5LU3

The Structure of Spirochaeta thermophila CBM64


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.5 Å
  • R-Value Free: 0.151 
  • R-Value Work: 0.124 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Stability and Ligand Promiscuity of Type A Carbohydrate-binding Modules Are Illustrated by the Structure of Spirochaeta thermophila StCBM64C.

Pires, V.M.Pereira, P.M.Bras, J.L.Correia, M.Cardoso, V.Bule, P.Alves, V.D.Najmudin, S.Venditto, I.Ferreira, L.M.Romao, M.J.Carvalho, A.L.Fontes, C.M.Prazeres, D.M.

(2017) J. Biol. Chem. 292: 4847-4860

  • DOI: 10.1074/jbc.M116.767541

  • PubMed Abstract: 
  • Deconstruction of cellulose, the most abundant plant cell wall polysaccharide, requires the cooperative activity of a large repertoire of microbial enzymes. Modular cellulases contain non-catalytic type A carbohydrate-binding modules (CBMs) that spec ...

    Deconstruction of cellulose, the most abundant plant cell wall polysaccharide, requires the cooperative activity of a large repertoire of microbial enzymes. Modular cellulases contain non-catalytic type A carbohydrate-binding modules (CBMs) that specifically bind to the crystalline regions of cellulose, thus promoting enzyme efficacy through proximity and targeting effects. Although type A CBMs play a critical role in cellulose recycling, their mechanism of action remains poorly understood. Here we produced a library of recombinant CBMs representative of the known diversity of type A modules. The binding properties of 40 CBMs, in fusion with an N-terminal GFP domain, revealed that type A CBMs possess the ability to recognize different crystalline forms of cellulose and chitin over a wide range of temperatures, pH levels, and ionic strengths. A Spirochaeta thermophila CBM64, in particular, displayed plasticity in its capacity to bind both crystalline and soluble carbohydrates under a wide range of extreme conditions. The structure of S. thermophila StCBM64C revealed an untwisted, flat, carbohydrate-binding interface comprising the side chains of four tryptophan residues in a co-planar linear arrangement. Significantly, two highly conserved asparagine side chains, each one located between two tryptophan residues, are critical to insoluble and soluble glucan recognition but not to bind xyloglucan. Thus, CBM64 compact structure and its extended and versatile ligand interacting platform illustrate how type A CBMs target their appended plant cell wall-degrading enzymes to a diversity of recalcitrant carbohydrates under a wide range of environmental conditions.


    Organizational Affiliation

    From the CIISA, Faculdade de Medicina Veterinária, Universidade de Lisboa, Pólo Universitário da Ajuda, 1300-477 Lisboa, Portugal.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Glycoside hydrolase family 12
A
92Spirochaeta thermophila (strain ATCC 700085 / DSM 6578 / Z-1203)Mutation(s): 0 
Find proteins for G0GE26 (Spirochaeta thermophila (strain ATCC 700085 / DSM 6578 / Z-1203))
Go to UniProtKB:  G0GE26
Small Molecules
Ligands 5 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
2NV
Query on 2NV

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A
3,6,9,12,15-pentaoxaoctadecan-17-amine
Jeffamine ED-2001
C13 H29 N O5
LPPZTQZWMYYVLK-UHFFFAOYSA-N
 Ligand Interaction
FMT
Query on FMT

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Download CCD File 
A
FORMIC ACID
C H2 O2
BDAGIHXWWSANSR-UHFFFAOYSA-N
 Ligand Interaction
CA
Query on CA

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

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Download CCD File 
A
4-oxobutanoic acid
Succinic semialdehyde
C4 H6 O3
UIUJIQZEACWQSV-UHFFFAOYSA-N
 Ligand Interaction
NI
Query on NI

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Download CCD File 
A
NICKEL (II) ION
Ni
VEQPNABPJHWNSG-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.5 Å
  • R-Value Free: 0.151 
  • R-Value Work: 0.124 
  • Space Group: P 43 21 2
Unit Cell:
Length (Å)Angle (°)
a = 56.703α = 90.00
b = 56.703β = 90.00
c = 66.738γ = 90.00
Software Package:
Software NamePurpose
REFMACrefinement
Aimlessdata scaling
XDSdata reduction
PHENIXphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2017-02-15
    Type: Initial release
  • Version 1.1: 2017-02-22
    Type: Database references
  • Version 1.2: 2017-04-05
    Type: Database references