Subsystem: DNA repair, bacterial photolyase

This subsystem's description is:

For more information, please check out the description and the additional notes tabs, below

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Domain
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CryPhrBPhr-ssPhrII
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Variant codes:

-1 = Nothing
+1 = RecA
+2 = Other repair-associated genes

Other sytems with related functions (this subsystem had gotten too big):
DNA repair, bacterial DinG and relatives
DNA repair, bacterial MutL-MutS system
DNA repair, bacterial RecFOR pathway
DNA repair, UvrABC system
DNA repair, bacterial UvrD and related helicases

Rec A should be found in all but a very few bacteria (such as Buchnera).


DNA repair protein RadA
Formerly called Sms, but to ensure a collision with the Archaeal RecA equivalent, it is now RadA


SbcCD is an ATP-dependent exonuclease that cleaves hairpin structures in DNA recombination and repair
YhaO (Bacillus subtilis nomenclature) is included to catch SbcD paralogs.


DNA polymerase IV (EC 2.7.7.7) = DinB = DinP = error-prone DNA polymerase responsible for replication at mispaired primers.

Error-prone repair protein UmuC = SamB (on plasmids)
Error-prone repair protein UmuD


Single-stranded DNA-binding protein
(just to hold it until it gets into DNA packaging and/or DNA replication)


Endonuclease IV (EC 3.1.21.2) cleaves DNA at apurinic or apyrimidinic sites (AP sites) for short patch repair.


Endonuclease V (EC 3.1.21.7) cleaves DNA near irreguarities including deoxyinosine, deoxyuridine, and base mismatches.
[Yao, M., and Kow, Y. W. 1997. Further characterization of Escherichia coli endonuclease V. Mechanism of recognition
for deoxyinosine, deoxyuridine, and base mismatches in DNA. J. Biol. Chem. 272: 30774-30779.]


Exodeoxyribonuclease III (EC 3.1.11.2)
3'-5'-exonuclease that removes damaged strand at apurinic or apyrimidinic sites (AP sites).
Also removes RNA from RNA/DNA duplex.


Methylated-DNA--protein-cysteine methyltransferase (EC 2.1.1.63)
also called
O6-methylguanine-DNA methyltransferase (EC 2.1.1.63)
transfers the methyl group from methylated DNA (where it is damage) to a cysteine on the protein. It is a single
turnover "enzyme".
It is not unusal to have at least two genes. In B. subtilis, one is damage inducible and the other is constitutive.
It is similar to the C-terminal domain of "ADA regulatory protein"


ADA regulatory protein is a bifunctional protein that regulates rexpression of alkylation reponse genes and at
the same time is itself a methylated-DNA--protein-cysteine methyltransferase.


Alkylated DNA repair protein AlkB
Provides resistance to the alkylating agents MMS and DMS.
[Chen, B. J., Carroll, P., and Samson, L. 1994. The Escherichia coli AlkB protein protects human cells against
alkylation-induced toxicity. J Bacteriol. 176: 6255-61.]