2X32

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

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.55 Å
  • R-Value Free: 0.194 
  • R-Value Work: 0.159 
  • R-Value Observed: 0.160 

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This is version 1.2 of the entry. See complete history. 


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

  • DOI: 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 ...

    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.

    Organizational Affiliation: 

    Architecture et Fonction des Macromolécules Biologiques, UMR6098, CNRS and Aix-Marseille Universities, Marseille, France. florence.vincent@afmb.univ-mrs.fr



Macromolecules
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(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
CELLULOSE-BINDING PROTEINA, B179Saccharophagus degradans 2-40Mutation(s): 0 
Gene Names: cbm2A, Sde_1182
UniProt
Find proteins for Q21LI5 (Saccharophagus degradans (strain 2-40 / ATCC 43961 / DSM 17024))
Explore Q21LI5 
Go to UniProtKB:  Q21LI5
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ21LI5
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
OTP
Query on OTP
Download Ideal Coordinates CCD File 
C [auth A],
E [auth B]		(2E,6E,10E,14E,18E,22E,26E)-3,7,11,15,19,23,27,31-OCTAMETHYLDOTRIACONTA-2,6,10,14,18,22,26,30-OCTAENYL TRIHYDROGEN DIPHOSPHATE
C40 H68 O7 P2
IKKLDISSULFFQO-DJMILUHSSA-N		 Ligand Interaction
IMD
Query on IMD
Download Ideal Coordinates CCD File 
D [auth A],
F [auth B],
G [auth B]		IMIDAZOLE
C3 H5 N2
RAXXELZNTBOGNW-UHFFFAOYSA-O		 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.55 Å
  • R-Value Free: 0.194 
  • R-Value Work: 0.159 
  • R-Value Observed: 0.160 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 63.378α = 90
b = 64.36β = 90
c = 84.732γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling
AMoREphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • 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: Source and taxonomy