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M. R. N. Murthy ¹

Affiliations
1 Molecular Biophysics Unit, Indian Institute of Science, Bengaluru 560 012, IN

Abstract

No Abstract.

Keywords

No Keywords.

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Sreeja Chellappan ¹, S. Mathivanan ¹, R. Thippeswamy ², M. Nagesh ², H. S. Savithri ³, M. R. N. Murthy ⁴

Affiliations
1 Molecular Biophysics Unit, Indian Institute of Science, Bengaluru 560 012, IN
2 Indian Council of Agricultural Research, Project Directorate of Biological Control, Bengaluru 560 024, IN
3 Department of Biochemistry, Indian Institute of Science, Bengaluru 560 012, IN
4 Indian Institute of Science Education and Research, Thiruvananthapuram 695 551, IN

Abstract

Photorhabdus luminescens is a Gram-negative, symbiotic bacterium associated with entomopathogenic nematodes of the genus Heterorhabditis. Several genes from this organism related to insecticidal properties are being examined for their potential in pest management. Oxalate decarboxylase (OXDC), an enzyme secreted by bacteria and fungi and putatively associated with insecticidal pathways catalyses the manganese dependent decarboxylation of oxalate to formate and CO₂. In this study, we report the X-ray crystal structure of OXDC isolated and purified from Photorhabdus luminescens (PlOXDC, MW 43 kDa) determined at 1.97 Å resolution. PlOXDC protomer has a bicupin structure. Each cupin domain consists of two antiparallel β sheets organized as a sandwich with a Mn²⁺ ion bound at the active site. PlOXDC exists as a mixture of monomeric and trimeric forms in solution but assumes a trimeric form in the crystal structure.

Keywords

Bicupin, Crystal Structure, Oxalate Decarboxylase, Photorhabdus luminescens.

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M. R. N. Murthy

Abstract

A hydration shell surrounds proteins in solution. The structures of proteins at atomic resolution presently available in the Protein Data Bank (PDB) provide detailed information on the mode of hydration and plausible roles of water molecules in protein structure and function. This article presents an analysis of water structure in proteins determined at atomic resolution. Water molecules bind to proteins by making hydrogen bonds with oxygen and nitrogen atoms with oxygen as the preferred atom. The mean length of hydrogen bonds between oxygen and water is shorter than that of nitrogen and water. However, the mean thermal parameter of water molecules hydrogenbonded to oxygen atoms is higher than that of water molecules hydrogen-bonded to nitrogen atoms. Water molecules of the first hydration shell are stabilized by hydrogen bonding with protein atoms, while the stability of the second hydration shell is derived from hydrogen bonding with molecules of the first shell. The number of molecules in the second and higher shells is less than half of that of the first shell. As could be expected, the mean thermal parameter of molecules is higher in the second shell compared to that of the first shell. The number of water molecules buried in protein interfaces increases with increasing size of protein. In several proteins, water molecules form hydrogen-bonded networks that could cover a large part of the protein surface. Pentagonal and tetrahedral arrangements of hydrogen-bonded water molecules could be observed in several structures. Strongly bound water molecules with low thermal parameters appear to be essential for maintaining the loops in appropriate positions. Tightly bound water molecules are also found at the active site of some proteins. These molecules may play important roles in protein function.

Keywords

Atomic Resolution, Hydration Shell, Hydrogen Bond Length, Protein Hydration, Water Cluster.

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D. Vaigundan ¹, I. Yuvaraj ², P. Sunita ³, K. Sekar ⁴, M. R. N. Murthy ⁵, P. R. Krishnaswamy ⁶

Affiliations
1 Genomics and Central Research Laboratory, Department of Cell Biology and Molecular Genetics, Sri Devaraj Urs Academy of Higher Education and Research, Tamaka, Kolar 563 101, India, IN
2 Computational Data Sciences, Indian Institute of Science, Bengaluru 560 012, India; Present address: National Institute for Plant Biotechnology, Indian Council of Agricultural Research, New Delhi 110 012, India, IN
3 Molecular Biophysics Unit, Indian Institute of Science, Bengaluru 560 012, India, IN
4 Computational Data Sciences, Indian Institute of Science, Bengaluru 560 012, India, IN
5 Molecular Biophysics Unit, Indian Institute of Science, Bengaluru 560 012, India; Institute of Bioinformatics and Applied Biotechnology, Bengaluru 560 100, India, IN
6 Genomics and Central Research Laboratory, Department of Cell Biology and Molecular Genetics, Sri Devaraj Urs Academy of Higher Education and Research, Tamaka, Kolar 563 101, India; Centre for Nanoscience and Engineering, Indian Institute of Science, Bengaluru 560 012, India, IN

Abstract

Amino acid oxidases (AOs) are flavin adenine dinucleotide (FAD)-dependent dimeric enzymes that stereo specifically catalyse the deamination of an a-amino acid leading to an a-keto acid. Putative Leptospira interrogans recombinant l-amino acid oxidase (Li-rLAO; lacking 20 residues corresponding to the N-terminal signal sequence) was cloned, expressed, purified, and its three-dimensional structure was determined by X-ray crystallography at a resolution of 1.8 Å. The active site could be easily identified by the presence of electron density corresponding to a non-covalently bound FAD in both protomers of the dimeric enzyme. Structural analysis of Li-rLAO revealed that its polypeptide fold is similar to those of the previously determined homologous structures as available in the Protein Data Bank. However, a substrate-binding residue found at the active site of other previously determined homologous structures was not conserved in Li-rLAO, suggesting that its specificity may differ from those of earlier reported structures. Not surprisingly, Li-rLAO showed no activity for most amino acids and amines; it exhibited a low activity only with l-arginine as the substrate. The catalytic properties of Li-rLAO could be rationalized in terms of its three-dimensional structure

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