Protein : Qrob_P0240460.2 Q. robur
Protein Identifier  ? Qrob_P0240460.2 Organism . Name  Quercus robur
Score  0.0 Score Type  egn
Protein Description  (M=2) K10862 - tyrosyl-DNA phosphodiesterase 1 [EC:3.1.4.-] Code Enzyme  EC:3.1.4.1
Gene Prediction Quality  validated Protein length 

Sequence

Length: 257  
Kegg Orthology  K10862
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0 Synonyms

4 GO Terms

Identifier Name Description
GO:0003677 DNA binding Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
GO:0005634 nucleus A membrane-bounded organelle of eukaryotic cells in which chromosomes are housed and replicated. In most cells, the nucleus contains all of the cell's chromosomes except the organellar chromosomes, and is the site of RNA synthesis and processing. In some species, or in specialized cell types, RNA metabolism or DNA replication may be absent.
GO:0008081 phosphoric diester hydrolase activity Catalysis of the hydrolysis of a phosphodiester to give a phosphomonoester and a free hydroxyl group.
GO:0006281 DNA repair The process of restoring DNA after damage. Genomes are subject to damage by chemical and physical agents in the environment (e.g. UV and ionizing radiations, chemical mutagens, fungal and bacterial toxins, etc.) and by free radicals or alkylating agents endogenously generated in metabolism. DNA is also damaged because of errors during its replication. A variety of different DNA repair pathways have been reported that include direct reversal, base excision repair, nucleotide excision repair, photoreactivation, bypass, double-strand break repair pathway, and mismatch repair pathway.

