3U4X

Crystal structure of a lectin from Camptosema pedicellatum seeds in complex with 5-bromo-4-chloro-3-indolyl-alpha-D-mannose


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.16 Å
  • R-Value Free: 0.237 
  • R-Value Work: 0.190 
  • R-Value Observed: 0.193 

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This is version 1.2 of the entry. See complete history


Literature

Crystal structure of the lectin of Camptosema pedicellatum: implications of a conservative substitution at the hydrophobic subsite.

Souza Teixeira, C.Colares da Silva, H.Rocha de Moura, T.Pereira-Junior, F.N.Santiago do Nascimento, K.Shiniti Nagano, C.Holanda Sampaio, A.Delatorre, P.Matias Rocha, B.A.Sousa Cavada, B.

(2012) J Biochem 152: 87-98

  • DOI: https://doi.org/10.1093/jb/mvs047
  • Primary Citation of Related Structures:  
    3U4X

  • PubMed Abstract: 

    Lectins have been used as models for studies of the molecular basis of protein-carbohydrate interaction and specificity by deciphering codes present in the glycan structures. The purpose of the present study was to purify and solve the complete primary and crystal structure of the lectin of Camptosema pedicellatum (CPL) complexed with 5-bromo-4-chloro-3-indolyl-α-d-mannose (X-Man) using tandem mass spectrometry. CPL was purified by single-step affinity chromatography. Mass spectrometry findings revealed that purified CPL features a combination of chains weighing 25,298 ± 2 (α-chain), 12,835 ± 2 (β-chain) and 12,481 ± 2 Da (γ-chain). The solved crystal structure of CPL features a conservative mutation in the hydrophobic subsite, a constituent of the carbohydrate recognition domain (CRD), indicating the relevance of hydrophobic interactions in the establishment of interactions with carbohydrates. The substitution and the analysis of the interactions with X-Man also revealed that the hydrophobic effect caused by a minor change in the hydrophobic subsite interferes in the formation of H-bonds due to the reorientation of the indolyl group in the CRD.


  • Organizational Affiliation

    BioMol-Lab, Laboratório de Moléculas Biologicamente Ativas, Departamento de Bioquímica e Biologia Molecular, Universidade Federal do Ceará, Fortaleza, Ceará 60440-970, Brazil.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Camptosema pedicellatum lectin (CPL)236Bionia pedicellataMutation(s): 0 
UniProt
Find proteins for J9PBR3 (Bionia pedicellata)
Explore J9PBR3 
Go to UniProtKB:  J9PBR3
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupJ9PBR3
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.16 Å
  • R-Value Free: 0.237 
  • R-Value Work: 0.190 
  • R-Value Observed: 0.193 
  • Space Group: I 2 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 65.94α = 90
b = 66.78β = 90
c = 107.7γ = 90
Software Package:
Software NamePurpose
MOLREPphasing
REFMACrefinement
PDB_EXTRACTdata extraction
MOSFLMdata reduction
SCALAdata scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2012-09-12
    Type: Initial release
  • Version 1.1: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Derived calculations, Structure summary
  • Version 1.2: 2024-02-28
    Changes: Data collection, Database references, Structure summary