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Conserved domains on  [gi|31615977|pdb|1P4E|D]
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List of domain hits

Name Accession Description Interval E-value
INT_Flp_C cd00217
Flp Tyrosine-based site-specific recombinases (also called integrases), C-terminal catalytic ...
6-420 0e+00

Flp Tyrosine-based site-specific recombinases (also called integrases), C-terminal catalytic domain; Yeast Flp-like recombinases mediate the amplification of the 2 micron circular plasmid copy number by catalyzing the intra-molecular recombination between two inverted repeats during replication. They belong to the DNA breaking-rejoining enzyme superfamily, which also includes prokaryotic tyrosine recombinases and type IB topoisomerases. These enzymes share the same fold in their catalytic domain containing six conserved active site residues and the overall reaction mechanism. Flp-like recombinases are almost exclusively found in yeast and are highly diverged in sequence from the prokaryotic tyrosine recombinases. They cleave their target DNA in trans with a composite active site in which the catalytic tyrosine is provided by a promoter bound to a site other than the one being cleaved. Thus each active site within Flp complexes is assembled by domain swapping and contains catalytic residues from two different monomers. Two DNA segments are synapsed by the tetrameric enzyme, carrying the nucleophilic tyrosine in each active site with only two of the four monomers active at a given time. The catalytic domain is linked through a flexible loop to the N-terminal domain, which is largely responsible for non-specific DNA binding and isomerization. Its overall fold is similar to the SAM domain fold also found in the N-terminal domains of lambda integrase and XerD recombinase.


:

Pssm-ID: 271174 [Multi-domain]  Cd Length: 410  Bit Score: 582.50  E-value: 0e+00
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
1P4E_D        6 LCKTPPKVLVRQFVERFERPSGEKIASCAAELTYLCWMITHNGTAIKRATFMSYNTIISNSLSFDIVNKSLQFKYKTQKA 85
Cdd:cd00217   1 LIPVRPAILIELFLELFGKDKIEDKRKLASLLTYLILMAFPAITEVKRGTFRKYKTIISNSLSFDYSRKTIQFKYRLKKN 80
                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
1P4E_D       86 TILEASLKKLIPAWEFTIIPYNGQKHQSDITDIVSSlqlqFESSEEADKGNSHSKKMLKALLSEGESIWEITEKILNSFE 165
Cdd:cd00217  81 RLLQKGLEDAEPPYKFVILSDKRQEENLFIIDKVPL----EPNTESKHIRNSEVNLEFTNILSEKESIWKIIYKILDSFE 156
                       170       180       190       200       210       220       230       240
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
1P4E_D      166 YTSRFTKTKTLYQFLFLATFINCGRFSDIKNVDPKSFKLVQNKYLGVIIQCLVTETKTSVSRHIYFFSARGRIDPLVYLD 245
Cdd:cd00217 157 ENTSRTTTKARYKLLLLATFTNCCRISDLKNLDPSTFELVKNKYLGTIVRAHVTETKTRISRTVYFFPARGRCDLLLALD 236
                       250       260       270       280       290       300       310       320
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
1P4E_D      246 EFLRNSEPVLKRVNRTGNsssNKQEYQLLKDNLVRSYNKALKKNAPYPIFAIKNGPKSHIGRHLMTSFLSMKGLTELTNV 325
Cdd:cd00217 237 EYLRICKPIPKTVVSDQN---VNQKYQLLKESLVRSYNKFLSKHPAEPIFKIKNGPKSHLGRHLMASFLSKNELDKEANS 313
                       330       340       350       360       370       380       390       400
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
1P4E_D      326 VGNFSDKRA--SAVARTT*THQITAIPDHYFALVSRYYAYDPISKEmIALKDETNPIEEWQHIEQLKGSA-EGSIRYPAW 402
Cdd:cd00217 314 LGNWSKVREigSAVARRNYTHTITPCPDSLFAFISGYYQISPEGSE-IELNNNKNPMERVHTIPELPTSEdELQLRYGHW 392
                       410
                ....*....|....*...
1P4E_D      403 NGIISQEVLDYLSSYINR 420
Cdd:cd00217 393 AKIISHDVLAFLSEYSRK 410
 
