3L1N

Crystal structure of Mp1p ligand binding domain 2 complexd with palmitic acid


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.3 Å
  • R-Value Free: 0.198 
  • R-Value Work: 0.182 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Crystal structure of the Mp1p ligand binding domain 2 reveals its function as a fatty acid-binding protein.

Liao, S.Tung, E.T.Zheng, W.Chong, K.Xu, Y.Dai, P.Guo, Y.Bartlam, M.Yuen, K.Y.Rao, Z.

(2010) J.Biol.Chem. 285: 9211-9220

  • DOI: 10.1074/jbc.M109.057760

  • PubMed Abstract: 
  • Penicillium marneffei is a dimorphic, pathogenic fungus in Southeast Asia that mostly afflicts immunocompromised individuals. As the only dimorphic member of the genus, it goes through a phase transition from a mold to yeast form, which is believed t ...

    Penicillium marneffei is a dimorphic, pathogenic fungus in Southeast Asia that mostly afflicts immunocompromised individuals. As the only dimorphic member of the genus, it goes through a phase transition from a mold to yeast form, which is believed to be a requisite for its pathogenicity. Mp1p, a cell wall antigenic mannoprotein existing widely in yeast, hyphae, and conidia of the fungus, plays a vital role in host immune response during infection. To understand the function of Mp1p, we have determined the x-ray crystal structure of its ligand binding domain 2 (LBD2) to 1.3 A. The structure reveals a dimer between the two molecules. The dimer interface forms a ligand binding cavity, in which electron density was observed for a palmitic acid molecule interacting with LBD2 indirectly through hydrogen bonding networks via two structural water molecules. Isothermal titration calorimetry experiments measured the ligand binding affinity (K(d)) of Mp1p at the micromolar level. Mutations of ligand-binding residues, namely S313A and S332A, resulted in a 9-fold suppression of ligand binding affinity. Analytical ultracentrifugation assays demonstrated that both LBD2 and Mp1p are mostly monomeric in vitro, no matter with or without ligand, and our dimeric crystal structure of LBD2 might be the result of crystal packing. Based on the conformation of the ligand-binding pocket in the dimer structure, a model for the closed, monomeric form of LBD2 is proposed. Further structural analysis indicated the biological importance of fatty acid binding of Mp1p for the survival and pathogenicity of the conditional pathogen.


    Organizational Affiliation

    From the Laboratory of Structural Biology, Tsinghua University, Beijing 100084, China.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Cell wall antigen
A
194Talaromyces marneffeiMutation(s): 2 
Gene Names: MP1
Find proteins for O42721 (Talaromyces marneffei)
Go to UniProtKB:  O42721
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
PLM
Query on PLM

Download SDF File 
Download CCD File 
A
PALMITIC ACID
C16 H32 O2
IPCSVZSSVZVIGE-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
MSE
Query on MSE
A
L-PEPTIDE LINKINGC5 H11 N O2 SeMET
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
PLMKd: 6340 nM BINDINGMOAD
PLMKd: 2340 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.3 Å
  • R-Value Free: 0.198 
  • R-Value Work: 0.182 
  • Space Group: P 41 21 2
Unit Cell:
Length (Å)Angle (°)
a = 46.510α = 90.00
b = 46.510β = 90.00
c = 149.380γ = 90.00
Software Package:
Software NamePurpose
SOLVEphasing
SCALEPACKdata scaling
REFMACrefinement
HKL-2000data reduction
ADSCdata collection

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2010-01-05
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Version format compliance