29 Blast

Analysis Hit Start End Strand Length Note Hit Coverage Hit Length Hit Pident E Val Hit Description
blastp_kegg lcl|pper:PRUPE_ppa002421mg 112 253 + 142 none 21.07 674 84.51 1e-80 hypothetical protein
blastp_kegg lcl|pmum:103324493 112 253 + 142 none 21.04 675 84.51 1e-80 tyrosyl-DNA phosphodiesterase 1
blastp_kegg lcl|pxb:103933010 112 253 + 142 none 21.29 667 83.10 6e-79 tyrosyl-DNA phosphodiesterase 1-like
blastp_kegg lcl|mdm:103422457 112 253 + 142 none 22.87 621 83.10 1e-78 tyrosyl-DNA phosphodiesterase 1-like
blastp_kegg lcl|mdm:103446679 112 253 + 142 none 22.87 621 83.10 1e-78 tyrosyl-DNA phosphodiesterase 1
blastp_kegg lcl|pxb:103948132 112 253 + 142 none 21.29 667 81.69 4e-77 tyrosyl-DNA phosphodiesterase 1-like
blastp_kegg lcl|csv:101208609 112 253 + 142 none 23.16 613 78.87 9e-76 tyrosyl-DNA phosphodiesterase 1-like
blastp_kegg lcl|vvi:100247070 115 253 + 139 none 22.38 621 82.73 2e-75 tyrosyl-DNA phosphodiesterase 1-like
blastp_kegg lcl|fve:101308644 112 253 + 142 Gaps:2 21.84 641 81.43 3e-75 tyrosyl-DNA phosphodiesterase 1-like
blastp_kegg lcl|cmo:103484589 112 253 + 142 none 21.98 646 77.46 1e-74 tyrosyl-DNA phosphodiesterase 1
blastp_pdb 1qzq_B 122 251 + 130 Gaps:12 28.16 483 37.50 1e-19 mol:protein length:483 tyrosyl-DNA phosphodiesterase 1
blastp_pdb 1qzq_A 122 251 + 130 Gaps:12 28.16 483 37.50 1e-19 mol:protein length:483 tyrosyl-DNA phosphodiesterase 1
blastp_pdb 1jy1_A 122 251 + 130 Gaps:12 29.31 464 36.76 2e-19 mol:protein length:464 TYROSYL-DNA PHOSPHODIESTERASE
blastp_pdb 1rh0_B 122 251 + 130 Gaps:12 28.04 485 36.76 3e-19 mol:protein length:485 Tyrosyl-DNA phosphodiesterase 1
blastp_pdb 1rh0_A 122 251 + 130 Gaps:12 28.04 485 36.76 3e-19 mol:protein length:485 Tyrosyl-DNA phosphodiesterase 1
blastp_pdb 1rgu_B 122 251 + 130 Gaps:12 28.04 485 36.76 3e-19 mol:protein length:485 Tyrosyl-DNA phosphodiesterase 1
blastp_pdb 1rgu_A 122 251 + 130 Gaps:12 28.04 485 36.76 3e-19 mol:protein length:485 Tyrosyl-DNA phosphodiesterase 1
blastp_pdb 1rgt_B 122 251 + 130 Gaps:12 28.04 485 36.76 3e-19 mol:protein length:485 Tyrosyl-DNA phosphodiesterase 1
blastp_pdb 1rgt_A 122 251 + 130 Gaps:12 28.04 485 36.76 3e-19 mol:protein length:485 Tyrosyl-DNA phosphodiesterase 1
blastp_pdb 1rg2_B 122 251 + 130 Gaps:12 28.04 485 36.76 3e-19 mol:protein length:485 Tyrosyl-DNA phosphodiesterase 1
blastp_uniprot_sprot sp|Q8BJ37|TYDP1_MOUSE 122 251 + 130 Gaps:8 22.33 609 39.71 4e-21 Tyrosyl-DNA phosphodiesterase 1 OS Mus musculus GN Tdp1 PE 2 SV 2
blastp_uniprot_sprot sp|Q9NUW8|TYDP1_HUMAN 122 251 + 130 Gaps:12 22.37 608 37.50 2e-19 Tyrosyl-DNA phosphodiesterase 1 OS Homo sapiens GN TDP1 PE 1 SV 2
blastp_uniprot_sprot sp|Q4G056|TYDP1_RAT 122 251 + 130 Gaps:8 22.33 609 37.50 2e-18 Tyrosyl-DNA phosphodiesterase 1 OS Rattus norvegicus GN Tdp1 PE 2 SV 1
blastp_uniprot_sprot sp|Q9VQM4|TYDP1_DROME 108 255 + 148 Gaps:14 26.55 580 35.06 2e-12 Probable tyrosyl-DNA phosphodiesterase OS Drosophila melanogaster GN gkt PE 2 SV 1
rpsblast_cdd gnl|CDD|197221 111 249 + 139 Gaps:12 100.00 145 42.76 9e-41 cd09122 PLDc_Tdp1_1 Catalytic domain repeat 1 of Tyrosyl-DNA phosphodiesterase. Catalytic domain repeat 1 of Tyrosyl-DNA phosphodiesterase (Tdp1 EC 3.1.4.-) which exists in eukaryotes but not in prokaryotes. Tdp1 acts as an important DNA repair enzyme that removes stalled topoisomerase I-DNA complexes by catalyzing the hydrolysis of a phosphodiester bond between a tyrosine side chain and a DNA 3'-phosphate. It is a monomeric protein that contains two copies of a variant HKD motif (H-x-K-x(4)-D where x represents any amino acid residue) which consists of the highly conserved histidine and lysine residues but lacks the aspartate residue that is well conserved in other phospholipase D (PLD EC 3.1.4.4) enzymes. Thus this family represents a distinct class within the PLD superfamily. Like other PLD enzymes Tdp1 may utilize a common two-step general acid/base catalytic mechanism involving a DNA-enzyme intermediate to cleave phosphodiester bonds. A single active site involved in phosphatidyl group transfer would be formed by the two variant HKD motifs from the N- and C-terminal domains in a pseudodimeric way.
rpsblast_cdd gnl|CDD|147962 94 256 + 163 Gaps:6 38.11 433 27.88 3e-29 pfam06087 Tyr-DNA_phospho Tyrosyl-DNA phosphodiesterase. Covalent intermediates between topoisomerase I and DNA can become dead-end complexes that lead to cell death. Tyrosyl-DNA phosphodiesterase can hydrolyse the bond between topoisomerase I and DNA.
rpsblast_cdd gnl|CDD|197289 108 251 + 144 Gaps:6 88.76 169 34.00 2e-26 cd09193 PLDc_mTdp1_1 Catalytic domain repeat 1 of metazoan tyrosyl-DNA phosphodiesterase. Catalytic domain repeat 1 of metazoan tyrosyl-DNA phosphodiesterase (Tdp1 EC 3.1.4.-). Human Tdp1 (hTdp1) acts as an important DNA repair enzyme with a preference for single-stranded or blunt-ended duplex oligonucleotides. It can remove stalled topoisomerase I-DNA complexes by catalyzing the hydrolysis of a phosphodiester bond between a tyrosine side chain and a DNA 3'-phosphate. It is therefore a potential molecular target for new anti-cancer drugs. hTdp1 has been shown to associate with additional proteins such as XRCC1 to form a multi-enzyme complex. These additional proteins may be involved in recognizing 3'-phoshotyrosyl DNA in vivo. hTdp1 is a monomeric protein containing two copies of a variant HKD motif (H-x-K-x(4)-D where x represents any amino acid residue) which consists of the highly conserved histidine and lysine residues but lacks the aspartate residue that is well conserved in other phospholipase D (PLD EC 3.1.4.4) enzymes. Like other PLD enzymes hTdp1 may utilize a common two-step general acid/base catalytic mechanism involving a DNA-enzyme intermediate to cleave phosphodiester bonds. A single active site involved in phosphatidyl group transfer would be formed by the two variant HKD motifs from the N- and C-terminal domains in a pseudodimeric way.
rpsblast_cdd gnl|CDD|197290 119 251 + 133 Gaps:6 83.73 166 29.50 2e-20 cd09194 PLDc_yTdp1_1 Catalytic domain repeat 1 of yeast tyrosyl-DNA phosphodiesterase. Catalytic domain repeat 1 of yeast tyrosyl-DNA phosphodiesterase (yTdp1 EC 3.1.4.-). yTdp1 is involved in the repair of topoisomerase I DNA lesions by hydrolyzing the topoisomerase from the 3'-end of the DNA during double-strand break repair. Unlike human Tdp1 whose substrate-binding pocket can accommodate a fairly large topoisomerase I peptide fragment yTdp1 has a preference for substrates containing one to four amino acid residues. The monomeric yTdp1 contains two copies of a variant HKD motif (H-x-K-x(4)-D where x represents any amino acid residue) which consists of the highly conserved histidine and lysine residues but lacks the aspartate residue that is well conserved in other phospholipase D (PLD EC 3.1.4.4) enzymes. Like other PLD enzymes yTdp1 may utilize a common two-step general acid/base catalytic mechanism involving a DNA-enzyme intermediate to cleave phosphodiester bonds. A single active site involved in phosphatidyl group transfer would be formed by the two variant HKD motifs from the N- and C-terminal domains in a pseudodimeric way.
rpsblast_kog gnl|CDD|37242 34 253 + 220 Gaps:3 42.58 519 28.51 4e-40 KOG2031 KOG2031 KOG2031 Tyrosyl-DNA phosphodiesterase [Replication recombination and repair].

