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PDBsum entry 1ceo

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Cellulose degradation PDB id
1ceo
Jmol
Contents
Protein chain
332 a.a. *
Waters ×288
* Residue conservation analysis
PDB id:
1ceo
Name: Cellulose degradation
Title: Cellulase (celc) mutant with glu 140 replaced by gln
Structure: Cellulase celc. Chain: a. Synonym: 1,4-beta-d-glucan-glucanohydrolase, endo-1,4-beta- glucanasE C. Engineered: yes. Mutation: yes
Source: Clostridium thermocellum. Organism_taxid: 1515. Strain: ncib 10682. Expressed in: escherichia coli. Expression_system_taxid: 562.
Resolution:
1.90Å     R-factor:   0.194     R-free:   0.222
Authors: R.Dominguez,P.M.Alzari
Key ref:
R.Domínguez et al. (1996). The crystal structure of a family 5 endoglucanase mutant in complexed and uncomplexed forms reveals an induced fit activation mechanism. J Mol Biol, 257, 1042-1051. PubMed id: 8632467 DOI: 10.1006/jmbi.1996.0222
Date:
04-Dec-95     Release date:   03-Apr-96    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
P0C2S3  (GUNC_CLOTM) -  Endoglucanase C
Seq:
Struc:
343 a.a.
332 a.a.*
Key:    PfamA domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 2 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     metabolic process   4 terms 
  Biochemical function     hydrolase activity     4 terms  

 

 
DOI no: 10.1006/jmbi.1996.0222 J Mol Biol 257:1042-1051 (1996)
PubMed id: 8632467  
 
 
The crystal structure of a family 5 endoglucanase mutant in complexed and uncomplexed forms reveals an induced fit activation mechanism.
R.Domínguez, H.Souchon, M.Lascombe, P.M.Alzari.
 
  ABSTRACT  
 
The structures of the Glu140-->Gln mutant of the Clostridium thermocellum endoglucanase CelC in unliganded form (CelC(E140Q)) and in complex with cellohexaose (CelC(E140Q)-Gl(C6)) have been refined to crystallographic R-factors of 19.4% at 1.9 A and 17.8% at 2.3 A resolution, respectively. The structure of CelC(E140Q)-Gl(C6) complex shows two D-glucosyl residues bound to the non-reducing end of the substrate-binding cleft. Comparison of the unliganded and complexes structures reveals conformational changes due to substrate binding, including a significant reorientation of the loop 138-141 which carries the general acid/base catalyst Glu140 in wild-type CelC. Endoglucanase CelC, a family 5 glycohydrolase, exhibits a (beta/alpha)8-fold with an additional subdomain of 54 amino acids inserted between beta-strand 6 and alpha-helix 6. Seven amino acid residues (Arg46, His90, Asn139, Glu140, His198, Tyr200, and Glu280) located close to the catalytic reaction center are strictly conserved in family 5 cellulases. Only three of these residues (His90, Gln140 and Glu280) make direct contacts with the substrate, but all participate in a network of hydrogen bonds which contribute to the stability of the active site architecture and may influence the protonation state of the two catalytic residues. Residue Trp313, which interacts with the nucleophile Glu280 and is within hydrogen bonding distance of the substrate, is involved in a non-proline cis-peptide bond. An aromatic residue occurs at an equivalent position in many other (beta/alpha)8-barrel glycosidases; the presence of a cis-peptide bond at this position in the structures of family 1 beta-glucosidases, family 2 beta-galactosidases, family 5 cellulases, family 17 beta-glucanases, and family 18 chitinases provides further evidence of an evolutionary relationship between glycosyl hydrolases with a (beta/alpha)8- architecture.
 
