2W47

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.4 Å
  • R-Value Free: 0.201 
  • R-Value Work: 0.188 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

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.USA 106: 3065

  • DOI: 10.1073/pnas.0808972106
  • Primary Citation of Related Structures:  2VZP, 2VZQ, 2VZR, 2W1W, 2W3J, 2W46, 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 i ...

    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.


    Organizational Affiliation

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




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
LIPOLYTIC ENZYME, G-D-S-L
A
144Clostridium thermocellum (strain ATCC 27405 / DSM 1237 / NBRC 103400 / NCIMB 10682 / NRRL B-4536 / VPI 7372)N/A
Find proteins for A3DK57 (Clostridium thermocellum (strain ATCC 27405 / DSM 1237 / NBRC 103400 / NCIMB 10682 / NRRL B-4536 / VPI 7372))
Go to UniProtKB:  A3DK57
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CA
Query on CA

Download SDF File 
Download CCD File 
A
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
UNF
Query on UNF

Download SDF File 
Download CCD File 
A
4-O-(4-deoxy-beta-L-threo-hex-4-enopyranuronosyl)-beta-D-galactopyranuronic acid
C12 H16 O12
LLVVMXFNKAHVEZ-KMBKDFKYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
UNFKd: 10500 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.4 Å
  • R-Value Free: 0.201 
  • R-Value Work: 0.188 
  • Space Group: P 65 2 2
Unit Cell:
Length (Å)Angle (°)
a = 86.033α = 90.00
b = 86.033β = 90.00
c = 75.905γ = 120.00
Software Package:
Software NamePurpose
MOSFLMdata reduction
SCALAdata scaling
REFMACrefinement
MOLREPphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Revision History 

  • Version 1.0: 2009-01-27
    Type: Initial release
  • Version 1.1: 2012-04-04
    Type: Derived calculations, Non-polymer description, Other, Refinement description, Structure summary, Version format compliance
  • Version 1.2: 2017-06-28
    Type: Data collection