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.

                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 57242805 352 VYLIGSTPGRFQGSQKDNWGHFRLKKLLKDHASSMPNAESWPVVGQFSSVGSLGADESKWLCSEFKESmltLGKESKTPG 431
Cdd:cd09195   1 VFLIGSVPGRHTGSSLDKWGHLRLRKLLKEHASLPPVAESWPVIAQFSSIGSLGPDPQKWLCSEFLES---LSGLGKTSG 77

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 57242805 432 KSSVPLYLIYPSVENVRTSLEGYPAGGSLPYSIQTAEKQNWLHSYFHKWSAETSGRSNAMPHIKTYMRPSPDFSKIAWFL 511
Cdd:cd09195  78 KSSPPLKLIYPSVENVRNSLEGYPAGGCLPYSKQTAEKQPWLKSYLHKWKADKRGRSRAMPHIKTYTRISPDLSKIAWFL 157

                       170       180       190
                ....*....|....*....|....*....|....
gi 57242805 512 VTSANLSKAAWGALEKNGTQLMIRSYELGVLFLP 545
Cdd:cd09195 158 LTSANLSKAAWGALEKNGTQLMIRSYEAGVLFLP 191

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.

                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 57242805 352 VYLIGSTPGRFQGSQKDNWGHFRLKKLLKDHASSMPNAESWPVVGQFSSVGSLGADESKWLCSEFKESmltLGKESKTPG 431
Cdd:cd09195   1 VFLIGSVPGRHTGSSLDKWGHLRLRKLLKEHASLPPVAESWPVIAQFSSIGSLGPDPQKWLCSEFLES---LSGLGKTSG 77

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 57242805 432 KSSVPLYLIYPSVENVRTSLEGYPAGGSLPYSIQTAEKQNWLHSYFHKWSAETSGRSNAMPHIKTYMRPSPDFSKIAWFL 511
Cdd:cd09195  78 KSSPPLKLIYPSVENVRNSLEGYPAGGCLPYSKQTAEKQPWLKSYLHKWKADKRGRSRAMPHIKTYTRISPDLSKIAWFL 157

                       170       180       190
                ....*....|....*....|....*....|....
gi 57242805 512 VTSANLSKAAWGALEKNGTQLMIRSYELGVLFLP 545
Cdd:cd09195 158 LTSANLSKAAWGALEKNGTQLMIRSYEAGVLFLP 191

Catalytic domain, repeat 2, of tyrosyl-DNA phosphodiesterase; Catalytic domain, repeat 2, 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.

                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 57242805 372 HFRLKKLLKDHASSM-PNAESWPVVGQFSSVGSLGadeSKWLCSEFKESMLTLGKES-------KTPGKSSVPLYLIYPS 443
Cdd:cd09123   1 LGRLRKLLQNLTLDNkEKEKSKPLVYQFSSIGSLD---EKWWLNEFASSLGGVSSRSelplvkkNSPSLGKPKLKIIFPT 77

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 57242805 444 VENVRTSLEGYPAGGSLPYSIQTAEKQNWLHSYFHKWSAETSG--RSNAMPHIKTYMRPSPD--FSKIAWFLVTSANLSK 519
Cdd:cd09123  78 VEEVRTSLEGYNGGGSIPFTIKNYESKEFLKKLFHRWKPRNNArrRQRAMPHIKTYIRYTDDgkIDKLGWVYLGSHNLSK 157

                       170       180
                ....*....|....*....|....*
gi 57242805 520 AAWGALEKNGTQLMIRSYELGVLFL 544
Cdd:cd09123 158 AAWGALQKNGSQLRIRNYELGVLFP 182

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.

                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 57242805 162 NPFQfyLTRVSGVKP--KYNSGALHIKDILSPlfGTLVSSAQFNYCFDVDWLVKQYPPEFRKKPILLVHGD--KREAKAH 237
Cdd:cd09194   1 SPFK--LVKSSAYDEeeEVNVDTITLKDLLGD--PDLKETWLFNFQYDLDFLLDQFHPNVNHVKITIVAGSgtIEPPTRR 76

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 57242805 238 LHAQAKPYENISLCQAKLDIAFGTHHTKMMLLLYEEG-LRVVIHTSNLIHADWHQKTQGIWLSPLYPRIADGTHKSGESp 316
Cdd:cd09194  77 RIKLNKIYPNVKLIEAYMPPPFGTHHSKMMINFYQDDsCQIVIPSANLTEMDTNLPQQVVWKSPRLPLKSETVPGSGSR- 155

                       170
                ....*....|.
gi 57242805 317 thFKADLISYL 327
Cdd:cd09194 156 --FKRDLLAYL 164

