3M8U

Crystal structure of glutathione-binding protein A (GbpA) from Haemophilus parasuis SH0165 in complex with glutathione disulfide (GSSG)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.85 Å
  • R-Value Free: 0.188 
  • R-Value Work: 0.158 
  • R-Value Observed: 0.160 

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Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history


Literature

Glutathione import in Haemophilus influenzae Rd is primed by the periplasmic heme-binding protein HbpA

Vergauwen, B.Elegheert, J.Dansercoer, A.Devreese, B.Savvides, S.N.

(2010) Proc Natl Acad Sci U S A 107: 13270-13275

  • DOI: 10.1073/pnas.1005198107
  • Primary Citation of Related Structures:  
    3M8U

  • PubMed Abstract: 
  • Glutathione (GSH) is a vital intracellular cysteine-containing tripeptide across all kingdoms of life and assumes a plethora of cellular roles. Such pleiotropic behavior relies on a finely tuned spatiotemporal distribution of glutathione and its conjugates, which is not only controlled by synthesis and breakdown, but also by transport ...

    Glutathione (GSH) is a vital intracellular cysteine-containing tripeptide across all kingdoms of life and assumes a plethora of cellular roles. Such pleiotropic behavior relies on a finely tuned spatiotemporal distribution of glutathione and its conjugates, which is not only controlled by synthesis and breakdown, but also by transport. Here, we show that import of glutathione in the obligate human pathogen Haemophilus influenzae, a glutathione auxotrophe, is mediated by the ATP-binding cassette (ABC)-like dipeptide transporter DppBCDF, which is primed for glutathione transport by a dedicated periplasmic-binding protein (PBP). We have identified the periplasmic lipoprotein HbpA, a protein hitherto implicated in heme acquisition, as the cognate PBP that specifically binds reduced (GSH) and oxidized glutathione (GSSG) forms of glutathione with physiologically relevant affinity, while it exhibits marginal binding to hemin. Dissection of the ligand preferences of HbpA showed that HbpA does not recognize bulky glutathione S conjugates or glutathione derivatives with C-terminal modifications, consistent with the need for selective import of useful forms of glutathione and the concomitant exclusion of potentially toxic glutathione adducts. Structural studies of the highly homologous HbpA from Haemophilus parasuis in complex with GSSG have revealed the structural basis of the proposed novel function for HbpA-like proteins, thus allowing a delineation of highly conserved structure-sequence fingerprints for the entire family of HbpA proteins. Taken together, our studies unmask the main physiological role of HbpA and establish a paradigm for glutathione import in bacteria. Accordingly, we propose a name change for HbpA to glutathione-binding protein A.


    Organizational Affiliation

    Laboratory for Protein Biochemistry and Biomolecular Engineering (L-ProBE), Department of Biochemistry and Microbiology, Ghent University, 9000 Ghent, Belgium. bjorn.vergauwen@ugent.be



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Heme-binding protein AA522Glaesserella parasuis SH0165Mutation(s): 6 
Gene Names: HAPS_1202hbpA
UniProt
Find proteins for B8F653 (Glaesserella parasuis serovar 5 (strain SH0165))
Explore B8F653 
Go to UniProtKB:  B8F653
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupB8F653
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GDS
Query on GDS

Download Ideal Coordinates CCD File 
B [auth A]OXIDIZED GLUTATHIONE DISULFIDE
C20 H32 N6 O12 S2
YPZRWBKMTBYPTK-BJDJZHNGSA-N
 Ligand Interaction
MLI
Query on MLI

Download Ideal Coordinates CCD File 
C [auth A],
D [auth A],
E [auth A]
MALONATE ION
C3 H2 O4
OFOBLEOULBTSOW-UHFFFAOYSA-L
 Ligand Interaction
Binding Affinity Annotations 
IDSourceBinding Affinity
GDS Binding MOAD:  3M8U Kd: 1.29e+4 (nM) from 1 assay(s)
PDBBind:  3M8U Kd: 1.29e+4 (nM) from 1 assay(s)
BindingDB:  3M8U Kd: min: 330, max: 2100 (nM) from 2 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.85 Å
  • R-Value Free: 0.188 
  • R-Value Work: 0.158 
  • R-Value Observed: 0.160 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 57.52α = 90
b = 68.47β = 90
c = 142.32γ = 90
Software Package:
Software NamePurpose
PHASERphasing
PHENIXrefinement
XDSdata reduction
XSCALEdata scaling

Structure Validation

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Ligand Structure Quality Assessment 



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2010-07-14
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance