Relaxase

A relaxase is a single-strand DNA transesterase enzyme produced by some prokaryotes and viruses. Relaxases are responsible for site- and strand-specific nicks in double-stranded DNA. Known relaxases belong to the Rolling Circle Replication (RCR) initiator superfamily of enzymes and fall into two broad classes: replicative (Rep) and mobilization (Mob).^[1] The nicks produced by Rep relaxases initiate plasmid or virus RCR. Mob relaxases nick at origin of transfer (oriT) to initiate the process of DNA mobilization and transfer known as bacterial conjugation. Relaxases are so named because the single-stranded DNA nick that they catalyze lead to relaxation of helical tension.

Structure and mechanism

Known relaxases are metal ion dependent tyrosine transesterases. This means that they use a metal ion to aid the transfer of an ester bond from the DNA phosphodiester backbone to a catalytic tyrosine side chain, resulting in a long-lived covalent phosphotyrosine intermediate that essentially unified the nicked DNA strand and the enzyme as one molecule. Preliminary reports of relaxase inhibition by small molecules that mimic intermediates of this reaction were first reported in 2007.^[2] Such inhibition has implications related to preventing the propagation of antibiotic resistance in clinical settings.

The first relaxase x-ray crystal and NMR structures - of Rep relaxases from tomato yellow leaf curl virus (TYLCV)^[3] and adeno associated virus serotype 5 (AAV-5)^[4] - were solved in 2002. These revealed compact molecules composed of five-stranded, antiparallel beta sheet cores and peripheral alpha helices. A histidine-rich motif, previously identified by sequence conservation, was shown to be a metal ion binding site located on the beta sheet core, nearby the carboxy-terminal catalytic tyrosine residue. Later structures of the Mob relaxases TrwC from plasmid R388^[5] and TraI from the F-plasmid^[6] confirmed that the Mob and Rep classes are evolutionarily related to one another through circular permutation. This means that they share a general fold, but the amino-terminal sequence of one is homologous to the C-terminus of the other, and vice versa. Thus the Catalytic tyrosines of TraI and TrwC are amino-terminal rather than carboxy-terminal.

Etymology

Relaxase nomenclature is varied. In conjugative bacterial plasmids, Mob-class relaxases go by names such as TraI (in plasmid RP4), VirD2 (pTi), TrwC (R388), TraI (F-plasmid), MobB (CloDF13), or TrsK (pGO1).

See also

• Virus
• Plasmid
• Rolling Circle Replication
• Bacterial conjugation
• Protein structure

References

1. Dyda F, Hickman AB (November 2003). "A mob of reps". Structure 11 (11): 1310–1. doi:10.1016/j.str.2003.10.010. PMID 14604517.
2. Lujan SA, Guogas LM, Ragonese H, Matson SW, Redinbo MR (2007). "Disrupting antibiotic resistance propagation by inhibiting the conjugative DNA relaxase". Proc. Natl. Acad. Sci. U.S.A. 104 (30): 12282–7. doi:10.1073/pnas.0702760104. JSTOR 25436291. PMC 1916486. PMID 17630285.
3. Campos-Olivas R, Louis JM, Clerot D, Gronenborn B, Gronenborn AM (August 2002). "The structure of a replication initiator unites diverse aspects of nucleic acid metabolism". Proc. Natl. Acad. Sci. U.S.A. 99 (16): 10310–5. doi:10.1073/pnas.152342699. PMC 124910. PMID 12130667.
4. Hickman AB, Ronning DR, Kotin RM, Dyda F (2002). "Structural unity among viral origin binding proteins: crystal structure of the nuclease domain of adeno-associated virus Rep". Mol Cell 10 (2): 327–37. doi:10.1016/S1097-2765(02)00592-0. PMID 12191478.
5. Guasch A, Lucas M, Moncalián G, Cabezas M, Pérez-Luque R, Gomis-Rüth FX, de la Cruz F, Coll M (2003). "Recognition and processing of the origin of transfer DNA by conjugative relaxase TrwC". Nat Struct Biol 10 (12): 1002–10. doi:10.1038/nsb1017. PMID 14625590.
6. Datta S, Larkin C, Schildbach JF (2003). "Structural insights into single-stranded DNA binding and cleavage by F factor TraI". Structure 11 (11): 1369–79. doi:10.1016/j.str.2003.10.001. PMID 14604527.