>TIGR01663 PNK-3'Pase polynucleotide kinase 3'-phosphatase; InterPro: IPR006550 These sequences represent the metazoan 5'-polynucleotide-kinase-3'-phosphatase, PNKP, which is believed to be involved in repair of oxidative DNA damage. Removal of 3'-phosphates is essential for the further processing of the break by DNA polymerases , . The central phosphatase domain is a member of the IIIA subfamily (IPR006549 from INTERPRO) of the haloacid dehalogenase (HAD) superfamily of aspartate-nucleophile hydrolases. As is common in this superfamily, the enzyme is magnesium dependent. A difference between this enzyme and other HAD-superfamily phosphatases is in the third conserved catalytic motif which usually contains two conserved aspartate residues believed to be involved in binding the magnesium ion. Here, the second aspartate is replaced by a conserved arginine residue which may indicate an interaction with the phosphate backbone of the substrate. Very close relatives of this domain are also found separate from the N- and C-terminal domains seen here, as in the 3'-phosphatase found in plants. The larger family of these domains is described by IPR006551 from INTERPRO. Outside of the phosphatase domain is a P-loop ATP-binding motif associated with the kinase activity. The entry for the mouse homolog appears to be missing a large piece of sequence corresponding to the first conserved catalytic motif of the phosphatase domain as well as the conserved threonine of the second motif. Either this is a sequencing artifact or this may represent a pseudo- or non-functional gene. .

Probab=94.91 E-value=0.061 Score=30.66 Aligned_cols=117 Identities=21% Similarity=0.230 Sum_probs=64.5 Q ss_pred CCCCCCCEEEECCCEEEEECCCCHHHHHHHHCCCHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHCCCC Q ss_conf 55553444872275026524520027887412232778887652024410012345568764200456898874211345 Q gi|254780960|r 75 HENRRKNLLIADMDSTMIEQECIDELADLIGIKEKVSLITARAMNGEIPFQDSLRERISLFKGTSTKIIDSLLEKKITYN 154 (297) Q Consensus 75 ~~~~~~~l~~~d~d~tli~~~~l~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 154 (297) T Consensus 163 GVK~~~K~AGyDlDGT~I~T~SG~V------------------------F------------P~~-------~~DW~I~y 199 (526) T TIGR01663 163 GVKGSEKVAGYDLDGTLIKTKSGKV------------------------F------------PKN-------TDDWRILY 199 (526) T ss_pred CCCCCCCEEEEECCCCEEECCCCEE------------------------C------------CCC-------CCCCEEEC T ss_conf 2257873442425773673134302------------------------0------------688-------88657845 Q ss_pred CCHHHHHHHHHHCCCEEEEEEC------------CCHHHHHHHHHHHCCCH--HHHHCCCCHHHCCCCCCCCCCCCHHHH Q ss_conf 4338999999841986999816------------72342232265508641--343101000000000015631052113 Q gi|254780960|r 155 PGGYELVHTMKQNGASTLLVTG------------GFSIFARFIAQHLGFDQ--YYANRFIEKDDRLTGQVMEPIIDGTAK 220 (297) Q Consensus 155 ~~~~~~i~~l~~~g~~v~iisg------------~~~~~~~~ia~~lgi~~--~~a~~~~~~~~~~~~~~~~~~~~~~~k 220 (297) T Consensus 200 PE~P~KL~~L~~~GyK~~~FTNQ~~I~RGK~~~~~FK~K~~~~V~KLGVP~QVl~A~~~GlYRKP~TGMW---------- 269 (526) T TIGR01663 200 PEVPRKLKELEKDGYKLVLFTNQGSIARGKLNLDDFKVKVKAVVEKLGVPIQVLVAIGDGLYRKPLTGMW---------- 269 (526) T ss_pred CCCCHHHHHHHHCCCEEEEEECCCCEECCCCCHHHHHHHHHHHHHHCCCCEEEEEECCCCCCCCCCCHHH---------- T ss_conf 6544578887418827999845773001555656766688888986189768876506872027752047---------- Q ss_pred HHHHHH-HHHHHCCCCCEEEEEECCC Q ss_conf 887753-2331037766799997892 Q gi|254780960|r 221 SQILLE-AIQKLQINPEDTIAVGDGN 245 (297) Q Consensus 221 ~~~~~~-l~~~~~~~~~~v~avGDg~ 245 (297) T Consensus 270 -~HL~~~~NDG~~I~~~~~~FVGDAA 294 (526) T TIGR01663 270 -DHLKEEANDGVEISIDDSIFVGDAA 294 (526) T ss_pred -HHHHHHCCCCCEEECCCEEEECCCC T ss_conf -8988753688123117757871667

HHsearch alignment for GI: 254780960 and conserved domain: TIGR01663