4Z2Q

The crystal structure of Sclerotium Rolfsii lectin variant 1 (SSR1) in complex with N-acetyl-glucosamine


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.9 Å
  • R-Value Free: 0.186 
  • R-Value Work: 0.146 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history

Literature

Molecular Cloning, Carbohydrate Specificity and the Crystal Structure of Two Sclerotium rolfsii Lectin Variants.

Peppa, V.I.Venkat, H.Kantsadi, A.L.Inamdar, S.R.Bhat, G.G.Eligar, S.Shivanand, A.Chachadi, V.B.Satisha, G.J.Swamy, B.M.Skamnaki, V.T.Zographos, S.E.Leonidas, D.D.

(2015) Molecules 20: 10848-10865

  • DOI: 10.3390/molecules200610848
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • SRL is a cell wall associated developmental-stage specific lectin secreted by Sclerotium rolfsii, a soil-born pathogenic fungus. SRL displays specificity for TF antigen (Galβ1→3GalNAc-α-Ser//Thr) expressed in all cancer types and has tumour suppressi ...

    SRL is a cell wall associated developmental-stage specific lectin secreted by Sclerotium rolfsii, a soil-born pathogenic fungus. SRL displays specificity for TF antigen (Galβ1→3GalNAc-α-Ser//Thr) expressed in all cancer types and has tumour suppressing effects in vivo. Considering the immense potential of SRL in cancer research, we have generated two variant gene constructs of SRL and expressed in E. coli to refine the sugar specificity and solubility by altering the surface charge. SSR1 and SSR2 are two different recombinant variants of SRL, both of which recognize TF antigen but only SSR1 binds to Tn antigen (GalNAcα-Ser/Thr). The glycan array analysis of the variants demonstrated that SSR1 recognizes TF antigen and their derivative with high affinity similar to SRL but showed highest affinity towards the sialylated Tn antigen, unlike SRL. The carbohydrate binding property of SSR2 remains unaltered compared to SRL. The crystal structures of the two variants were determined in free form and in complex with N-acetylglucosamine at 1.7 Å and 1.6 Å resolution, respectively. Structural analysis highlighted the structural basis of the fine carbohydrate specificity of the two SRL variants and results are in agreement with glycan array analysis.


    Organizational Affiliation

    Department of Post Graduate Studies in Biochemistry, Karnatak University, Dharwad 580003, India. anupamas.biochem@gmail.com.,Department of Biochemistry and Biotechnology, University of Thessaly, 26 Ploutonos Street, Larissa 41221, Greece. natassakan@windowslive.com.,Department of Post Graduate Studies in Biochemistry, Karnatak University, Dharwad 580003, India. sawmy_bm@yahoo.co.in.,Department of Biochemistry and Biotechnology, University of Thessaly, 26 Ploutonos Street, Larissa 41221, Greece. ddleonidas@bio.uth.gr.,Department of Post Graduate Studies in Biochemistry, Karnatak University, Dharwad 580003, India. ganapati.bd@gmail.com.,Department of Post Graduate Studies in Biochemistry, Karnatak University, Dharwad 580003, India. vishwanath1014@yahoo.co.in.,Department of Biochemistry, Kuvempu University, Shimoga, Karnataka 577451, India. satishlec@gmail.com.,Department of Post Graduate Studies in Biochemistry, Karnatak University, Dharwad 580003, India. sachinbchem@gmail.com.,Department of Biochemistry and Biotechnology, University of Thessaly, 26 Ploutonos Street, Larissa 41221, Greece. vskamnaki@bio.uth.gr.,Department of Post Graduate Studies in Biochemistry, Karnatak University, Dharwad 580003, India. srinamdar2009@gmail.com.,Department of Biochemistry, Kuvempu University, Shimoga, Karnataka 577451, India. hemalatha.venkat@enzene.com.,Department of Biochemistry and Biotechnology, University of Thessaly, 26 Ploutonos Street, Larissa 41221, Greece. vikpeppa@gmail.com.,Institute of Biology, Medicinal Chemistry & Biotechnology, National Hellenic Research Foundation, 48 Vas. Constantinou Ave, Athens 11635, Greece. sez@eie.gr.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Lectin
A, B
141Athelia rolfsiiMutation(s): 0 
Gene Names: l1
Find proteins for A0A0M3KL30 (Athelia rolfsii)
Go to UniProtKB:  A0A0M3KL30
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NDG
Query on NDG

Download SDF File 
Download CCD File 
A, B
2-(ACETYLAMINO)-2-DEOXY-A-D-GLUCOPYRANOSE
C8 H15 N O6
OVRNDRQMDRJTHS-PVFLNQBWSA-N
 Ligand Interaction
NAG
Query on NAG

Download SDF File 
Download CCD File 
A, B
N-ACETYL-D-GLUCOSAMINE
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
 Ligand Interaction
MPD
Query on MPD

Download SDF File 
Download CCD File 
B
(4S)-2-METHYL-2,4-PENTANEDIOL
C6 H14 O2
SVTBMSDMJJWYQN-YFKPBYRVSA-N
 Ligand Interaction
TRS
Query on TRS

Download SDF File 
Download CCD File 
A
2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL
TRIS BUFFER
C4 H12 N O3
LENZDBCJOHFCAS-UHFFFAOYSA-O
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.9 Å
  • R-Value Free: 0.186 
  • R-Value Work: 0.146 
  • Space Group: P 42 21 2
Unit Cell:
Length (Å)Angle (°)
a = 99.919α = 90.00
b = 99.919β = 90.00
c = 63.810γ = 90.00
Software Package:
Software NamePurpose
REFMACrefinement
PHENIXphasing
SCALAdata scaling
CrysalisProdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2015-07-01
    Type: Initial release