3CX3

Crystal structure Analysis of the Streptococcus pneumoniae AdcAII protein

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free: 0.295 
  • R-Value Work: 0.225 
  • R-Value Observed: 0.229 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history. 


Literature

AdcAII, a new pneumococcal Zn-binding protein homologous with ABC transporters: biochemical and structural analysis.

Loisel, E., Jacquamet, L., Serre, L., Bauvois, C., Ferrer, J.L., Vernet, T., Di Guilmi, A.M., Durmort, C.

(2008) J Mol Biol 381: 594-606

  • DOI: 10.1016/j.jmb.2008.05.068
  • Primary Citation of Related Structures:  
    3CX3

  • PubMed Abstract: 

    • Regulation of metal homeostasis is vital for pathogenic bacteria facing drastic metal concentration changes in various locations within the host during invasion. Metal-binding receptors (MBRs), one of the extracellular components of ATP-binding cassette transporters, have been shown to be essential in this process ...

    Regulation of metal homeostasis is vital for pathogenic bacteria facing drastic metal concentration changes in various locations within the host during invasion. Metal-binding receptors (MBRs), one of the extracellular components of ATP-binding cassette transporters, have been shown to be essential in this process. Streptococcus pneumoniae expresses two characterized MBRs: PsaA and AdcA, two extracellular lipoproteins encoded by the psaABCD and adcRCBA operons, respectively. The Mn- and Zn-uptake functions of PsaA and AdcA, respectively, have been well established. Here we describe AdcAII as a third putative S. pneumoniae MBR. The analysis of a phylogenetic tree built from the sequence alignment of 68 proteins reveals a subgroup of members displaying an unusual genetic operon organisation. The adcAII gene belongs to a 6670-nucleotide-long transcript spanning the spr0903 to spr0907 loci encoding for the CcdA, thioredoxine, YfnA, AdcAII and PhtD proteins. Two adjacent repeats of imperfect AdcR-binding consensus sequence were identified upstream of the adcAII gene, suggesting a transcriptional co-regulation of adcAII and phtD genes. Biophysical and structural studies of recombinant AdcAII were performed to identify the metal specificity of the protein. Using electrospray mass spectrometry in native conditions, we found that Zn was bound to recombinant AdcAII. Screening of the effect of 10 cationic ions on the thermal stability of AdcAII revealed that Zn had the most pronounced stabilizing effect. The crystal structure of AdcAII has been solved to 2.4 A resolution. One Zn ion is bound to each AdcAII molecule in a symmetrical active site composed of three His and one Glu. The structure almost perfectly superimposed on the known MBR structures. The presence of a flexible 15-residue-long loop close to the metal-binding site is specific to those specialized in Zn transport. Taken together, these functional and structural data provide new perspectives related to the physiological role of AdcAII in pneumococcus Zn homeostasis.

    Organizational Affiliation: 

    Institut de Biologie Structurale Jean-Pierre Ebel UMR 5075 (CNRS/CEA/UJF/PSB), Laboratoire d'Ingénierie des Macromolécules, 41 rue Jules Horowitz, 38027 Grenoble, France.



Macromolecules
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(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
LipoproteinA, B284Streptococcus pneumoniae R6Mutation(s): 0 
Gene Names: lmb, spr0906
UniProt
Find proteins for Q8DQ09 (Streptococcus pneumoniae (strain ATCC BAA-255 / R6))
Explore Q8DQ09 
Go to UniProtKB:  Q8DQ09
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ8DQ09
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN
Download Ideal Coordinates CCD File 
E [auth A],
F [auth B]		ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N		 Ligand Interaction
NA
Query on NA
Download Ideal Coordinates CCD File 
C [auth A],
D [auth A]		SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N		 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
MSE
Query on MSE		A, B L-PEPTIDE LINKINGC5 H11 N O2 SeMET
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free: 0.295 
  • R-Value Work: 0.225 
  • R-Value Observed: 0.229 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 55.76α = 90
b = 63.26β = 90
c = 151.66γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
PDB_EXTRACTdata extraction
XDSdata reduction
XSCALEdata scaling
SHARPphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2008-08-05
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance