In silico Study of Iron, Zinc and Copper Binding Proteins of Pseudomonas syringae pv. lapsa: Emphasis on Secreted Metalloproteins

Abstract

The phytopathogenic bacteria, Pseudomonas syringae pv. lapsa (P. syringae pv. lapsa) infects the staple food crop wheat. Metalloproteins play important roles in plant-pathogen interactions. Hence, the present work is aimed to predict and analyze the iron (Fe), zinc (Zn), and copper (Cu) binding proteins of P. syringae pv. lapsa which help in its growth, adaptation, survival and pathogenicity. A total of 232 Fe, 307 Zn, and 38 Cu-binding proteins have been identified. The functional annotation, subcellular localization and gene ontology enriched network analysis revealed their role in wide range of biological activities of the phytopathogen. Among the identified metalloproteins, a total of 29 Fe-binding, 31 Zn-binding, and 5 Cu-binding proteins were found to be secreted in nature. These putative secreted metalloproteins may perform diverse cellular and biological functions ranging from transport, response to oxidative stress, proteolysis, antimicrobial resistance, metabolic processes, protein folding and DNA repair. The observations obtained here may provide initial information required to draft new schemes to control microbial infections of staple food crops and will further help in developing sustainable agriculture.

A novel FRET peptide assay reveals efficient Helicobacter pylori HtrA inhibition through zinc and copper binding

“…This allosteric pocket contains the amino acid motif S 164 , D 165 , S 166 , and D 168 , which is not only required for the stability and activity of HtrA oligomers 45 , but also for binding small molecule inhibitors that block HtrA activity 46 . Although typical Zn ++ -or Cu ++ -binding motifs characterized by histidine-rich regions are not present in this region, HpHtrA and, in particular, the allosteric loop may exhibit additional Zn ++ -and Cu ++ -binding sites composed of aspartic acid (D), glutamic acid (E), or cysteine (C), which can bind Zn ++ or Cu ++ equally well 47 . Therefore, we wanted to investi- www.nature.com/scientificreports/ www.nature.com/scientificreports/ gate whether Zn ++ and Cu ++ could target the aspartic acids exposed in this loop, which have previously been suggested as ligand-binding motifs 47,48 .…”

“…Although typical Zn ++ -or Cu ++ -binding motifs characterized by histidine-rich regions are not present in this region, HpHtrA and, in particular, the allosteric loop may exhibit additional Zn ++ -and Cu ++ -binding sites composed of aspartic acid (D), glutamic acid (E), or cysteine (C), which can bind Zn ++ or Cu ++ equally well 47 . Therefore, we wanted to investi- www.nature.com/scientificreports/ www.nature.com/scientificreports/ gate whether Zn ++ and Cu ++ could target the aspartic acids exposed in this loop, which have previously been suggested as ligand-binding motifs 47,48 . The individual amino acids S 164 , D 165 , S 166 , and D 168 were mutated to alanine and analyzed for oligomer stability (Fig.…”

The l-Thr Kinase/l-Thr-Phosphate Decarboxylase (CobD) Enzyme from Methanosarcina mazei Gö1 Contains Metallocenters Needed for Optimal Activity

“…One potential explanation for the high number of Fe atoms is the number of aspartate (4 Asp) and glutamate (14 Glu) residues in the C -terminus of Mm CobD. Other than histidine and cysteine, aspartate and glutamate are known to strongly interact with metals in general and Fe in particular 38 . The His and Cys residues might form covalent bonds with Fe to form [Fe-S] clusters while the Asp and Glu residues could coordinate single Fe ions.…”

Targeting metabolic pathways proteins of Orientia tsutsugamushi using combined hierarchical approach to combat scrub typhus

“…The complete genome sequences of human pathogen Ott strain Ikeda are publicly available and are pivotal for obtaining biological information about this pathogen. The computational analysis of the genome and extraction of information from them is one of the convenient, fast, and time saving strategies . The profound interpretation of metabolic pathways unique to pathogen can help us to understand the factors responsible for its survival and pathogenesis, which can further expedite the identification of novel drug targets.…”

“…The computational analysis of the genome and extraction of information from them is one of the convenient, fast, and time saving strategies. [21][22][23][24] The profound interpretation of metabolic pathways unique to pathogen can help us to understand the factors responsible for its survival and pathogenesis, which can further expedite the identification of novel drug targets. This study reports in silico mining of unique metabolic pathways proteins from Ott strain Ikeda for identification of potential therapeutic targets.…”