Name Accession Description Interval E-value
INT_Flp_C cd00217
Flp Tyrosine-based site-specific recombinases (also called integrases), C-terminal catalytic ...
6-420 0e+00

Flp Tyrosine-based site-specific recombinases (also called integrases), C-terminal catalytic domain; Yeast Flp-like recombinases mediate the amplification of the 2 micron circular plasmid copy number by catalyzing the intra-molecular recombination between two inverted repeats during replication. They belong to the DNA breaking-rejoining enzyme superfamily, which also includes prokaryotic tyrosine recombinases and type IB topoisomerases. These enzymes share the same fold in their catalytic domain containing six conserved active site residues and the overall reaction mechanism. Flp-like recombinases are almost exclusively found in yeast and are highly diverged in sequence from the prokaryotic tyrosine recombinases. They cleave their target DNA in trans with a composite active site in which the catalytic tyrosine is provided by a promoter bound to a site other than the one being cleaved. Thus each active site within Flp complexes is assembled by domain swapping and contains catalytic residues from two different monomers. Two DNA segments are synapsed by the tetrameric enzyme, carrying the nucleophilic tyrosine in each active site with only two of the four monomers active at a given time. The catalytic domain is linked through a flexible loop to the N-terminal domain, which is largely responsible for non-specific DNA binding and isomerization. Its overall fold is similar to the SAM domain fold also found in the N-terminal domains of lambda integrase and XerD recombinase.


Pssm-ID: 271174 [Multi-domain]  Cd Length: 410  Bit Score: 582.50  E-value: 0e+00
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
1P4E_D        6 LCKTPPKVLVRQFVERFERPSGEKIASCAAELTYLCWMITHNGTAIKRATFMSYNTIISNSLSFDIVNKSLQFKYKTQKA 85
Cdd:cd00217   1 LIPVRPAILIELFLELFGKDKIEDKRKLASLLTYLILMAFPAITEVKRGTFRKYKTIISNSLSFDYSRKTIQFKYRLKKN 80
                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
1P4E_D       86 TILEASLKKLIPAWEFTIIPYNGQKHQSDITDIVSSlqlqFESSEEADKGNSHSKKMLKALLSEGESIWEITEKILNSFE 165
Cdd:cd00217  81 RLLQKGLEDAEPPYKFVILSDKRQEENLFIIDKVPL----EPNTESKHIRNSEVNLEFTNILSEKESIWKIIYKILDSFE 156
                       170       180       190       200       210       220       230       240
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
1P4E_D      166 YTSRFTKTKTLYQFLFLATFINCGRFSDIKNVDPKSFKLVQNKYLGVIIQCLVTETKTSVSRHIYFFSARGRIDPLVYLD 245
Cdd:cd00217 157 ENTSRTTTKARYKLLLLATFTNCCRISDLKNLDPSTFELVKNKYLGTIVRAHVTETKTRISRTVYFFPARGRCDLLLALD 236
                       250       260       270       280       290       300       310       320
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
1P4E_D      246 EFLRNSEPVLKRVNRTGNsssNKQEYQLLKDNLVRSYNKALKKNAPYPIFAIKNGPKSHIGRHLMTSFLSMKGLTELTNV 325
Cdd:cd00217 237 EYLRICKPIPKTVVSDQN---VNQKYQLLKESLVRSYNKFLSKHPAEPIFKIKNGPKSHLGRHLMASFLSKNELDKEANS 313
                       330       340       350       360       370       380       390       400
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
1P4E_D      326 VGNFSDKRA--SAVARTT*THQITAIPDHYFALVSRYYAYDPISKEmIALKDETNPIEEWQHIEQLKGSA-EGSIRYPAW 402
Cdd:cd00217 314 LGNWSKVREigSAVARRNYTHTITPCPDSLFAFISGYYQISPEGSE-IELNNNKNPMERVHTIPELPTSEdELQLRYGHW 392
                       410
                ....*....|....*...
1P4E_D      403 NGIISQEVLDYLSSYINR 420
Cdd:cd00217 393 AKIISHDVLAFLSEYSRK 410
Flp_C pfam05202
Recombinase Flp protein;
135-379 2.64e-129

