PDBsum entry 2vn6

Go to PDB code: 
protein metals Protein-protein interface(s) links
Cell adhesion PDB id
Protein chains
151 a.a. *
64 a.a. *
_CA ×2
Waters ×329
* Residue conservation analysis
PDB id:
Name: Cell adhesion
Title: The clostridium cellulolyticum dockerin displays a dual binding mode for its cohesin partner
Structure: Scaffolding protein. Chain: a. Fragment: residues 277-427. Synonym: cohesin. Engineered: yes. Endoglucanase a. Chain: b. Fragment: residues 410-473. Synonym: dockerin, endo-1,4-beta-glucanase a, egcca,
Source: Clostridium cellulolyticum. Organism_taxid: 1521. Expressed in: escherichia coli. Expression_system_taxid: 562.
1.49Å     R-factor:   0.177     R-free:   0.210
Authors: B.A.Pinheiro,J.A.M.Prates,M.R.Proctor,H.J.Gilbert, G.J.Davies,V.A.Money,C.Martinez-Fleites,E.A.Bayer, C.M.G.A.Fontes,H.P.Fierobe
Key ref:
B.A.Pinheiro et al. (2008). The Clostridium cellulolyticum Dockerin Displays a Dual Binding Mode for Its Cohesin Partner. J Biol Chem, 283, 18422-18430. PubMed id: 18445585 DOI: 10.1074/jbc.M801533200
31-Jan-08     Release date:   13-May-08    
Go to PROCHECK summary

Protein chain
Pfam   ArchSchema ?
Q45996  (Q45996_9CLOT) -  Scaffolding protein
1546 a.a.
151 a.a.
Protein chain
Pfam   ArchSchema ?
P17901  (GUNA_CLOCE) -  Endoglucanase A
475 a.a.
64 a.a.*
Key:    PfamA domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 3 residue positions (black crosses)

 Enzyme reactions 
   Enzyme class: Chain B: 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     carbohydrate metabolic process   2 terms 
  Biochemical function     carbohydrate binding     2 terms  


DOI no: 10.1074/jbc.M801533200 J Biol Chem 283:18422-18430 (2008)
PubMed id: 18445585  
The Clostridium cellulolyticum Dockerin Displays a Dual Binding Mode for Its Cohesin Partner.
B.A.Pinheiro, M.R.Proctor, C.Martinez-Fleites, J.A.Prates, V.A.Money, G.J.Davies, E.A.Bayer, C.M.Fontesm, H.P.Fierobe, H.J.Gilbert.
The plant cell wall degrading apparatus of anaerobic bacteria includes a large multienzyme complex termed the "cellulosome." The complex assembles through the interaction of enzyme-derived dockerin modules with the multiple cohesin modules of the noncatalytic scaffolding protein. Here we report the crystal structure of the Clostridium cellulolyticum cohesin-dockerin complex in two distinct orientations. The data show that the dockerin displays structural symmetry reflected by the presence of two essentially identical cohesin binding surfaces. In one binding mode, visualized through the A16S/L17T dockerin mutant, the C-terminal helix makes extensive interactions with its cohesin partner. In the other binding mode observed through the A47S/F48T dockerin variant, the dockerin is reoriented by 180 degrees and interacts with the cohesin primarily through the N-terminal helix. Apolar interactions dominate cohesin-dockerin recognition that is centered around a hydrophobic pocket on the surface of the cohesin, formed by Leu-87 and Leu-89, which is occupied, in the two binding modes, by the dockerin residues Phe-19 and Leu-50, respectively. Despite the structural similarity between the C. cellulolyticum and Clostridium thermocellum cohesins and dockerins, there is no cross-specificity between the protein partners from the two organisms. The crystal structure of the C. cellulolyticum complex shows that organism-specific recognition between the protomers is dictated by apolar interactions primarily between only two residues, Leu-17 in the dockerin and the cohesin amino acid Ala-129. The biological significance of the plasticity in dockerin-cohesin recognition, observed here in C. cellulolyticum and reported previously in C. thermocellum, is discussed.
  Selected figure(s)  
Figure 2.
FIGURE 2. The three-dimensional structures of the C. cellulolyticum cohesin-dockerin complexes. a depicts the structure of Coh-DocA16S/L17T with the dockerin color-ramped from N terminus (blue) to C terminus (red) and the cohesin in pale brown. In this complex the hydrophobic residues Phe-48 and Ala-47 dominate the hydrophobic contribution of the dockerin, and these residues are shown as ball-and-stick. Ca^2+ ions are shown as shaded spheres. b shows the CohDocA47S/F48T complex, similarly colored. Here Leu-17 and Ala-16 of the dockerin form the basis of the hydrophobic surface of the dockerin. c depicts an overlap of the two binding modes showing the very high degree of overall similarity reflecting the internal 2-fold symmetry of the dockerin itself (see text). A47S/F48T is shown in blue and A16S/L17T in yellow.
Figure 4.
FIGURE 4. Overlap of the C. cellulolyticum and C. thermocellum cohesin-dockerin complexes in both binding modes highlighting the key recognition signature. A, C. cellulolyticum Coh-Doc A16S/L17T mutant complex (light green) is overlaid with the equivalent C. thermocellum cohesin-dockerin (wild type) complex (crimson) (PDB 1OHZ [PDB] ). B depicts the C. cellulolyticum Coh-Doc A47S/F48T mutant complex (yellow) overlaid with the equivalent C. thermocellum cohesin-dockerin S45A/T46A complex (pale blue) (PDB 2CCL).
  The above figures are reprinted by permission from the ASBMB: J Biol Chem (2008, 283, 18422-18430) copyright 2008.  
  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.  
20229062 D.Niu, X.X.Zhou, T.Y.Yuan, Z.W.Lin, H.Ruan, and W.F.Li (2010).
Effect of the C-terminal domains and terminal residues of catalytic domain on enzymatic activity and thermostability of lichenase from Clostridium thermocellum.
  Biotechnol Lett, 32, 963-967.  
19025568 A.Peer, S.P.Smith, E.A.Bayer, R.Lamed, and I.Borovok (2009).
Noncellulosomal cohesin- and dockerin-like modules in the three domains of life.
  FEMS Microbiol Lett, 291, 1.  
19758121 B.A.Pinheiro, H.J.Gilbert, K.Sakka, K.Sakka, V.O.Fernandes, J.A.Prates, V.D.Alves, D.N.Bolam, L.M.Ferreira, and C.M.Fontes (2009).
Functional insights into the role of novel type I cohesin and dockerin domains from Clostridium thermocellum.
  Biochem J, 424, 375-384.  
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.