrier in the processive action.

Literature references that cite this PDB file's key reference

  PubMed id Reference
20967294 M.Saharay, H.Guo, and J.C.Smith (2010).
Catalytic mechanism of cellulose degradation by a cellobiohydrolase, CelS.
  PLoS One, 5, e12947.  
20538726 T.C.Freeman, and W.C.Wimley (2010).
A highly accurate statistical approach for the prediction of transmembrane beta-barrels.
  Bioinformatics, 26, 1965-1974.  
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
18078545 C.D.Putnam, M.Hammel, G.L.Hura, and J.A.Tainer (2007).
X-ray solution scattering (SAXS) combined with crystallography and computation: defining accurate macromolecular structures, conformations and assemblies in solution.
  Q Rev Biophys, 40, 191-285.  
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
16595672 C.Regni, A.M.Schramm, and L.J.Beamer (2006).
The reaction of phosphohexomutase from Pseudomonas aeruginosa: structural insights into a simple processive enzyme.
  J Biol Chem, 281, 15564-15571.
PDB codes: 2fkf 2fkm
17022659 M.Desvaux (2006).
Unravelling carbon metabolism in anaerobic cellulolytic bacteria.
  Biotechnol Prog, 22, 1229-1238.  
15755956 A.L.Demain, M.Newcomb, and J.H.Wu (2005).
Cellulase, clostridia, and ethanol.
  Microbiol Mol Biol Rev, 69, 124-154.  
15853815 J.Jänis, J.Hakanpää, N.Hakulinen, F.M.Ibatullin, A.Hoxha, P.J.Derrick, J.Rouvinen, and P.Vainiotalo (2005).
Determination of thioxylo-oligosaccharide binding to family 11 xylanases using electrospray ionization Fourier transform ion cyclotron resonance mass spectrometry and X-ray crystallography.
  FEBS J, 272, 2317-2333.
PDB code: 1xnk
16102601 M.Desvaux (2005).
Clostridium cellulolyticum: model organism of mesophilic cellulolytic clostridia.
  FEMS Microbiol Rev, 29, 741-764.  
15073875 D.B.Wilson (2004).
Studies of Thermobifida fusca plant cell wall degrading enzymes.
  Chem Rec, 4, 72-82.  
14679233 E.Devillard, D.B.Goodheart, S.K.Karnati, E.A.Bayer, R.Lamed, J.Miron, K.E.Nelson, and M.Morrison (2004).
Ruminococcus albus 8 mutants defective in cellulose degradation are deficient in two processive endocellulases, Cel48A and Cel9B, both of which possess a novel modular architecture.
  J Bacteriol, 186, 136-145.  
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.  
15148314 T.Itoh, S.Akao, W.Hashimoto, B.Mikami, and K.Murata (2004).
Crystal structure of unsaturated glucuronyl hydrolase, responsible for the degradation of glycosaminoglycan, from Bacillus sp. GL1 at 1.8 A resolution.
  J Biol Chem, 279, 31804-31812.
PDB code: 1vd5
12842048 A.Varrot, T.P.Frandsen, I.von Ossowski, V.Boyer, S.Cottaz, H.Driguez, M.Schülein, and G.J.Davies (2003).
Structural basis for ligand binding and processivity in cellobiohydrolase Cel6A from Humicola insolens.
  Structure, 11, 855-864.
PDB codes: 1oc5 1oc6 1oc7 1ocb 1ocj
12837787 D.Mandelman, A.Belaich, J.P.Belaich, N.Aghajari, H.Driguez, and R.Haser (2003).
X-Ray crystal structure of the multidomain endoglucanase Cel9G from Clostridium cellulolyticum complexed with natural and synthetic cello-oligosaccharides.
  J Bacteriol, 185, 4127-4135.
PDB codes: 1g87 1ga2 1k72 1kfg
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.  
12023973 M.Hrmova, T.Imai, S.J.Rutten, J.K.Fairweather, L.Pelosi, V.Bulone, H.Driguez, and G.B.Fincher (2002).
Mutated barley (1,3)-beta-D-glucan endohydrolases synthesize crystalline (1,3)-beta-D-glucans.
  J Biol Chem, 277, 30102-30111.  
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
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.