Pathways & interactions
Polymerase/histidinol phosphatase, N-terminal (IPR003141)
Short name: Pol/His_phosphatase_N
Overlapping homologous superfamilies
- Polymerase/histidinol phosphatase-like (IPR016195)
- PHP domain (IPR004013)
- Polymerase/histidinol phosphatase, N-terminal (IPR003141)
This domain is associated with the N terminus of members of the PHP superfamily, this includes:
- subunit of bacterial DNA polymerase III,
- eukaryotic DNA polymerase,
- X-family of DNA polymerases,
- histidinol phosphatases,
- and a number of uncharacterised protein families.
In common for all PHP proteins is the presence of four conserved sequence motifs that contain invariant histidine and aspartate residues implicated in metal ion coordination. As part of DNA polymerases, the PHP domain was suggested to hydrolyse pyrophosphate and thereby shift the reaction equilibrium toward nucleotide polymerisation. However, it cannot be ruled out that the PHP domain possesses a nuclease activity, particularly in the repair polymerases of the X-family. No functional information is available for standalone proteins that belong to the PHP superfamily.
The crystal structure of the YcdX protein from Escherichia coli has been determined to 1.6-A resolution. YcdX has an unusual topology of a alpha 7_beta 7 barrel compared with the more common alpha 8_beta 8 (TIM) barrel. The C-terminal helix caps the barrel on the N-terminal side. The deep cleft at the C-terminal side of the barrel contains the three zinc binding residues. These residues are invariant in the YcdX family confirming their functional importance.
Only four proteins with known structures have a similar trinuclear zinc catalytic site. All four (nuclease P1, endonuclease IV, alkaline phosphatase, and phospholipase C) hydrolyse the phosphoester bond. This finding suggests a similar activity for YcdX. YcdX is among the genes significantly induced in response to the DNA damage, therefore indicating that members of the YcdX family may be involved in DNA repair [PMID: 12661000].
- SM00481 (POLIIIAc)