4Z2S | pdb_00004z2s

The crystal structure of Sclerotium Rolfsii lectin variant 2 (SSR2) in complex with N-acetyl-glucosamine

• PDB DOI: https://doi.org/10.2210/pdb4Z2S/pdb

• Classification: SUGAR BINDING PROTEIN
• Organism(s): Agroathelia rolfsii
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2015-03-30 Released: 2015-07-01 
• Deposition Author(s): Kantsadi, A.L., Peppa, V.I., Leonidas, D.D.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free: 
  0.203 (Depositor), 0.209 (DCC) 
• R-Value Work: 
  0.165 (Depositor), 0.176 (DCC) 
• R-Value Observed: 
  0.167 (Depositor) 

Starting Model: experimental

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

• PubMed: 26076107 
• DOI: https://doi.org/10.3390/molecules200610848
• Primary Citation Related Structures: 
  4YLD, 4Z2F, 4Z2Q, 4Z2S


• 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 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.

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Organizational Affiliation: 
• Department of Biochemistry and Biotechnology, University of Thessaly, 26 Ploutonos Street, Larissa 41221, Greece. [e-mail].
Department of Biochemistry, Kuvempu University, Shimoga, Karnataka 577451, India. [e-mail].
Department of Biochemistry and Biotechnology, University of Thessaly, 26 Ploutonos Street, Larissa 41221, Greece. [e-mail].
Department of Post Graduate Studies in Biochemistry, Karnatak University, Dharwad 580003, India. [e-mail].
Department of Post Graduate Studies in Biochemistry, Karnatak University, Dharwad 580003, India. [e-mail].
Department of Post Graduate Studies in Biochemistry, Karnatak University, Dharwad 580003, India. [e-mail].
Department of Post Graduate Studies in Biochemistry, Karnatak University, Dharwad 580003, India. [e-mail].
Department of Post Graduate Studies in Biochemistry, Karnatak University, Dharwad 580003, India. [e-mail].
Department of Biochemistry, Kuvempu University, Shimoga, Karnataka 577451, India. [e-mail].
Department of Post Graduate Studies in Biochemistry, Karnatak University, Dharwad 580003, India. [e-mail].
Department of Biochemistry and Biotechnology, University of Thessaly, 26 Ploutonos Street, Larissa 41221, Greece. [e-mail].
Institute of Biology, Medicinal Chemistry & Biotechnology, National Hellenic Research Foundation, 48 Vas. Constantinou Ave, Athens 11635, Greece. [e-mail].
Department of Biochemistry and Biotechnology, University of Thessaly, 26 Ploutonos Street, Larissa 41221, Greece. [e-mail].

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 33.48 kDa 
• Atom Count: 2,764 
• Modeled Residue Count: 284 
• Deposited Residue Count: 284 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Sclerotium Rolfsii lectin variant	A, B	142	Agroathelia rolfsii	Mutation(s): 0
UniProt
Find proteins for A0A0M3KL31 (Agroathelia rolfsii) Explore A0A0M3KL31  Go to UniProtKB:  A0A0M3KL31

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAG	E [auth A], H [auth B]	2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N
NDG	D [auth A], G [auth B]	2-acetamido-2-deoxy-alpha-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-PVFLNQBWSA-N
TRS	C [auth A]	2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL C4 H12 N O3 LENZDBCJOHFCAS-UHFFFAOYSA-O
MPD	F [auth B]	(4S)-2-METHYL-2,4-PENTANEDIOL C6 H14 O2 SVTBMSDMJJWYQN-YFKPBYRVSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free:  0.203 (Depositor), 0.209 (DCC) 
• R-Value Work:  0.165 (Depositor), 0.176 (DCC) 
• R-Value Observed: 0.167 (Depositor) 

Space Group: P 4₂ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 100.025	α = 90
b = 100.025	β = 90
c = 63.783	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
CrysalisPro	data reduction
SCALA	data scaling
PHENIX	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2015-07-01 
Deposition Author(s): Kantsadi, A.L., Peppa, V.I., Leonidas, D.D.

Revision History  

• Version 1.0: 2015-07-01
  Type: Initial release
  
• Version 2.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Atomic model, Data collection, Derived calculations, Structure summary
• Version 2.1: 2024-01-10
  Changes: Data collection, Database references, Refinement description, Structure summary