5FRE

Characterization of a novel CBM from Clostridium perfringens


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.9 Å
  • R-Value Free: 0.209 
  • R-Value Work: 0.173 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history

Literature

Characterization of a High-Affinity Sialic Acid-Specific Cbm40 from Clostridium Perfringens and Engineering of a Divalent Form.

Ribeiro, J.P.Pau, W.Pifferi, C.Renaudet, O.Varrot, A.Mahal, L.K.Imberty, A.

(2016) Biochem.J. 473: 2109

  • DOI: 10.1042/BCJ20160340
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • CBMs (carbohydrate-binding modules) are a class of polypeptides usually associated with carbohydrate-active enzymatic sites. We have characterized a new member of the CBM40 family, coded from a section of the gene NanI from Clostridium perfringens Gl ...

    CBMs (carbohydrate-binding modules) are a class of polypeptides usually associated with carbohydrate-active enzymatic sites. We have characterized a new member of the CBM40 family, coded from a section of the gene NanI from Clostridium perfringens Glycan arrays revealed its preference towards α(2,3)-linked sialosides, which was confirmed and quantified by calorimetric studies. The CBM40 binds to α(2,3)-sialyl-lactose with a Kd of ∼30 μM, the highest affinity value for this class of proteins. Inspired by lectins' structure and their arrangement as multimeric proteins, we have engineered a dimeric form of the CBM, and using SPR (surface plasmon resonance) we have observed 6-11-fold binding increases due to the avidity affect. The structures of the CBM, resolved by X-ray crystallography, in complex with α(2,3)- or α(2,6)-sialyl-lactose explain its binding specificity and unusually strong binding.


    Organizational Affiliation

    CERMAV, UPR5301, CNRS and Université Grenoble Alpes, 601 rue de la Chimie, BP 53, 38041, Grenoble, France lkmahal@nyu.edu imberty@cermav.cnrs.fr.,Biomedical Chemistry Institute, New York University Department of Chemistry, 100 Washington Square East, Room 1001, New York, NY 10003, U.S.A.,Université Grenoble Alpes, DCM, BP 53, 38041 Grenoble cedex 9, France.,Biomedical Chemistry Institute, New York University Department of Chemistry, 100 Washington Square East, Room 1001, New York, NY 10003, U.S.A. lkmahal@nyu.edu imberty@cermav.cnrs.fr.,Biomedical Chemistry Institute, New York University Department of Chemistry, 100 Washington Square East, Room 1001, New York, NY 10003, U.S.A. CERMAV, UPR5301, CNRS and Université Grenoble Alpes, 601 rue de la Chimie, BP 53, 38041, Grenoble, France.,CERMAV, UPR5301, CNRS and Université Grenoble Alpes, 601 rue de la Chimie, BP 53, 38041, Grenoble, France.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
EXO-ALPHA-SIALIDASE
A, B, C
194Clostridium perfringens (strain ATCC 13124 / DSM 756 / JCM 1290 / NCIMB 6125 / NCTC 8237 / Type A)Mutation(s): 0 
Gene Names: nanI
Find proteins for A0A0H2YQR1 (Clostridium perfringens (strain ATCC 13124 / DSM 756 / JCM 1290 / NCIMB 6125 / NCTC 8237 / Type A))
Go to UniProtKB:  A0A0H2YQR1
Small Molecules
Ligands 5 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
1PG
Query on 1PG

Download SDF File 
Download CCD File 
A, B
2-(2-{2-[2-(2-METHOXY-ETHOXY)-ETHOXY]-ETHOXY}-ETHOXY)-ETHANOL
C11 H24 O6
SLNYBUIEAMRFSZ-UHFFFAOYSA-N
 Ligand Interaction
ACT
Query on ACT

Download SDF File 
Download CCD File 
B
ACETATE ION
C2 H3 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-M
 Ligand Interaction
CA
Query on CA

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Download CCD File 
A, B, C
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
GAL
Query on GAL

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Download CCD File 
A, B, C
BETA-D-GALACTOSE
C6 H12 O6
WQZGKKKJIJFFOK-FPRJBGLDSA-N
 Ligand Interaction
SIA
Query on SIA

Download SDF File 
Download CCD File 
A, B, C
O-SIALIC ACID
C11 H19 N O9
SQVRNKJHWKZAKO-YRMXFSIDSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.9 Å
  • R-Value Free: 0.209 
  • R-Value Work: 0.173 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 64.348α = 90.00
b = 76.714β = 93.46
c = 67.254γ = 90.00
Software Package:
Software NamePurpose
PHASERphasing
XDSdata reduction
REFMACrefinement
Aimlessdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2016-07-20
    Type: Initial release