Proteomics

Dataset Information

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Bacterial Superoxide Dismutase variants, metal-loaded or apo - structural dynamics study

ABSTRACT: The proteins are a pair of closely related superoxide dismutase (SOD) enzymes from the Gram positive bacterium, Staphylococcus aureus. SodA is a Mn-specific SOD (MnSOD), which is inactive when loaded with Fe, whereas SodM is a 'cambialistic' SOD (camSOD), which is catalytically active with either Mn or Fe as a cofactor. Their sequences are 75% identical across their 199 amino acid sequences: the crystal structures of each enzyme in each metal-loaded form: Mn-loaded MnSOD SodA: PDB ID 5N56 Fe-loaded MnSOD SodA: PDB ID 6EX3 Mn-loaded camSOD SodM: PDB ID 5N57 Fe-loaded camSOD SodM: PDB ID 6EX4 The resulting structures (all to approximately 2A resolution) showed no significant differences that indicated molecular reasons for the differences in activity. Because of the differences in activity, therefore, the project aimed to compare three forms of these enzymes to determine whether there are any differences in the dynamics of regions of their structure, most notably those within the active site and the putative substrate access route(s).

INSTRUMENT(S): Synapt MS

ORGANISM(S): Bacteria Staphylococcus Aureus

SUBMITTER: Agata Malinowska  

LAB HEAD: Michał Dadlez

PROVIDER: PXD057066 | Pride | 2025-05-07

REPOSITORIES: Pride

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Dataset's files

Source:
Action DRS
20240222SodM_Fe.DnX Other
20240222SodM_Fe.csv Csv
20240222SodM_Mn.DnX Other
20240222SodM_Mn.csv Csv
20240223SodMFeandMn.csv Csv
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Publications

HRaDeX: R Package and Web Server for Computing High-Resolution Deuterium Uptake Rates for HDX-MS Data.

Puchała Weronika W   Kistowski Michał M   Zhukova Liliya L   Burdukiewicz Michał M   Dadlez Michał M  

Journal of proteome research 20250319 4

Hydrogen-deuterium exchange monitored by mass spectrometry (HDX-MS) is a well-established and powerful technique used to study protein dynamics and stability by capturing local and global unfolding events in protein structures. However, in this technique, obtaining region-specific information requires proteolytic digestion that breaks the protein into peptide fragments, causing the HDX data to reflect averages over these fragments rather than individual amino acids. We propose a new computationa  ...[more]

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