ATP-dependent LonBA proteases of bacilli and clostridia

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Abstract

The Lon protease family belongs to the key peptide hydrolases of the protein quality control (PQC) system, which plays a leading role in maintaining the integrity of the cellular proteome in all natural kingdoms. Moreover, Lon proteases are the only family of ATP-dependent proteases of PQC which comprises a number of structurally distinct subfamilies. Recently, it has been suggested that the Lon family contains a previously unclassified LonBA subfamily, which includes enzymes from bacteria of the Bacilli and Clostridia classes. Using bioinformatics analysis, data were obtained on the structural features of enzymes of the putative new subfamily and on the existence of two different groups of Lon proteases in this subfamily.

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About the authors

A. G. Andrianova

Shemyakin–Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences

Email: tatyana.rotanova@ibch.ru
Russian Federation, ul. Mikluho-Maklaya 16/10, Moscow, 117997

A. M. Kudzhaev

Shemyakin–Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences

Email: tatyana.rotanova@ibch.ru
Russian Federation, ul. Mikluho-Maklaya 16/10, Moscow, 117997

I. V. Smirnov

Shemyakin–Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences

Email: tatyana.rotanova@ibch.ru
Russian Federation, ul. Mikluho-Maklaya 16/10, Moscow, 117997

T. V. Rotanova

Shemyakin–Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences

Author for correspondence.
Email: tatyana.rotanova@ibch.ru
Russian Federation, ul. Mikluho-Maklaya 16/10, Moscow, 117997

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Supplementary files

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2. Fig. 1. Domain organization and consensus elements of the active centers of Lon proteases of different subfamilies. (a) – Lon proteases of subfamilies A, B and C; (b) – Lon proteases of subfamily BA. Subdomains NSD, NTD5H and NTD3H form the N-terminal region of LonA proteases. NB, NC, Nsh and Nlg are N-terminal fragments of enzymes of subfamilies B, C and BA. The nucleotide-binding (NB) and α-helical (H) subdomains in light blue and blue color characterize AAA+ modules of types A and B, respectively. Walker motifs represent the ATPase active center. I (MA, Membrane Anchoring) and I* (HHE, Helical Harpin Extension) are insertion domains. The coral-colored protease domains (P) contain A-type active centers, while the turquoise-colored ones contain B-type centers. F are the residues of hydrophobic amino acids, X are the residues of any amino acids. The catalytic residues of serine (S) and lysine (K) are highlighted in red.

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3. Fig. 2. Comparison of the sequences of LonBA proteases from Bacillus subtilis and Clostridium botulinum with the sequence of the model LonA protease from Escherichia coli, taking into account the structural data obtained for EcLonA and BsLonBA [2]. Sources of Lon proteases: E. coli – EcLonA (MER0000485, PDB: 1RRE, 1RR9, 6U5Z); B. subtilis – BsLonBA (MER0002228, PDB: 8DVH); C. botulinum – CbBA-sh1 (MER0078974), CbBA-sh2 (MER0245087), CbBA-sh3 (MER0475680), CbBA-lg1 (MER0078953), CbBA-lg2 (MER0245321), CbBA-lg3 (MER0114077). The notations “sh” and “lg” mean “short” and “long” LonBA proteases, respectively. The amino acid residue numbers are given for the sequences of EcLonA, BsLonBA and CbLonBA-lg1. The alignment of the primary structures was performed using the program https://www.ebi.ac.uk/jdispatcher/msa/clustalo. For EcLonA and BsLonBA, the secondary structure elements are presented according to the work of Gustchina et al. [2], and for CbLonBA-lg1 – as predicted (https://zhanggroup.org/PSSpred/). α-helices are shown in red, 310-helices in pink, β-strands in blue, and fragments not included in the secondary structure elements in black. Consensus elements are underlined: Walker motifs (Walker A and Walker B), key residues Y and LH/D of Pore loop-1 and Pore loop-2, respectively, residues sensor-1 and sensor-2 (s1 and s2), “arginine finger” (RF), the environment of the catalytic serine (S*) and lysine (K*) residues. In the sequences of all LonBA proteases, the inserted 14-member fragments of the NB subdomains are underlined, and in short LonBA proteases, the 14-member fragments corresponding to the region (E392–K405) of BsLonBA, which forms a unique inserted β-barrel in the P-domain structure, are underlined.

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