9 Domain Motifs

Analysis Begin End Length Domain Identifier Cross Ref Description Inter Pro
Pfam 108 253 146 PF06087 none Tyrosyl-DNA phosphodiesterase IPR010347
Gene3D 108 255 148 G3DSA:3.30.870.10 none none none
SUPERFAMILY 107 255 149 SSF56024 none none none
PANTHER 122 254 133 PTHR12415 none none IPR010347
SMART 52 104 53 SM00614 none BED zinc finger IPR003656
PANTHER 122 254 133 PTHR12415:SF0 none none none
Pfam 55 102 48 PF02892 none BED zinc finger IPR003656
ProSiteProfiles 52 108 57 PS50808 none Zinc finger BED-type profile. IPR003656
SUPERFAMILY 55 103 49 SSF57667 none none none

0 Localization

6 Qtllist

Qtl Name Chromosome Name Linkage Group Prox Marker Dist Marker Position QTL Pos One Pos Two Test Type Test Value R 2
Bourran2_2014_nSecLBD_A4 Qrob_Chr07 7 v_8327_222 s_1A4WGY_363 16,04 0 44,69 lod 2,6373 6,5
Bourran2_2014_nP_A4 Qrob_Chr11 11 s_1B58GB_1413 s_1A5BYY_1671 11,15 0 42,38 lod 1,8913 4,5
Bourran2_2015_nSeqBC_3P Qrob_Chr11 11 s_1DG9PM_867 s_1BZ083_1312 26,06 25,47 27,72 lod 3.6 7.1
Bourran2_2015_nEpis_A4 Qrob_Chr09 9 v_15847_485 v_8329_369 34,94 34,88 37,45 lod 3.1 7
Bourran2_2015_nEpiBC_A4 Qrob_Chr07 7 s_1DP9TW_798 v_8128_173 22,61 22,14 22,73 lod 3.1 8.5
Bourran2_2014_nEpiBC_A4 Qrob_Chr07 7 s_2FI9D9_500 s_1AXDMJ_325 12,26 0 34,9 lod 2,2306 6,1

0 Targeting