Catalytic domain of phospholipase D superfamily proteins; Catalytic domain of phospholipase D (PLD) superfamily proteins. The PLD superfamily is composed of a large and diverse group of proteins including plant, mammalian and bacterial PLDs, bacterial cardiolipin (CL) synthases, bacterial phosphatidylserine synthases (PSS), eukaryotic phosphatidylglycerophosphate (PGP) synthase, eukaryotic tyrosyl-DNA phosphodiesterase 1 (Tdp1), and some bacterial endonucleases (Nuc and BfiI), among others. PLD enzymes hydrolyze phospholipid phosphodiester bonds to yield phosphatidic acid and a free polar head group. They can also catalyze the transphosphatidylation of phospholipids to acceptor alcohols. The majority of members in this superfamily contain a short conserved sequence motif (H-x-K-x(4)-D, where x represents any amino acid residue), called the HKD signature motif. There are varying expanded forms of this motif in different family members. Some members contain variant HKD motifs. Most PLD enzymes are monomeric proteins with two HKD motif-containing domains. Two HKD motifs from two domains form a single active site. Some PLD enzymes have only one copy of the HKD motif per subunit but form a functionally active dimer, which has a single active site at the dimer interface containing the two HKD motifs from both subunits. Different PLD enzymes may have evolved through domain fusion of a common catalytic core with separate substrate recognition domains. Despite their various catalytic functions and a very broad range of substrate specificities, the diverse group of PLD enzymes can bind to a phosphodiester moiety. Most of them are active as bi-lobed monomers or dimers, and may possess similar core structures for catalytic activity. They are generally thought to utilize a common two-step ping-pong catalytic mechanism, involving an enzyme-substrate intermediate, to cleave phosphodiester bonds. The two histidine residues from the two HKD motifs play key roles in the catalysis. Upon substrate binding, a histidine from one HKD motif could function as the nucleophile, attacking the phosphodiester bond to create a covalent phosphohistidine intermediate, while the other histidine residue from the second HKD motif could serve as a general acid, stabilizing the leaving group.

                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 57242805 186 KDILSPLFGTLVSSAQFNYCFD---VDWLVKQYPPEF-RKKPILLVHGDKREAKAHLHAQ---AKPYENISLCQAKLDIA 258
Cdd:cd00138   1 EALLELLKNAKESIFIATPNFSfnsADRLLKALLAAAeRGVDVRLIIDKPPNAAGSLSAAlleALLRAGVNVRSYVTPPH 80

                        90       100       110       120
                ....*....|....*....|....*....|....*....|..
gi 57242805 259 F-GTHHTKMMLLlyeEGLRVVIHTSNLIHADWHQKTQGIWLS 299
Cdd:cd00138  81 FfERLHAKVVVI---DGEVAYVGSANLSTASAAQNREAGVLV 119

Catalytic domain of phospholipase D superfamily proteins; Catalytic domain of phospholipase D (PLD) superfamily proteins. The PLD superfamily is composed of a large and diverse group of proteins including plant, mammalian and bacterial PLDs, bacterial cardiolipin (CL) synthases, bacterial phosphatidylserine synthases (PSS), eukaryotic phosphatidylglycerophosphate (PGP) synthase, eukaryotic tyrosyl-DNA phosphodiesterase 1 (Tdp1), and some bacterial endonucleases (Nuc and BfiI), among others. PLD enzymes hydrolyze phospholipid phosphodiester bonds to yield phosphatidic acid and a free polar head group. They can also catalyze the transphosphatidylation of phospholipids to acceptor alcohols. The majority of members in this superfamily contain a short conserved sequence motif (H-x-K-x(4)-D, where x represents any amino acid residue), called the HKD signature motif. There are varying expanded forms of this motif in different family members. Some members contain variant HKD motifs. Most PLD enzymes are monomeric proteins with two HKD motif-containing domains. Two HKD motifs from two domains form a single active site. Some PLD enzymes have only one copy of the HKD motif per subunit but form a functionally active dimer, which has a single active site at the dimer interface containing the two HKD motifs from both subunits. Different PLD enzymes may have evolved through domain fusion of a common catalytic core with separate substrate recognition domains. Despite their various catalytic functions and a very broad range of substrate specificities, the diverse group of PLD enzymes can bind to a phosphodiester moiety. Most of them are active as bi-lobed monomers or dimers, and may possess similar core structures for catalytic activity. They are generally thought to utilize a common two-step ping-pong catalytic mechanism, involving an enzyme-substrate intermediate, to cleave phosphodiester bonds. The two histidine residues from the two HKD motifs play key roles in the catalysis. Upon substrate binding, a histidine from one HKD motif could function as the nucleophile, attacking the phosphodiester bond to create a covalent phosphohistidine intermediate, while the other histidine residue from the second HKD motif could serve as a general acid, stabilizing the leaving group.

                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 57242805 409 SKWLCSEFKESMLTLGKesktpgkSSVPLYLIYPSVENVRTSLEGypaggslpysiQTAEKQNWLHSYFHKWsaETSGRS 488
Cdd:cd00138  22 SFNSADRLLKALLAAAE-------RGVDVRLIIDKPPNAAGSLSA-----------ALLEALLRAGVNVRSY--VTPPHF 81

                        90       100       110       120       130
                ....*....|....*....|....*....|....*....|....*....|....*
gi 57242805 489 NAMPHIKTYMRPSpdfskiAWFLVTSANLSKAAWGalekngtqlmiRSYELGVLF 543
Cdd:cd00138  82 FERLHAKVVVIDG------EVAYVGSANLSTASAA-----------QNREAGVLV 119