H
IPR011604

PD-(D/E)XK endonuclease-like domain superfamily

InterPro entry
Short namePDDEXK-like_dom_sf
Overlapping entries
 

Description

This entry represent a PD-(D/E)XK endonuclease-like domain superfamily
[4]
. PD-(D/E)XK nucleases constitute a large and highly diverse superfamily of enzymes that display little sequence similarity. However, they share a common core fold and a few critical active site residues
[3]
. This domain can be found at the C terminus of nuclease/helicase AddA, AddB, and RecB.

There are two classes of helicase-nuclease complex involved in the initiation step for recombinational repair. AddAB-type enzymes (also called RexAB) are found mainly in Gram-positive bacteria, whereas heterotrimeric RecBCD-type enzymes are found mainly in Gram-negative bacteria
[6]
. The RecBCD holoenzyme has a single nuclease domain found in RecB
[5]
. Exodeoxyribonuclease V, or RecBCD holoenzyme, is a multifunctional nuclease with potent ATP-dependent exodeoxyribonuclease activity. Ejection of RecD, as occurs at chi recombinational hotspots, cripples exonuclease activity in favor of recombinagenic helicase activity. All proteins in this family for which functions are known are DNA-DNA helicases that are used as part of an exonuclease-helicase complex (made up of RecBCD homologues) that function to generate substrates for the initiation of recombination and recombinational repair. The complex catalyses exonucleolytic cleavage in either the 5' to 3' or 3' to 5' direction to yield 5-phosphooligonucleotides in the presence of ATP
[2]
.

This superfamily includes phage-type exonucleases (
3.1.11.3
), the C-terminal domain of Exonuclease/helicase subunit RexA and RexB
[7]
and RecB exodeoxyribonuclease V exonuclease (
3.1.11.5
), which are closely related in sequence and structure, containing a restriction enzyme-like core fold.

Exonuclease from Bacteriophage lambda facilitates phage DNA recombination through the double-strand break repair (DSBR) and single-strand annealing pathways; it is also important for the late, rolling-circle mode of lambda DNA replication. This magnesium-dependent enzyme catalyses the exonucleolytic cleavage of DNA in the 5'- to 3'-direction to yield nucleoside 5'-phosphates. Lambda exonuclease is a trimer of three subunits that form a toroid structure with a tapered channel passing through the middle
[1]
.

References

1.Toroidal structure of lambda-exonuclease. Kovall R, Matthews BW. Science 277, 1824-7, (1997). View articlePMID: 9295273

2.Crystal structure of RecBCD enzyme reveals a machine for processing DNA breaks. Singleton MR, Dillingham MS, Gaudier M, Kowalczykowski SC, Wigley DB. Nature 432, 187-93, (2004). View articlePMID: 15538360

3.Realm of PD-(D/E)XK nuclease superfamily revisited: detection of novel families with modified transitive meta profile searches. Knizewski L, Kinch LN, Grishin NV, Rychlewski L, Ginalski K. BMC Struct. Biol. 7, 40, (2007). View articlePMID: 17584917

4.Identification of novel restriction endonuclease-like fold families among hypothetical proteins. Kinch LN, Ginalski K, Rychlewski L, Grishin NV. Nucleic Acids Res. 33, 3598-605, (2005). View articlePMID: 15972856

5.A single nuclease active site of the Escherichia coli RecBCD enzyme catalyzes single-stranded DNA degradation in both directions. Wang J, Chen R, Julin DA. J. Biol. Chem. 275, 507-13, (2000). View articlePMID: 10617645

6.A dual-nuclease mechanism for DNA break processing by AddAB-type helicase-nucleases. Yeeles JT, Dillingham MS. J. Mol. Biol. 371, 66-78, (2007). View articlePMID: 17570399

7.rexAB mutants in Streptococcus pneumoniae. Halpern D, Gruss A, Claverys JP, Karoui ME. Microbiology (Reading) 150, 2409-2414, (2004). View articlePMID: 15256582

Cross References

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