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Homology modeling and molecular docking studies of ArnA protein from Erwinia amylovora: role in polymyxin antibiotic resistance

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Abstract

The resistivity of plant pathogen Erwinia amylovora against the polymyxin group of antibiotics is enhanced by modification of lipid A from lipopolysaccharide with 4-amino-4-deoxy L-arabinose (Ara4N) catalyzed by a bifunctional protein ArnA. ArnA is the first enzyme in the lipid A modification pathway with distinct dehydrogenase and transformylase domains which has been known in development of resistivity to polymyxin group of antibiotics. Thus, three dimensional structure of ArnA protein from Erwinia amylovora was constructed using homology modeling technique. The quality and reliability of the generated 3-D model was then assessed by different online available programs such as What if, PROCHECK, QMEAN, ProSA along with superimposition by UCSF Chimera. Sequence analysis study of ArnA protein from E. coli, Erwinia amylovora, Yersinia pestis, Ps. aeruginosa and Salmonella showed conserved domains with exact active site residues. Molecular docking study of ArnA protein with substrate UDP-GlcA and different inhibitors such as 5-formyl-5,6,7,8 tetrahydrofolate, leucovorin and 5-methyl tetrahydrofolate revealed similar binding pocket. The residues ASN492, ARG510, SER433 and ARG619 of ArnA protein are involved in interactions with inhibitors. Thus, this study could be useful to understand the proper binding mode of inhibitors to inhibit the lipid A modification pathway of ArnA protein from plant pathogen Erwinia amylovora.

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Abbreviations

BLAST:

Basic local alignment search tool

NCBI:

National centre for biotechnology information

PDB:

Protein data bank

RMSD:

Root mean square deviation

SDF:

Structure data file

UDP-GlcA:

Uridine-di-phosphate glucoronic acid

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Acknowledgments

Authors are gratefully acknowledged for the infrastructural facility provided by Structural Bioinformatics Unit, Department of Biochemistry, Shivaji University, Kolhapur. RSP is thankful to University Grants Commission, New Delhi for providing project fellowship through UGC-SAP-DRS-Phase I Programme sanctioned to Department of Biochemistry, Shivaji University, Kolhapur. KDS is thankful to University Grants Commission, New Delhi for providing infrastructural grants.

Conflict of interest

All authors have no conflict of interest.

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Authors and Affiliations

  1. Department of Biochemistry, Structural Bioinformatics Unit, Shivaji University, Kolhapur, 416004, Maharashtra, India

    Kailas D. Sonawane, Radhika S. Malkar & Pranhita R. Nimbalkar

  2. Department of Microbiology, Shivaji University, Kolhapur, 416 004, Maharashtra, India

    Kailas D. Sonawane, Rishikesh S. Parulekar & Deepak B. Jadhav

  3. Department of Biotechnology, Shivaji University, Kolhapur, 416 004, Maharashtra, India

    Sagar H. Barage

Authors
  1. Kailas D. Sonawane
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  2. Rishikesh S. Parulekar
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  3. Radhika S. Malkar
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  4. Pranhita R. Nimbalkar
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  5. Sagar H. Barage
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  6. Deepak B. Jadhav
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Corresponding author

Correspondence to Kailas D. Sonawane.

Electronic supplementary material

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Supplementary Table 1

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Supplementary Table 2

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Supplementary Table 3

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Supplementary Table 4

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Supplementary Table 5

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Supplementary Fig. 1

Multiple sequence alignment by CLUSTALW. Conserved substrate (UDP-GlcA) binding residues in red from ArnA protein sequence of different organisms such as E. coli (template), S. typhi, Erwinia amylovora (target- YP_003530443), Yersinia pestis and Ps. aeruginosa showing conserved substrate binding residues SER433, ASN492 and ARG619 in all the organisms (red) (DOCX 15 kb)

Supplementary Fig. 2

PsiPred secondary structure prediction of ArnA protein from plant pathogen Erwinia amylovora (DOCX 1706 kb)

Supplementary Fig. 3

ProSA Z-score and energy plot comparison between template and target showing valid model. The model ProSA plot with Z-score of −11.5 indicated overall quality of 3D structure of modeled ArnA protein along with negative values of energy for amino acid residues as per knowledge based energy plot. The template ProSA plot with Z-score of −12.7 represents overall quality of 3D structure of template (PDB ID 1Z7E) with negative values of energy for amino acid residues as per knowledge based energy plot. When compared with model Z-score it was found that the overall quality of the 3D structure of template and model are very similar in terms of their Z-score (DOCX 836 kb)

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Sonawane, K.D., Parulekar, R.S., Malkar, R.S. et al. Homology modeling and molecular docking studies of ArnA protein from Erwinia amylovora: role in polymyxin antibiotic resistance. J. Plant Biochem. Biotechnol. 24, 425–432 (2015). https://doi.org/10.1007/s13562-014-0293-3

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  • DOI: https://doi.org/10.1007/s13562-014-0293-3

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