The tertiary structure of an i-type lysozyme isolated from the common orient clam (<i>Meretrix lusoria</i>)

Kuwano, Yuko; Yoneda, Kazunari; Kawaguchi, Yuya; Araki, Toshimitsu

doi:10.1107/s1744309113028170

Cited by 9 publications

(5 citation statements)

References 22 publications

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“…The structure of the bacterial produced mutanolysin is quite distinct from C-type lysozymes like hen egg white lysozyme [ 72 , 73 ]. In contrast G-type and I-type lysozymes produced by eukaryotes are structurally similar to C-type lysozyme and likely the result of divergent evolution [ 74 , 75 ]. However, at this time it is not known if RsiV can bind to G-type or I-type lysozymes.…”

Section: Discussionmentioning

confidence: 99%

The Anti-sigma Factor RsiV Is a Bacterial Receptor for Lysozyme: Co-crystal Structure Determination and Demonstration That Binding of Lysozyme to RsiV Is Required for σV Activation

et al. 2016

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σ factors provide RNA polymerase with promoter specificity in bacteria. Some σ factors require activation in order to interact with RNA polymerase and transcribe target genes. The Extra-Cytoplasmic Function (ECF) σ factor, σV, is encoded by several Gram-positive bacteria and is specifically activated by lysozyme. This activation requires the proteolytic destruction of the anti-σ factor RsiV via a process of regulated intramembrane proteolysis (RIP). In many cases proteases that cleave at site-1 are thought to directly sense a signal and initiate the RIP process. We previously suggested binding of lysozyme to RsiV initiated the proteolytic destruction of RsiV and activation of σV. Here we determined the X-ray crystal structure of the RsiV-lysozyme complex at 2.3 Å which revealed that RsiV and lysozyme make extensive contacts. We constructed RsiV mutants with altered abilities to bind lysozyme. We find that mutants that are unable to bind lysozyme block site-1 cleavage of RsiV and σV activation in response to lysozyme. Taken together these data demonstrate that RsiV is a receptor for lysozyme and binding of RsiV to lysozyme is required for σV activation. In addition, the co-structure revealed that RsiV binds to the lysozyme active site pocket. We provide evidence that in addition to acting as a sensor for the presence of lysozyme, RsiV also inhibits lysozyme activity. Thus we have demonstrated that RsiV is a protein with multiple functions. RsiV inhibits σV activity in the absence of lysozyme, RsiV binds lysozyme triggering σV activation and RsiV inhibits the enzymatic activity of lysozyme.

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Section: Discussionmentioning

confidence: 99%

The Anti-sigma Factor RsiV Is a Bacterial Receptor for Lysozyme: Co-crystal Structure Determination and Demonstration That Binding of Lysozyme to RsiV Is Required for σV Activation

et al. 2016

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“…However, electron density maps did not reveal the presence of NAG3 molecule, suggesting that the inhibitory effect of sodium ions was at play. Interestingly, both sodium ions and NAG3 were present in the crystallization conditions of TjL (PDB ID: 2DQA 23 ) and MlL lysozyme (PDB ID: 3AB6 33 ). In contrast to our study, these structures contained NAG3 molecules but no sodium ions.…”

Section: Resultsmentioning

confidence: 99%

Structural insights into thrombolytic activity of destabilase from medicinal leech

Marin

Kornilov

Bukhdruker

et al. 2023

Sci Rep

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Destabilase from the medical leech Hirudo medicinalis belongs to the family of i-type lysozymes. It has two different enzymatic activities: microbial cell walls destruction (muramidase activity), and dissolution of the stabilized fibrin (isopeptidase activity). Both activities are known to be inhibited by sodium chloride at near physiological concentrations, but the structural basis remains unknown. Here we present two crystal structures of destabilase, including a 1.1 Å-resolution structure in complex with sodium ion. Our structures reveal the location of sodium ion between Glu34/Asp46 residues, which were previously recognized as a glycosidase active site. While sodium coordination with these amino acids may explain inhibition of the muramidase activity, its influence on previously suggested Ser49/Lys58 isopeptidase activity dyad is unclear. We revise the Ser49/Lys58 hypothesis and compare sequences of i-type lysozymes with confirmed destabilase activity. We suggest that the general base for the isopeptidase activity is His112 rather than Lys58. pKa calculations of these amino acids, assessed through the 1 μs molecular dynamics simulation, confirm the hypothesis. Our findings highlight the ambiguity of destabilase catalytic residues identification and build foundations for further research of structure–activity relationship of isopeptidase activity as well as structure-based protein design for potential anticoagulant drug development.

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“…The activity of enzymes is an important index of mollusk physiology and immune status. The invertebrate-type LZM plays an important role in the immunity of invertebrates, including bivalves (Itoh et al 2007 ; Xue et al 2007 ; Kuwano et al 2013 ). Gagnaire et al ( 2006 ) reported that the activity of LZM in the blood cells of the oyster Crassostrea gigas decreased significantly under the stress of exposure to polycyclic aromatic hydrocarbons.…”

Section: Discussionmentioning

confidence: 99%

Integrated RNA-seq and RNAi Analysis of the Roles of the Hsp70 and SP Genes in Red-Shell Meretrix meretrix Tolerance to the Pathogen Vibrio parahaemolyticus

et al. 2022

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The “Wanlihong” Meretrix meretrix (WLH-M) clam is a new variety of this species that has a red shell and stronger Vibrio tolerance than ordinary M. meretrix (ORI-M). To investigate the molecular mechanisms responsible for the WLH-M strain’s tolerance to Vibrio , we challenged clams with Vibrio parahaemolyticus and then assessed physiological indexes and conducted transcriptome analysis and RNA interference experiments. The mortality, tissue bacterial load, and hemocyte reactive oxygen species level of ORI-M were significantly higher than those of WLH-M, whereas the content and activity of lysozyme were significantly lower. Gene Ontology functional annotation analysis and Kyoto Encyclopedia of Genes and Genomes pathway enrichment analysis revealed that immune and metabolic pathways were enriched in Vibrio -challenged clams. The expressions of the heat shock protein 70 ( Hsp70 ) and serine protease ( SP ) genes, which are involved in antibacterial immunity, were significantly upregulated in WLH-M but not in ORI-M, while the expression of the kynurenine 3-monooxygenase gene, a proinflammatory factor, was significantly downregulated in WLH-M. RNA interference experiments confirmed that Hsp70 and SP downregulation could result in increased mortality of WLH-M. Therefore, we speculate that Hsp70 and SP may be involved in the antibacterial immunity of WLH-M in vivo. Our data provided a valuable resource for further studies of the antibacterial mechanism of WLH-M and provided a foundation for the breeding of pathogen-resistant strains. Supplementary Information The online version contains supplementary material available at 10.1007/s10126-022-10156-6.

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The tertiary structure of an i-type lysozyme isolated from the common orient clam (Meretrix lusoria)

Cited by 9 publications

References 22 publications

The Anti-sigma Factor RsiV Is a Bacterial Receptor for Lysozyme: Co-crystal Structure Determination and Demonstration That Binding of Lysozyme to RsiV Is Required for σV Activation

The Anti-sigma Factor RsiV Is a Bacterial Receptor for Lysozyme: Co-crystal Structure Determination and Demonstration That Binding of Lysozyme to RsiV Is Required for σV Activation

Structural insights into thrombolytic activity of destabilase from medicinal leech

Integrated RNA-seq and RNAi Analysis of the Roles of the Hsp70 and SP Genes in Red-Shell Meretrix meretrix Tolerance to the Pathogen Vibrio parahaemolyticus

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