  Selected figure(s)  
 
Figure 2.
Figure 2. Stereo view of the active site of the CelCE140Q--Glc6 complex illustrating the hydrogen-bonding network (broken lines) involving Trp313 and seven amino acid residues conserved in family 5 cellulases. The corresponding distances are listed in Table 1. The drawing was generated with MOLSCRIPT (Kraulis, 1991).
Figure 6.
Figure 6. The cis-peptide bond between Trp313 and Asn314 of CelC is stabilized by an internal water molecule which is involved in a tetrahedral arrangement of hydrogen bonds with protein atoms.
 
  The above figures are reprinted by permission from Elsevier: J Mol Biol (1996, 257, 1042-1051) copyright 1996.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
20622123 A.Beloqui, T.Y.Nechitaylo, N.López-Cortés, A.Ghazi, M.E.Guazzaroni, J.Polaina, A.W.Strittmatter, O.Reva, A.Waliczek, M.M.Yakimov, O.V.Golyshina, M.Ferrer, and P.N.Golyshin (2010).
Diversity of glycosyl hydrolases from cellulose-depleting communities enriched from casts of two earthworm species.
  Appl Environ Microbiol, 76, 5934-5946.  
20875088 W.M.Patrick, Y.Nakatani, S.M.Cutfield, M.L.Sharpe, R.J.Ramsay, and J.F.Cutfield (2010).
Carbohydrate binding sites in Candida albicans exo-β-1,3-glucanase and the role of the Phe-Phe 'clamp' at the active site entrance.
  FEBS J, 277, 4549-4561.
PDB codes: 2pc8 2pf0 3n9k 3o6a
18981178 M.Kitamura, M.Okuyama, F.Tanzawa, H.Mori, Y.Kitago, N.Watanabe, A.Kimura, I.Tanaka, and M.Yao (2008).
Structural and Functional Analysis of a Glycoside Hydrolase Family 97 Enzyme from Bacteroides thetaiotaomicron.
  J Biol Chem, 283, 36328-36337.
PDB codes: 2d73 2zq0
15073875 D.B.Wilson (2004).
Studies of Thermobifida fusca plant cell wall degrading enzymes.
  Chem Rec, 4, 72-82.  
14573597 G.Golan, D.Shallom, A.Teplitsky, G.Zaide, S.Shulami, T.Baasov, V.Stojanoff, A.Thompson, Y.Shoham, and G.Shoham (2004).
Crystal structures of Geobacillus stearothermophilus alpha-glucuronidase complexed with its substrate and products: mechanistic implications.
  J Biol Chem, 279, 3014-3024.
PDB codes: 1k9d 1k9e 1k9f 1l8n 1mqp 1mqq 1mqr
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
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.  
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
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
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
9556600 M.Hrmova, E.A.MacGregor, P.Biely, R.J.Stewart, and G.B.Fincher (1998).
Substrate binding and catalytic mechanism of a barley beta-D-Glucosidase/(1,4)-beta-D-glucan exohydrolase.
  J Biol Chem, 273, 11134-11143.  
9665697 M.S.Hasson, A.Muscate, M.J.McLeish, L.S.Polovnikova, J.A.Gerlt, G.L.Kenyon, G.A.Petsko, and D.Ringe (1998).
The crystal structure of benzoylformate decarboxylase at 1.6 A resolution: diversity of catalytic residues in thiamin diphosphate-dependent enzymes.
  Biochemistry, 37, 9918-9930.
PDB code: 1bfd
9790669 P.J.Focia, S.P.Craig, R.Nieves-Alicea, R.J.Fletterick, and A.E.Eakin (1998).
A 1.4 A crystal structure for the hypoxanthine phosphoribosyltransferase of Trypanosoma cruzi.
  Biochemistry, 37, 15066-15075.
PDB code: 1tc1
9345622 A.White, and D.R.Rose (1997).
Mechanism of catalysis by retaining beta-glycosyl hydrolases.
  Curr Opin Struct Biol, 7, 645-651.  
9345621 B.Henrissat, and G.Davies (1997).
Structural and sequence-based classification of glycoside hydrolases.
  Curr Opin Struct Biol, 7, 637-644.  
  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.  
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.