Recombinase Flp protein;


Pssm-ID: 253081  Cd Length: 244  Bit Score: 375.97  E-value: 2.64e-129
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
1P4E_D        135 GNSHSKKMLKALLSEgESIWEITEKILNSFEYTSRFTKTKTLYQFLFLATFINCGRFSDIKNVDPKSFKLVQNKYLGVII 214
Cdd:pfam05202   1 GNSVGDEITKIVETE-ESIWKIVEKTMDSIEARTRTTTTRAEYRFLLLATFFNCCRHSDLKNADPKTFEIVKNKFLGRIL 79
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
1P4E_D        215 QCLVTETKTSVSRHIYFFSARGRIDPLVYLDEFLRNSEPVLKrvNRTGNSSSNkQEYQLLKDNLVRSYNKALKKNAPYPI 294
Cdd:pfam05202  80 RALVTETKTRKSRFIYFFPVNGRCDPLLALHDYLRETEPVPK--SRTSNRESN-QEYQLLRDSLVRSYDRFLAKHAPEPI 156
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
1P4E_D        295 FAIKNGPKSHIGRHLMTSFLSMKGLTELTNVVGNFS---DKRASAVARTT*THQITAIPDHYFALVSRYYAYDPISKEMI 371
Cdd:pfam05202 157 FAIKNGPKSHLGRHLMASYLSNNELGEWVSPYGNWSagdDEIESAVARSKYTHGQADIPDHLFAFLSGYYKRTPEGKEVI 236

                  ....*...
1P4E_D        372 ALKDETNP 379
Cdd:pfam05202 237 ALKLIDNL 244
 
Name Accession Description Interval E-value
INT_Flp_C cd00217
Flp Tyrosine-based site-specific recombinases (also called integrases), C-terminal catalytic ...
6-420 0e+00

Flp Tyrosine-based site-specific recombinases (also called integrases), C-terminal catalytic domain; Yeast Flp-like recombinases mediate the amplification of the 2 micron circular plasmid copy number by catalyzing the intra-molecular recombination between two inverted repeats during replication. They belong to the DNA breaking-rejoining enzyme superfamily, which also includes prokaryotic tyrosine recombinases and type IB topoisomerases. These enzymes share the same fold in their catalytic domain containing six conserved active site residues and the overall reaction mechanism. Flp-like recombinases are almost exclusively found in yeast and are highly diverged in sequence from the prokaryotic tyrosine recombinases. They cleave their target DNA in trans with a composite active site in which the catalytic tyrosine is provided by a promoter bound to a site other than the one being cleaved. Thus each active site within Flp complexes is assembled by domain swapping and contains catalytic residues from two different monomers. Two DNA segments are synapsed by the tetrameric enzyme, carrying the nucleophilic tyrosine in each active site with only two of the four monomers active at a given time. The catalytic domain is linked through a flexible loop to the N-terminal domain, which is largely responsible for non-specific DNA binding and isomerization. Its overall fold is similar to the SAM domain fold also found in the N-terminal domains of lambda integrase and XerD recombinase.


