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Secondary structure preferences of mn (2+) binding sites in bacterial proteins

Tatyana Aleksandrovna Khrustaleva1

  • 1Regulatory Proteins and Peptides Laboratory, Institute of Physiology of the National Academy of Sciences of Belarus, Akademicheskaya 28, 220072 Minsk, Belarus.

Advances in Bioinformatics
|April 30, 2014
PubMed

Insights

Bacterial protein structures reveal manganese (Mn2+) primarily binds to aspartic acid, histidine, and glutamic acid. A specific secondary structure motif near these binders is common across bacteria, irrespective of their genomic GC-content.

Area of Science:

  • Biochemistry
  • Structural Biology
  • Genomics

Background:

  • Genomic GC-content influences bacterial protein structures and functions.
  • Manganese (Mn2+) is a crucial cofactor in many bacterial enzymes.
  • Understanding Mn2+ coordination in proteins provides insights into metalloenzyme mechanisms.

Purpose of the Study:

  • To analyze the 3D structures of bacterial proteins coordinating Mn2+ ions.
  • To investigate the relationship between genomic GC-content and Mn2+ binding sites.
  • To identify common structural motifs involved in Mn2+ coordination.

Main Methods:

  • Analysis of 149 protein data bank (PDB) files of bacterial proteins with Mn2+.
  • Identification of major Mn2+ coordinating amino acid residues (Asp, His, Glu).
  • Characterization of secondary structure motifs surrounding Mn2+ binding sites.

Main Results:

  • Aspartic acid, histidine, and glutamic acid are the primary Mn2+ binders.
  • A "beta strand-major binder-random coil" motif is significantly overrepresented around Mn2+ binding sites.
  • This motif's prevalence (77.88%) is independent of bacterial genomic GC-content.
  • GC-rich bacteria show increased Mn2+ coordination by glutamic acid in alpha helices, potentially due to reduced lysine usage.

Conclusions:

  • A conserved secondary structure motif facilitates Mn2+ binding in bacterial proteins.
  • Genomic GC-content may influence specific amino acid choices for Mn2+ coordination (e.g., Glu in alpha helices in GC-rich bacteria).
  • The identified motif represents a stable and common feature for Mn2+ binding across diverse bacterial genomes.

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