5LU3

The Structure of Spirochaeta thermophila CBM64


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.50 Å
  • R-Value Free: 0.151 
  • R-Value Work: 0.124 
  • R-Value Observed: 0.125 

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This is version 2.0 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: https://doi.org/10.1074/jbc.M116.767541
  • Primary Citation of Related Structures:  
    5LU3

  • 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 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 St CBM64C 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:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Glycoside hydrolase family 1292Spirochaeta thermophila DSM 6578Mutation(s): 0 
Gene Names: Spith_0373
UniProt
Find proteins for G0GE26 (Spirochaeta thermophila (strain ATCC 700085 / DSM 6578 / Z-1203))
Explore G0GE26 
Go to UniProtKB:  G0GE26
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupG0GE26
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 5 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
2NV
Query on 2NV

Download Ideal Coordinates CCD File 
B [auth A]3,6,9,12,15-pentaoxaoctadecan-17-amine
C13 H29 N O5
LPPZTQZWMYYVLK-CYBMUJFWSA-N
SSN
Query on SSN

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C [auth A]4-oxobutanoic acid
C4 H6 O3
UIUJIQZEACWQSV-UHFFFAOYSA-N
NI
Query on NI

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E [auth A]NICKEL (II) ION
Ni
VEQPNABPJHWNSG-UHFFFAOYSA-N
FMT
Query on FMT

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F [auth A]FORMIC ACID
C H2 O2
BDAGIHXWWSANSR-UHFFFAOYSA-N
CA
Query on CA

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D [auth A]CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.50 Å
  • R-Value Free: 0.151 
  • R-Value Work: 0.124 
  • R-Value Observed: 0.125 
  • Space Group: P 43 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 56.703α = 90
b = 56.703β = 90
c = 66.738γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
PHENIXphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2017-02-15
    Type: Initial release
  • Version 1.1: 2017-02-22
    Changes: Database references
  • Version 1.2: 2017-04-05
    Changes: Database references
  • Version 2.0: 2024-05-08
    Changes: Atomic model, Data collection, Database references, Derived calculations