Pssm-ID: 271174 [Multi-domain]  Cd Length: 410  Bit Score: 582.50  E-value: 0e+00
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
1P4E_D        6 LCKTPPKVLVRQFVERFERPSGEKIASCAAELTYLCWMITHNGTAIKRATFMSYNTIISNSLSFDIVNKSLQFKYKTQKA 85
Cdd:cd00217   1 LIPVRPAILIELFLELFGKDKIEDKRKLASLLTYLILMAFPAITEVKRGTFRKYKTIISNSLSFDYSRKTIQFKYRLKKN 80
                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
1P4E_D       86 TILEASLKKLIPAWEFTIIPYNGQKHQSDITDIVSSlqlqFESSEEADKGNSHSKKMLKALLSEGESIWEITEKILNSFE 165
Cdd:cd00217  81 RLLQKGLEDAEPPYKFVILSDKRQEENLFIIDKVPL----EPNTESKHIRNSEVNLEFTNILSEKESIWKIIYKILDSFE 156
                       170       180       190       200       210       220       230       240
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
1P4E_D      166 YTSRFTKTKTLYQFLFLATFINCGRFSDIKNVDPKSFKLVQNKYLGVIIQCLVTETKTSVSRHIYFFSARGRIDPLVYLD 245
Cdd:cd00217 157 ENTSRTTTKARYKLLLLATFTNCCRISDLKNLDPSTFELVKNKYLGTIVRAHVTETKTRISRTVYFFPARGRCDLLLALD 236
                       250       260       270       280       290       300       310       320
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
1P4E_D      246 EFLRNSEPVLKRVNRTGNsssNKQEYQLLKDNLVRSYNKALKKNAPYPIFAIKNGPKSHIGRHLMTSFLSMKGLTELTNV 325
Cdd:cd00217 237 EYLRICKPIPKTVVSDQN---VNQKYQLLKESLVRSYNKFLSKHPAEPIFKIKNGPKSHLGRHLMASFLSKNELDKEANS 313
                       330       340       350       360       370       380       390       400
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
1P4E_D      326 VGNFSDKRA--SAVARTT*THQITAIPDHYFALVSRYYAYDPISKEmIALKDETNPIEEWQHIEQLKGSA-EGSIRYPAW 402
Cdd:cd00217 314 LGNWSKVREigSAVARRNYTHTITPCPDSLFAFISGYYQISPEGSE-IELNNNKNPMERVHTIPELPTSEdELQLRYGHW 392
                       410
                ....*....|....*...
1P4E_D      403 NGIISQEVLDYLSSYINR 420
Cdd:cd00217 393 AKIISHDVLAFLSEYSRK 410
Flp_C pfam05202
Recombinase Flp protein;
135-379 2.64e-129

Recombinase Flp protein;


Pssm-ID: 253081  Cd Length: 244  Bit Score: 375.97  E-value: 2.64e-129
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
1P4E_D        135 GNSHSKKMLKALLSEgESIWEITEKILNSFEYTSRFTKTKTLYQFLFLATFINCGRFSDIKNVDPKSFKLVQNKYLGVII 214
Cdd:pfam05202   1 GNSVGDEITKIVETE-ESIWKIVEKTMDSIEARTRTTTTRAEYRFLLLATFFNCCRHSDLKNADPKTFEIVKNKFLGRIL 79
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
1P4E_D        215 QCLVTETKTSVSRHIYFFSARGRIDPLVYLDEFLRNSEPVLKrvNRTGNSSSNkQEYQLLKDNLVRSYNKALKKNAPYPI 294
Cdd:pfam05202  80 RALVTETKTRKSRFIYFFPVNGRCDPLLALHDYLRETEPVPK--SRTSNRESN-QEYQLLRDSLVRSYDRFLAKHAPEPI 156
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
1P4E_D        295 FAIKNGPKSHIGRHLMTSFLSMKGLTELTNVVGNFS---DKRASAVARTT*THQITAIPDHYFALVSRYYAYDPISKEMI 371
Cdd:pfam05202 157 FAIKNGPKSHLGRHLMASYLSNNELGEWVSPYGNWSagdDEIESAVARSKYTHGQADIPDHLFAFLSGYYKRTPEGKEVI 236

                  ....*...
1P4E_D        372 ALKDETNP 379
Cdd:pfam05202 237 ALKLIDNL 244
Flp_N pfam03930
Recombinase Flp protein N-terminus;
43-127 3.49e-29

