2K78

Solution Structure of the IsdC NEAT domain bound to Zinc Protoporphyrin


Experimental Data Snapshot

  • Method: SOLUTION NMR
  • Conformers Calculated: 200 
  • Conformers Submitted: 30 
  • Selection Criteria: structures with the lowest energy 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

The IsdC Protein from Staphylococcus aureus Uses a Flexible Binding Pocket to Capture Heme.

Villareal, V.A.Pilpa, R.M.Robson, S.A.Fadeev, E.A.Clubb, R.T.

(2008) J Biol Chem 283: 31591-31600

  • DOI: 10.1074/jbc.M801126200
  • Primary Citation of Related Structures:  
    2K78

  • PubMed Abstract: 
  • Staphylococcus aureus scavenges heme-iron from host hemoproteins using iron-regulated surface determinant (Isd) proteins. IsdC is the central conduit through which heme is passed across the cell wall and binds this molecule using a NEAr Transporter (NEAT) domain ...

    Staphylococcus aureus scavenges heme-iron from host hemoproteins using iron-regulated surface determinant (Isd) proteins. IsdC is the central conduit through which heme is passed across the cell wall and binds this molecule using a NEAr Transporter (NEAT) domain. NMR spectroscopy was used to determine the structure of IsdC in complex with a heme analog, zinc-substituted protoporphyrin IX (ZnPPIX). The backbone coordinates of the ensemble of conformers representing the structure exhibit a root mean square deviation to the mean structure of 0.53 +/- 0.11 angstroms. IsdC partially buries protoporphyrin within a large hydrophobic pocket that is located at the end of its beta-barrel structure. The central metal ion of the analog adopts a pentacoordinate geometry in which a highly conserved tyrosine residue serves as a proximal ligand. Consistent with the structure and its role in heme transfer across the cell wall, we show that IsdC weakly binds heme (K(D) = 0.34 +/- 0.12 microm) and that ZnPPIX rapidly dissociates from the protein at a rate of 126 +/- 30 s(-1). NMR studies of the apo-form of IsdC reveal that a 3(10) helix within the binding pocket undergoes a flexible to rigid transition as heme is captured. This structural plasticity may increase the efficiency of heme transfer across the cell wall by facilitating protein-protein interactions between apoIsdC and upstream hemoproteins.


    Organizational Affiliation

    Department of Chemistry and Biochemistry, UCLA-DOE Institute for Genomics and Proteomics, University of California, Los Angeles, California 90095, USA.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Iron-regulated surface determinant protein CA147Staphylococcus aureus subsp. aureus MW2Mutation(s): 0 
Gene Names: isdCsirDMW1013
UniProt
Find proteins for Q7A151 (Staphylococcus aureus (strain MW2))
Explore Q7A151 
Go to UniProtKB:  Q7A151
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZNH (Subject of Investigation/LOI)
Query on ZNH

Download Ideal Coordinates CCD File 
B [auth A]PROTOPORPHYRIN IX CONTAINING ZN
C34 H32 N4 O4 Zn
FUTVBRXUIKZACV-UMRYFLQFDI
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: SOLUTION NMR
  • Conformers Calculated: 200 
  • Conformers Submitted: 30 
  • Selection Criteria: structures with the lowest energy 
  • OLDERADO: 2K78 Olderado

Structure Validation

View Full Validation Report




Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2008-08-19
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance