2VNV | pdb_00002vnv

Crystal structure of BclA lectin from burkholderia cenocepacia in complex with alpha-methyl-mannoside at 1.7 Angstrom resolution


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.70 Å
  • R-Value Free: 
    0.203 (Depositor), 0.203 (DCC) 
  • R-Value Work: 
    0.169 (Depositor), 0.168 (DCC) 
  • R-Value Observed: 
    0.171 (Depositor) 

wwPDB Validation 3D Report Full Report

Validation slider image for 2VNV

Ligand Structure Quality Assessment 


This is version 1.4 of the entry. See complete history

Literature

Structural Basis for Mannose Recognition by a Lectin from Opportunistic Bacteria Burkholderia Cenocepacia

Lameignere, E.Malinovska, L.Slavikova, M.Duchaud, E.Mitchell, E.P.Varrot, A.Sedo, O.Imberty, A.Wimmerova, M.

(2008) Biochem J 411: 307

  • DOI: https://doi.org/10.1042/bj20071276
  • Primary Citation Related Structures: 
    2VNV

  • PubMed Abstract: 

    Chronic colonization of the lungs by opportunist bacteria such as Pseudomonas aeruginosa and members of the Bcc (Burkholderia cepacia complex) is the major cause of morbidity and mortality among CF (cystic fibrosis) patients. PA-IIL (lecB gene), a soluble lectin from Ps. aeruginosa, has been the subject of much interest because of its very strong affinity for fucose. Orthologues have been identified in the opportunist bacteria Ralstonia solanacearum, Chromobacterium violaceum and Burkholderia of Bcc. The genome of the J2315 strain of B. cenocepacia, responsible for epidemia in CF centres, contains three genes that code for proteins with PA-IIL domains. The shortest gene was cloned in Escherichia coli and pure recombinant protein, BclA (B. cenocepacia lectin A), was obtained. The presence of native BclA in B. cenocepacia extracts was checked using a proteomic approach. The specificity of recombinant BclA was characterized using surface plasmon resonance showing a preference for mannosides and supported with glycan array experiments demonstrating a strict specificity for oligomannose-type N-glycan structures. The interaction thermodynamics of BclA with methyl alpha-D-mannoside demonstrates a dissociation constant (K(d)) of 2.75 x 10(-6) M. The X-ray crystal structure of the complex with methyl alpha-D-mannoside was determined at 1.7 A (1 A=0.1 nm) resolution. The lectin forms homodimers with one binding site per monomer, acting co-operatively with the second dimer site. Each monomer contains two Ca2+ ions and one sugar ligand. Despite strong sequence similarity, the differences between BclA and PA-IIL in their specificity, binding site and oligomerization mode indicate that the proteins should have different roles in the bacteria.


  • Organizational Affiliation
    • CERMAV-CNRS, BP 53, F-38041, Grenoble, Cedex 09, France.

Macromolecule Content 

  • Total Structure Weight: 71.31 kDa 
  • Atom Count: 6,374 
  • Modeled Residue Count: 631 
  • Deposited Residue Count: 645 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
BCLA
A, B, C, D, E
129Burkholderia cenocepacia J2315Mutation(s): 0 
UniProt
Find proteins for B4EH87 (Burkholderia cenocepacia (strain ATCC BAA-245 / DSM 16553 / LMG 16656 / NCTC 13227 / J2315 / CF5610))
Explore B4EH87 
Go to UniProtKB:  B4EH87
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupB4EH87
Sequence Annotations
Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
MMA

Query on MMA



Download:Ideal Coordinates CCD File
F [auth A],
J [auth B],
N [auth C],
Q [auth D],
U [auth E]
methyl alpha-D-mannopyranoside
C7 H14 O6
HOVAGTYPODGVJG-VEIUFWFVSA-N
SO4

Query on SO4



Download:Ideal Coordinates CCD File
I [auth A],
M [auth B],
T [auth D],
X [auth E]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
CA

Query on CA



Download:Ideal Coordinates CCD File
G [auth A]
H [auth A]
K [auth B]
L [auth B]
O [auth C]
G [auth A],
H [auth A],
K [auth B],
L [auth B],
O [auth C],
P [auth C],
R [auth D],
S [auth D],
V [auth E],
W [auth E]
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.70 Å
  • R-Value Free:  0.203 (Depositor), 0.203 (DCC) 
  • R-Value Work:  0.169 (Depositor), 0.168 (DCC) 
  • R-Value Observed: 0.171 (Depositor) 
Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 50.01α = 90
b = 185.702β = 90
c = 187.551γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling
MOLREPphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2008-04-08
    Type: Initial release
  • Version 1.1: 2011-05-10
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Data collection, Derived calculations, Other, Structure summary
  • Version 1.4: 2024-05-08
    Changes: Data collection, Database references, Structure summary