Lysine-cysteine NOS bonds

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spinqualitylabelsall models Show:Asymmetric Unit Biological Assembly Drag the structure with the mouse to rotate   Export Animated Image Covalent Lysine-Cysteine protein crosslinks were first reported in 2016, interpreted at the time as Lys-CH2-Cys[1][2]. Lysine-cysteine "Nitrogen-Oxygen-Sulfur" (NOS) bonds () were first reported in 2021 in transaldolases[3]. The sidechains of a lysine and a cysteine, joined by an NOS bond, make a covalent linkage between polypeptide chains. For comparison, the disulfide bond is a far more common type of covalent linkage between polypeptide chains, and the isopeptide bond is another rare type. near the N-terminus of the 352 amino acid Neisseria gonorrhoeae transaldolase chain 6zx4, between Lys8 and Cys38, near the surface.  Amino Terminus                 Carboxy Terminus  Reduction breaks the NOS bond. In transaldolase, breaking the NOS bond causes subtle allosteric shifts in the catalytic site, increasing enzymatic activity by several orders of magnitude[3]. Thus, the NOS bond is described as an allosteric redox switch[3]. Reduced: NOS bond broken, enzyme active. Oxidized: NOS bond present, enzyme inactive. Prevalence A survey of the data in the Protein Data Bank revealed that the NOS bond likely exists "in diverse protein families across all domains of life (including Homo sapiens) and that it is often located at catalytic or regulatory hotspots."[3] Because the NOS bond was unknown before 2021, it could easily have been overlooked in earlier interpretations of electron density maps.[3] Three examples are given illustrating putative NOS bonds in active sites of enzymes which, if correct, were previously overlooked: 1m3q, a DNA glycosylase: Lys249 – Cys253. 5y72, a prenyltransferase: Lys275 – Cys223. 6t3x, a cytomegalovirus nuclear egress protein: Lys132 – Cys54.

Contents 1 Methods 2 See Also 3 Other Protein Crosslinks 4 References

Methods

This is a summary of the observations supporting the NOS bond^[3]. 6zx4 (oxidized form, NOS present, enzyme inactive) has a resolution of 0.96 Å, with a better than average R_free of 0.136. Neisseria gonorrhoeae transaldolase has 3 cysteines (no disulfide bonds). It does not form disulfide-linked oligomers. Each Cys was individually mutated to Ser. Only the mutation Cys38Ser abolished redox control, producing a constitutively active enzyme.

Electron density for an unidentified atom appeared between the sidechain nitrogen of Lys8 and the sulfur of Cys38 for several crystals under nonreducing conditions, as well as in data from a low-dose non-synchrotron source, arguing against a radiation damage artifact. Competitive refinements indicated that the unidentified atom was oxygen, rather than carbon. Mass spectrometry analysis was consistent with this conclusion.

In crystals of reduced (active) enzyme, the Lys8-O-Cys38 bridge was absent. However, electron density near the Cys38 sulfur was consistent with molecular oxygen O₂. Molecular oxygen was absent in this position in the oxidized (inactive) enzyme.

See Also

• Electron density maps shows density maps for the bona fide NOS bond in 6zx4, as well as a presumably overlooked NOS bond in a structure published in 2011, and a case of Lys close to Cys where the electron density rules out an NOS bond.

Other Protein Crosslinks

In addition to the thioester bonds discussed above, other covalent cross-links between polypeptide chains include:

• Disulfide bonds
• Isopeptide bonds
• Thioester protein crosslinks
• Thioether protein crosslinks
• Ester protein crosslinks
• Histidine-tyrosine protein crosslinks

References

1. ↑ Ruszkowski M, Dauter Z. On methylene-bridged cysteine and lysine residues in proteins. Protein Sci. 2016 Sep;25(9):1734-6. doi: 10.1002/pro.2958. Epub 2016 Jun 17. PMID:27261771 doi:http://dx.doi.org/10.1002/pro.2958
2. ↑ Matthews BW. Recognizing lysine-cysteine crosslinks in proteins. Protein Sci. 2021 Aug;30(8):1491-1492. doi: 10.1002/pro.4149. Epub 2021 Jul 5. PMID:34180568 doi:http://dx.doi.org/10.1002/pro.4149
3. ↑ ^{3.0 3.1 3.2 3.3 3.4 3.5} Wensien M, von Pappenheim FR, Funk LM, Kloskowski P, Curth U, Diederichsen U, Uranga J, Ye J, Fang P, Pan KT, Urlaub H, Mata RA, Sautner V, Tittmann K. A lysine-cysteine redox switch with an NOS bridge regulates enzyme function. Nature. 2021 May 5. pii: 10.1038/s41586-021-03513-3. doi:, 10.1038/s41586-021-03513-3. PMID:33953398 doi:http://dx.doi.org/10.1038/s41586-021-03513-3