2X34

Structure of a polyisoprenoid binding domain from Saccharophagus degradans implicated in plant cell wall breakdown

• PDB DOI: https://doi.org/10.2210/pdb2X34/pdb

• Classification: CARBOHYDRATE-BINDING PROTEIN
• Organism(s): Saccharophagus degradans 2-40
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2010-01-19 Released: 2010-03-23 
• Deposition Author(s): Vincent, F., Dal Molin, D., Weiner, R.M., Bourne, Y., Henrissat, B.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 0.223 
• R-Value Work: 0.175 
• R-Value Observed: 0.178 

Literature

Structure of a Polyisoprenoid Binding Domain from Saccharophagus Degradans Implicated in Plant Cell Wall Breakdown

Vincent, F., Dalmolin, D., Weiner, R.M., Bourne, Y., Henrissat, B.

(2010) FEBS Lett 584: 1577

• PubMed: 20227408 
• DOI: https://doi.org/10.1016/j.febslet.2010.03.015
• Primary Citation of Related Structures:  
  2X32, 2X34


• PubMed Abstract: 
  

  Saccharophagus degradans belongs to a recently discovered group of marine bacteria equipped with an arsenal of sugar cleaving enzymes coupled to carbohydrate-binding domains to degrade various insoluble complex polysaccharides. The modular Sde-1182 protein consists of a family 2 carbohydrate binding module linked to a X158 domain of unknown function. The 1.9 A and 1.55 A resolution crystal structures of the isolated X158 domain bound to the two related polyisoprenoid molecules, ubiquinone and octaprenyl pyrophosphate, unveil a beta-barrel architecture reminiscent of the YceI-like superfamily that resembles the architecture of the lipocalin fold. This unprecedented association coupling oxidoreduction and carbohydrate recognition events may have implications for effective nutrient uptake in the marine environment.

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Organizational Affiliation: 

Architecture et Fonction des Macromolécules Biologiques, UMR6098, CNRS and Aix-Marseille Universities, Marseille, France. [e-mail]

Biological Assembly 1  

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

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

Biological Assembly 2  

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

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

Macromolecule Content

• Total Structure Weight: 41 kDa 
• Atom Count: 3,126 
• Modelled Residue Count: 349 
• Deposited Residue Count: 362 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
CELLULOSE-BINDING PROTEIN, X158	A, B	181	Saccharophagus degradans 2-40	Mutation(s): 0
UniProt
Find proteins for Q21LI5 (Saccharophagus degradans (strain 2-40 / ATCC 43961 / DSM 17024)) Explore Q21LI5  Go to UniProtKB:  Q21LI5

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
UQ8	C [auth A], D [auth B]	Ubiquinone-8 C49 H74 O4 ICFIZJQGJAJRSU-SGHXUWJISA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE	A, B	L-PEPTIDE LINKING	C5 H11 N O2 Se		MET

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 0.223 
• R-Value Work: 0.175 
• R-Value Observed: 0.178 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 62.979	α = 90
b = 64.964	β = 90
c = 84.191	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2010-03-23 
Deposition Author(s): Vincent, F., Dal Molin, D., Weiner, R.M., Bourne, Y., Henrissat, B.

Revision History  

• Version 1.0: 2010-03-23
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Advisory, Version format compliance
• Version 1.2: 2018-03-07
  Changes: Advisory, Source and taxonomy
• Version 1.3: 2024-10-23
  Changes: Advisory, Data collection, Database references, Derived calculations, Other, Structure summary