4X1U

The structure of AhpE from Mycobacterium tuberculosis revisited

Summary for 4X1U

• Entry DOI: 10.2210/pdb4x1u/pdb
• Descriptor: Putative peroxiredoxin MT2298, GLYCEROL (3 entities in total)
• Functional Keywords: peroxiredoxins, oxidoreductase
• Biological source: Mycobacterium tuberculosis
• Total number of polymer chains: 2
• Total formula weight: 35548.01

Authors

Pallo, A.,Messens, J. (deposition date: 2014-11-25, release date: 2016-07-27, Last modification date: 2024-10-23)

Primary citation

van Bergen, L.A.,Alonso, M.,Pallo, A.,Nilsson, L.,De Proft, F.,Messens, J.
Revisiting sulfur H-bonds in proteins: The example of peroxiredoxin AhpE.
Sci Rep, 6:30369-30369, 2016

PubMed Abstract: In many established methods, identification of hydrogen bonds (H-bonds) is primarily based on pairwise comparison of distances between atoms. These methods often give rise to systematic errors when sulfur is involved. A more accurate method is the non-covalent interaction index, which determines the strength of the H-bonds based on the associated electron density and its gradient. We applied the NCI index on the active site of a single-cysteine peroxiredoxin. We found a different sulfur hydrogen-bonding network to that typically found by established methods, and we propose a more accurate equation for determining sulfur H-bonds based on geometrical criteria. This new algorithm will be implemented in the next release of the widely-used CHARMM program (version 41b), and will be particularly useful for analyzing water molecule-mediated H-bonds involving different atom types. Furthermore, based on the identification of the weakest sulfur-water H-bond, the location of hydrogen peroxide for the nucleophilic attack by the cysteine sulfur can be predicted. In general, current methods to determine H-bonds will need to be reevaluated, thereby leading to better understanding of the catalytic mechanisms in which sulfur chemistry is involved.

PubMed: 27468924
DOI: 10.1038/srep30369

Experimental method

X-RAY DIFFRACTION (1.87 Å)