2W47

Clostridium thermocellum CBM35 in complex with delta-4,5- anhydrogalacturonic acid

• PDB DOI:  https://doi.org/10.2210/pdb2W47/pdb

• Classification: HYDROLASE
• Organism(s): Acetivibrio thermocellus
• Expression System: Escherichia coli BL21
• Mutation(s): No 


• Deposited: 2008-11-21 Released: 2009-01-27 
• Deposition Author(s): Montainer, C., Lammerts van Bueren, A., Dumon, C., Flint, J.E., Correia, M.A., Prates, J.A., Firbank, S.J., Lewis, R.J., Grondin, G.G., Ghinet, M.G., Gloster, T.M., Herve, C., Knox, J.P., Talbot, B.G., Turkenburg, J.P., Kerovuo, J., Brzezinski, R., Fontes, C.M.G.A., Davies, G.J., Boraston, A.B., Gilbert, H.J.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.40 Å
• R-Value Free: 0.201 
• R-Value Work: 0.188 
• R-Value Observed: 0.188 

Literature

Evidence that Family 35 Carbohydrate Binding Modules Display Conserved Specificity But Divergent Function.

Montanier, C., Van Bueren, A.L., Dumon, C., Flint, J.E., Correia, M.A., Prates, J.A., Firbank, S.J., Lewis, R.J., Grondin, G.G., Ghinet, M.G., Gloster, T.M., Herve, C., Knox, J.P., Talbot, B.G., Turkenburg, J.P., Kerovuo, J., Brzezinski, R., Fontes, C.M.G.A., Davies, G.J., Boraston, A.B., Gilbert, H.J.

(2009) Proc Natl Acad Sci U S A 106: 3065

• PubMed: 19218457 
• DOI: https://doi.org/10.1073/pnas.0808972106
• Primary Citation of Related Structures:  
  2VZP, 2VZQ, 2VZR, 2W1W, 2W3J, 2W46, 2W47, 2W87


• PubMed Abstract: 
  

Enzymes that hydrolyze complex carbohydrates play important roles in numerous biological processes that result in the maintenance of marine and terrestrial life. These enzymes often contain noncatalytic carbohydrate binding modules (CBMs) that have important substrate-targeting functions. In general, there is a tight correlation between the ligands recognized by bacterial CBMs and the substrate specificity of the appended catalytic modules. Through high-resolution structural studies, we demonstrate that the architecture of the ligand binding sites of 4 distinct family 35 CBMs (CBM35s), appended to 3 plant cell wall hydrolases and the exo-beta-D-glucosaminidase CsxA, which contributes to the detoxification and metabolism of an antibacterial fungal polysaccharide, is highly conserved and imparts specificity for glucuronic acid and/or Delta4,5-anhydrogalaturonic acid (Delta4,5-GalA). Delta4,5-GalA is released from pectin by the action of pectate lyases and as such acts as a signature molecule for plant cell wall degradation. Thus, the CBM35s appended to the 3 plant cell wall hydrolases, rather than targeting the substrates of the cognate catalytic modules, direct their appended enzymes to regions of the plant that are being actively degraded. Significantly, the CBM35 component of CsxA anchors the enzyme to the bacterial cell wall via its capacity to bind uronic acid sugars. This latter observation reveals an unusual mechanism for bacterial cell wall enzyme attachment. This report shows that the biological role of CBM35s is not dictated solely by their carbohydrate specificities but also by the context of their target ligands.

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Organizational Affiliation: 

Institute for Cell and Molecular Biosciences, The Medical School, Newcastle University, Newcastle upon Tyne NE2 4HH, United Kingdom.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

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

Macromolecule Content

• Total Structure Weight: 16.11 kDa 
• Atom Count: 1,315 
• Modelled Residue Count: 135 
• Deposited Residue Count: 144 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
LIPOLYTIC ENZYME, G-D-S-L	A	144	Acetivibrio thermocellus	Mutation(s): 0
UniProt
Find proteins for A3DK57 (Acetivibrio thermocellus (strain ATCC 27405 / DSM 1237 / JCM 9322 / NBRC 103400 / NCIMB 10682 / NRRL B-4536 / VPI 7372)) Explore A3DK57  Go to UniProtKB:  A3DK57

Oligosaccharides

Help

Entity ID: 2
Molecule	Chains	Chain Length	2D Diagram	Glycosylation
4-deoxy-beta-L-threo-hex-4-enopyranuronic acid-(1-4)-beta-D-galactopyranuronic acid	B	2		N/A
Glycosylation Resources
GlyTouCan:  G81894HG GlyCosmos:  G81894HG

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CA	C [auth A]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.40 Å
• R-Value Free: 0.201 
• R-Value Work: 0.188 
• R-Value Observed: 0.188 
• Space Group: P 6₅ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 86.033	α = 90
b = 86.033	β = 90
c = 75.905	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement
MOSFLM	data reduction
SCALA	data scaling
MOLREP	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2009-01-27 
Deposition Author(s): Montainer, C., Lammerts van Bueren, A., Dumon, C., Flint, J.E., Correia, M.A., Prates, J.A., Firbank, S.J., Lewis, R.J., Grondin, G.G., Ghinet, M.G., Gloster, T.M., Herve, C., Knox, J.P., Talbot, B.G., Turkenburg, J.P., Kerovuo, J., Brzezinski, R., Fontes, C.M.G.A., Davies, G.J., Boraston, A.B., Gilbert, H.J.

Revision History  

• Version 1.0: 2009-01-27
  Type: Initial release
  
• Version 1.1: 2012-04-04
  Changes: Derived calculations, Non-polymer description, Other, Refinement description, Structure summary, Version format compliance
• Version 1.2: 2017-06-28
  Changes: Data collection
• Version 2.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Advisory, Atomic model, Data collection, Derived calculations, Non-polymer description, Other, Structure summary