Biological Assembly 1  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report | Ligand Interaction

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 1 assigned by authors and generated by PQS (software)

Biological Assembly 2  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report | Ligand Interaction

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 2 assigned by authors and generated by PQS (software)

Macromolecule Content

• Total Structure Weight: 45.85 kDa 
• Atom Count: 3264 
• Modelled Residue Count: 401 
• Deposited Residue Count: 434 
• Unique protein chains: 2

2VN5

The Clostridium cellulolyticum dockerin displays a dual binding mode for its cohesin partner

• PDB DOI: 10.2210/pdb2VN5/pdb

• Classification: CELL ADHESION
• Organism(s): Ruminiclostridium cellulolyticum
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2008-01-31 Released: 2008-05-20 
• Deposition Author(s): Pinheiro, B.A., Prates, J.A.M., Proctor, M.R., Gilbert, H.J., Davies, G.J., Money, V.A., Martinez-Fleites, C., Bayer, E.A., Fontes, C.M.G.A., Fierobe, H.P.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 0.234 
• R-Value Work: 0.179 
• R-Value Observed: 0.182 

Literature

The Clostridium Cellulolyticum Dockerin Displays a Dual Binding Mode for its Cohesin Partner.

Pinheiro, B.A., Proctor, M.R., Martinez-Fleites, C., Prates, J.A.M., Money, V.A., Davies, G.J., Bayer, E.A., Fontes, C.M.G.A., Fierobe, H.P., Gilbert, H.J.

(2008) J Biol Chem 283: 18422

• PubMed: 18445585 
• DOI: 10.1074/jbc.M801533200
• Primary Citation of Related Structures:  
  2VN5, 2VN6


• PubMed Abstract: 
  

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.

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Organizational Affiliation: 

Centro Interdisciplinar de Investigação em Sanidade Animal, Faculdade de Medicina Veterinária, Universidade Técnica de Lisboa, Lisboa, Portugal.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
SCAFFOLDING PROTEIN	A, C	151	Ruminiclostridium cellulolyticum	Mutation(s): 0  Gene Names: cipC
UniProt
Find proteins for Q45996 (Ruminiclostridium cellulolyticum) Explore Q45996  Go to UniProtKB:  Q45996

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
ENDOGLUCANASE A	B, D	66	Ruminiclostridium cellulolyticum	Mutation(s): 0  EC: 3.2.1.4
UniProt
Find proteins for P17901 (Ruminiclostridium cellulolyticum (strain ATCC 35319 / DSM 5812 / JCM 6584 / H10)) Explore P17901  Go to UniProtKB:  P17901

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CA	E [auth B], F [auth B], G [auth D], H [auth D]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 0.234 
• R-Value Work: 0.179 
• R-Value Observed: 0.182 
• Space Group: P 3₂ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 76.42	α = 90
b = 76.42	β = 90
c = 111.095	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement
DENZO	data reduction
SCALEPACK	data scaling
MOLREP	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2008-01-31 
• Released Date: 2008-05-20 
Deposition Author(s): Pinheiro, B.A., Prates, J.A.M., Proctor, M.R., Gilbert, H.J., Davies, G.J., Money, V.A., Martinez-Fleites, C., Bayer, E.A., Fontes, C.M.G.A., Fierobe, H.P.

Revision History  

• Version 1.0: 2008-05-20
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Advisory, Version format compliance