POSTER PRESENTATION Open Access
In silico analysis of a family of extracellular
polysaccharide deacetylases involved in virulence
of pathogenic gram-positive cocci
Ramy Karam Aziz
From UT-ORNL-KBRIN Bioinformatics Summit 2010
Cadiz, KY, USA. 19-21 March 2010
Background
Pathogenic bacteria incessantly evolve mechanisms to
resist their host’s innate immunity. One such mechan-
ism is molecular camouflage: the modification of bacter-
ial surface molecules to make them unrecognizable by
the host’s immune system or resistant to its effector
molecules. Recently, a peptidoglycan deacetylase (PgdA)
was discovered in Streptococcus pneumoniae that ren-
ders bacterial peptidoglycan resistant to human lyso-
zyme, thus preventing host-mediated cell wall damage
[1-3]. In addition, polysaccharide deacetylases with dif-
ferent substrate specificities were identified in other
Correspondence: ramy.aziz@salmonella.org
Department of Microbiology and Immunology, Faculty of Pharmacy, Cairo
University, Cairo, Egypt
Figure 1 ConSurf [7,8] analysis of peptidoglycan and polysaccharide deacetylases of gram-positive cocci. The analysis involves the surface
mapping of aligned amino acid sequences to the three-dimensional structure of S. pneumoniae PgdA (Protein Data Bank ID 2c1g). Highly
conserved residues are shown in red (some are labeled for reference). These residues, conserved among the aligned proteins, are located within
one region of the enzyme, surrounding the acetyl-binding groove.
Aziz BMC Bioinformatics 2010, 11(Suppl 4):P8
http://www.biomedcentral.com/1471-2105/11/S4/P8
? 2010 Aziz; licensee BioMed Central Ltd.

gram-positive bacteria and shown to contribute to viru-
lence (e.g., IcaB of Staphylococcus epidermidis [4] and
Pdi or Streptococcus iniae [5]).
Materials and methods
In this study, genomes of streptococci and other repre-
sentative gram-positive cocci were screened for the pre-
sence of functional homologs of PgdA, the prototypic
pneumococcal peptidoglycan deacetylase. Subsequently,
amino acid sequences of homologous proteins were
aligned[6] and mapped to the three-dimensional struc-
ture of PgdA (Protein Data Bank ID: 2c1g). The Con-
Surf tool[7,8] was used for surface mapping of the
phylogenetic information calculated from the multiple
sequence alignments.
Results
Primary screening identified at least one intact pgdA
orthologous gene in every sequenced pathogenic strep-
tococcal species and other paralogous polysaccharide
deacetylases. Multiple sequence alignment of PgdA
homologs proteins, phylogenetic analysis, and chromo-
somal context analysis suggest that these proteins are
under host selective pressure. All PgdA orthologs share
a conserved Pfam protein domain (PF01522), and 40
amino acid residues are 100% identical, but non-ran-
domly distributed in beta-sheets in the C-terminal half
of each streptococcal PgdA. ConSurf structural conser-
vation analysis revealed that highly conserved residues
in PgdA orthologs and paralogs surround the enzyme’s
acetyl-binding groove (Figure 1).
Conclusion
Taken together, these data suggest the conservation of
PgdA in pathogenic streptococci, the presence of PgdA
orthologs and paralogs in gram-positive cocci, and the
high conservation of amino acid residues surrounding
the active site of these enzymes. These residues may be
tested as potential targets for the rational design of
novel, immune-assisted antibacterial agents.
Published: 23 July 2010
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doi:10.1186/1471-2105-11-S4-P8
Cite this article as: Aziz: In silico analysis of a family of extracellular
polysaccharide deacetylases involved in virulence of pathogenic gram-
positive cocci. BMC Bioinformatics 2010 11(Suppl 4):P8.
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Aziz BMC Bioinformatics 2010, 11(Suppl 4):P8
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