Recombinase Flp protein N-terminus;


Pssm-ID: 112730  Cd Length: 82  Bit Score: 109.05  E-value: 3.49e-29
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
1P4E_D         43 MITHNGTAIKRATFMSYNTIISNSLSFDIVNKSLQFKYKTQKATILEASLKKLIPAWEFTIipyNGQKHQSDITDIVSSL 122
Cdd:pfam03930   1 MATRKLTEIKRSTFTKYRRIISQSLQYDSSNKTVSFEYHLKRPTELKEGLSKAFKPYNFVI---KSHKKPTSMTTLFSSL 77

                  ....*
1P4E_D        123 QLQFE 127
Cdd:pfam03930  78 HLKKE 82
DNA_BRE_C cd00397
DNA breaking-rejoining enzymes, C-terminal catalytic domain; The DNA breaking-rejoining enzyme ...
158-318 9.74e-04

DNA breaking-rejoining enzymes, C-terminal catalytic domain; The DNA breaking-rejoining enzyme superfamily includes type IB topoisomerases and tyrosine based site-specific recombinases (integrases) that share the same fold in their catalytic domain containing conserved active site residues. The best-studied members of this diverse superfamily include Human topoisomerase I, the bacteriophage lambda integrase, the bacteriophage P1 Cre recombinase, the yeast Flp recombinase, and the bacterial XerD/C recombinases. Their overall reaction mechanism is essentially identical and involves cleavage of a single strand of a DNA duplex by nucleophilic attack of a conserved tyrosine to give a 3' phosphotyrosyl protein-DNA adduct. In the second rejoining step, a terminal 5' hydroxyl attacks the covalent adduct to release the enzyme and generate duplex DNA. The enzymes differ in that topoisomerases cleave and then rejoin the same 5' and 3' termini, whereas a site-specific recombinase transfers a 5' hydroxyl generated by recombinase cleavage to a new 3' phosphate partner located in a different duplex region. Many DNA breaking-rejoining enzymes also have N-terminal domains, which show little sequence or structure similarity.


Pssm-ID: 271175  Cd Length: 167  Bit Score: 38.62  E-value: 9.74e-04
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
1P4E_D      158 EKILNSFEytsRFTKTKTLYQFLFLATFINCGRFSDIKNVDPKSFKLVQNkylgvIIQCLVTETKTSVSRHIYFfSARGR 237
Cdd:cd00397   3 EKLLDAID---EDKKIDLRDRAILLLLLETGLRISELLALKVKDIDLDNG-----TIRVRGKKTKGGKERTVPL-PKELA 73
                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
1P4E_D      238 IDPLVYLDEFLRNSEPVLKRVNRTGNSSSNkqeyqLLKDNLVRSYNKALKKNAPypifAIKNGPKSHIGRHLMTSFLSMK 317
Cdd:cd00397  74 EELKEYLKERRDKRGPLLKSLYLNKLFGTK-----LGERLSRRTLRRIFKKAGI----EAGRKITPHSLRHTFATNLLEN 144

                .
1P4E_D      318 G 318
Cdd:cd00397 145 G 145
 
Blast search parameters
Data Source: Precalculated data, version = cdd.v.3.14
Preset Options:Database: CDSEARCH/cdd   Low complexity filter: no  Composition Based Adjustment: yes   E-value threshold: 0.01

References:

  • Marchler-Bauer A et al. (2015), "CDD: NCBI's conserved domain database.", Nucleic Acids Res.43(D)222-6.
  • Marchler-Bauer A et al. (2011), "CDD: a Conserved Domain Database for the functional annotation of proteins.", Nucleic Acids Res.39(D)225-9.
  • Marchler-Bauer A et al. (2009), "CDD: specific functional annotation with the Conserved Domain Database.", Nucleic Acids Res.37(D)205-10.
  • Marchler-Bauer A, Bryant SH (2004), "CD-Search: protein domain annotations on the fly.", Nucleic Acids Res.32(W)327-331.
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