Protein : Qrob_P0240420.2 Q. robur
Protein Identifier  ? Qrob_P0240420.2 Organism . Name  Quercus robur
Score  97.0 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: 641  
Kegg Orthology  K10862
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0 Synonyms

4 GO Terms

Identifier Name Description
GO:0005515 protein binding Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules).
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.

33 Blast

Analysis Hit Start End Strand Length Note Hit Coverage Hit Length Hit Pident E Val Hit Description
blastp_kegg lcl|cic:CICLE_v10014587mg 1 640 + 640 Gaps:80 100.00 636 66.82 0.0 hypothetical protein
blastp_kegg lcl|pmum:103324493 1 640 + 640 Gaps:89 100.00 675 62.96 0.0 tyrosyl-DNA phosphodiesterase 1
blastp_kegg lcl|cit:102627995 1 640 + 640 Gaps:80 100.00 636 66.51 0.0 tyrosyl-DNA phosphodiesterase 1-like
blastp_kegg lcl|pper:PRUPE_ppa002421mg 1 640 + 640 Gaps:88 100.00 674 62.76 0.0 hypothetical protein
blastp_kegg lcl|pxb:103948132 1 640 + 640 Gaps:101 100.00 667 62.07 0.0 tyrosyl-DNA phosphodiesterase 1-like
blastp_kegg lcl|pxb:103933010 1 640 + 640 Gaps:77 100.00 667 61.62 0.0 tyrosyl-DNA phosphodiesterase 1-like
blastp_kegg lcl|mdm:103446679 1 640 + 640 Gaps:101 100.00 621 65.70 0.0 tyrosyl-DNA phosphodiesterase 1
blastp_kegg lcl|mdm:103422457 1 640 + 640 Gaps:101 100.00 621 65.54 0.0 tyrosyl-DNA phosphodiesterase 1-like
blastp_kegg lcl|fve:101308644 1 640 + 640 Gaps:85 100.00 641 64.12 0.0 tyrosyl-DNA phosphodiesterase 1-like
blastp_kegg lcl|gmx:100793746 5 630 + 626 Gaps:69 99.07 647 61.62 0.0 tyrosyl-DNA phosphodiesterase 1-like
blastp_pdb 1qzq_B 182 628 + 447 Gaps:106 91.72 483 35.89 7e-54 mol:protein length:483 tyrosyl-DNA phosphodiesterase 1
blastp_pdb 1qzq_A 182 628 + 447 Gaps:106 91.72 483 35.89 7e-54 mol:protein length:483 tyrosyl-DNA phosphodiesterase 1
blastp_pdb 1jy1_A 182 628 + 447 Gaps:106 95.47 464 35.67 1e-53 mol:protein length:464 TYROSYL-DNA PHOSPHODIESTERASE
blastp_pdb 1rh0_B 182 628 + 447 Gaps:106 91.34 485 35.67 2e-53 mol:protein length:485 Tyrosyl-DNA phosphodiesterase 1
blastp_pdb 1rh0_A 182 628 + 447 Gaps:106 91.34 485 35.67 2e-53 mol:protein length:485 Tyrosyl-DNA phosphodiesterase 1
blastp_pdb 1rgu_B 182 628 + 447 Gaps:106 91.34 485 35.67 2e-53 mol:protein length:485 Tyrosyl-DNA phosphodiesterase 1
blastp_pdb 1rgu_A 182 628 + 447 Gaps:106 91.34 485 35.67 2e-53 mol:protein length:485 Tyrosyl-DNA phosphodiesterase 1
blastp_pdb 1rgt_B 182 628 + 447 Gaps:106 91.34 485 35.67 2e-53 mol:protein length:485 Tyrosyl-DNA phosphodiesterase 1
blastp_pdb 1rgt_A 182 628 + 447 Gaps:106 91.34 485 35.67 2e-53 mol:protein length:485 Tyrosyl-DNA phosphodiesterase 1
blastp_pdb 1rg2_B 182 628 + 447 Gaps:106 91.34 485 35.67 2e-53 mol:protein length:485 Tyrosyl-DNA phosphodiesterase 1
blastp_uniprot_sprot sp|Q9NUW8|TYDP1_HUMAN 149 628 + 480 Gaps:122 79.61 608 34.71 1e-52 Tyrosyl-DNA phosphodiesterase 1 OS Homo sapiens GN TDP1 PE 1 SV 2
blastp_uniprot_sprot sp|Q8BJ37|TYDP1_MOUSE 182 628 + 447 Gaps:102 72.74 609 35.44 4e-51 Tyrosyl-DNA phosphodiesterase 1 OS Mus musculus GN Tdp1 PE 2 SV 2
blastp_uniprot_sprot sp|Q4G056|TYDP1_RAT 182 628 + 447 Gaps:102 72.74 609 35.21 4e-51 Tyrosyl-DNA phosphodiesterase 1 OS Rattus norvegicus GN Tdp1 PE 2 SV 1
blastp_uniprot_sprot sp|Q9TXV7|TYDP1_CAEEL 206 628 + 423 Gaps:92 86.70 451 30.43 2e-27 Probable tyrosyl-DNA phosphodiesterase OS Caenorhabditis elegans GN F52C12.1 PE 3 SV 1
blastp_uniprot_sprot sp|Q9VQM4|TYDP1_DROME 194 535 + 342 Gaps:52 56.21 580 31.29 2e-26 Probable tyrosyl-DNA phosphodiesterase OS Drosophila melanogaster GN gkt PE 2 SV 1
blastp_uniprot_sprot sp|Q9USG9|TYDP1_SCHPO 177 554 + 378 Gaps:98 75.75 536 28.08 4e-15 Probable tyrosyl-DNA phosphodiesterase OS Schizosaccharomyces pombe (strain 972 / ATCC 24843) GN SPCP31B10.05 PE 3 SV 1
rpsblast_cdd gnl|CDD|147962 198 584 + 387 Gaps:84 95.84 433 29.40 4e-58 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|197221 202 337 + 136 Gaps:11 100.00 145 44.14 4e-44 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|197291 372 540 + 169 Gaps:31 80.63 191 48.05 2e-33 cd09195 PLDc_mTdp1_2 Catalytic domain repeat 2 of metazoan tyrosyl-DNA phosphodiesterase. Catalytic domain repeat 2 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|197289 185 339 + 155 Gaps:11 97.04 169 33.54 1e-25 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.

14 Domain Motifs

Analysis Begin End Length Domain Identifier Cross Ref Description Inter Pro
SUPERFAMILY 182 396 215 SSF56024 none none none
PANTHER 603 631 29 PTHR12415:SF0 none none none
PANTHER 425 580 156 PTHR12415 none none IPR010347
PANTHER 153 405 253 PTHR12415 none none IPR010347
PANTHER 425 580 156 PTHR12415:SF0 none none none
PANTHER 153 405 253 PTHR12415:SF0 none none none
PANTHER 603 631 29 PTHR12415 none none IPR010347
Pfam 197 542 346 PF06087 none Tyrosyl-DNA phosphodiesterase IPR010347
Gene3D 16 109 94 G3DSA:2.60.200.20 none none IPR000253
Gene3D 179 370 192 G3DSA:3.30.870.10 none none none
Gene3D 560 630 71 G3DSA:3.30.870.20 none none IPR027415
Gene3D 372 537 166 G3DSA:3.30.870.20 none none IPR027415
SUPERFAMILY 372 629 258 SSF56024 none none none
SUPERFAMILY 14 109 96 SSF49879 none none IPR008984

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