NCBI Home Page NCBI Site Search page NCBI Guide that lists and describes the NCBI resources
Conserved domains on  [gi|1772356063|gb|QFZ80736|]
View 

tyrosine-type recombinase/integrase [Bifidobacterium breve]

Protein Classification

site-specific integrase( domain architecture ID 332)

tyrosine based site-specific recombinase (integrase) is involved in cleavage of a single strand of a DNA duplex by nucleophilic attack of a conserved tyrosine to give a 3' phosphotyrosyl protein-DNA adduct

CATH:  1.10.443.10
Gene Ontology:  GO:0015074|GO:0003677|GO:0006310
PubMed:  10577069|10047575|9278480
SCOP:  4002347

Graphical summary

 Zoom to residue level

show extra options »

Show site features     Horizontal zoom: ×

List of domain hits

 Name Accession Description Interval E-value
DNA_BRE_C super family cl00213
DNA breaking-rejoining enzymes, C-terminal catalytic domain; The DNA breaking-rejoining enzyme ...
 23-65 1.79e-13

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.


The actual alignment was detected with superfamily member cd01189:

Pssm-ID: 469662 [Multi-domain]  Cd Length: 147  Bit Score: 61.04  E-value: 1.79e-13
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|...
gi 1772356063  23 DYMTPHDLRHTAVSLAIHAGVNPKLVQRIAGHHTFAQTMETYA 65
Cdd:cd01189   104 PRITPHDLRHTFASLLLEAGVPLKVIAERLGHSDISTTLDVYA 146
 
Name Accession Description Interval E-value
INT_ICEBs1_C_like cd01189
C-terminal catalytic domain of integrases from bacterial phages and conjugate transposons; ...
 23-65 1.79e-13

C-terminal catalytic domain of integrases from bacterial phages and conjugate transposons; This family of tyrosine based site-specific integrases is has origins in bacterial phages and conjugate transposons. One member is the integrase from Bacillus subtilis conjugative transposon ICEBs1. ICEBs1 can be excised and transfered to various recipients in response to DNA damage or high concentrations of potential mating partners. The family belongs to the superfamily of DNA breaking-rejoining enzymes, which share the same fold in their catalytic domain and the overall reaction mechanism. The catalytic domain contains six conserved active site residues. Their overall reaction mechanism 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.


Pssm-ID: 271189 [Multi-domain]  Cd Length: 147  Bit Score: 61.04  E-value: 1.79e-13
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|...
gi 1772356063  23 DYMTPHDLRHTAVSLAIHAGVNPKLVQRIAGHHTFAQTMETYA 65
Cdd:cd01189   104 PRITPHDLRHTFASLLLEAGVPLKVIAERLGHSDISTTLDVYA 146
XerD COG4974
Site-specific recombinase XerD [Replication, recombination and repair];
20-74 9.31e-11

Site-specific recombinase XerD [Replication, recombination and repair];


Pssm-ID: 443999 [Multi-domain]  Cd Length: 291  Bit Score: 55.77  E-value: 9.31e-11
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 1772356063  20 GVPDYMTPHDLRHTAVSLAIHAGVNPKLVQRIAGHHTfAQTMETYADLYDSDLDE 74
Cdd:COG4974   231 GIPKRVTPHSLRHTFATHLLEAGVDLRTVQELLGHSS-ISTTQIYTHVSDEELRE 284
Phage_integrase pfam00589
Phage integrase family; Members of this family cleave DNA substrates by a series of staggered ...
 20-69 4.46e-06

Phage integrase family; Members of this family cleave DNA substrates by a series of staggered cuts, during which the protein becomes covalently linked to the DNA through a catalytic tyrosine residue at the carboxy end of the alignment. The catalytic site residues in CRE recombinase are Arg-173, His-289, Arg-292 and Tyr-324.


Pssm-ID: 395471 [Multi-domain]  Cd Length: 169  Bit Score: 41.92  E-value: 4.46e-06
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|
gi 1772356063  20 GVPDYMTPHDLRHTAVSLAIHAGVNPKLVQRIAGHHTFAQTMeTYADLYD 69
Cdd:pfam00589 121 GLELPLHPHMLRHSFATHLLEAGVDLRVVQKLLGHSSISTTQ-IYTHVAD 169
 
Name Accession Description Interval E-value
INT_ICEBs1_C_like cd01189
C-terminal catalytic domain of integrases from bacterial phages and conjugate transposons; ...
 23-65 1.79e-13

C-terminal catalytic domain of integrases from bacterial phages and conjugate transposons; This family of tyrosine based site-specific integrases is has origins in bacterial phages and conjugate transposons. One member is the integrase from Bacillus subtilis conjugative transposon ICEBs1. ICEBs1 can be excised and transfered to various recipients in response to DNA damage or high concentrations of potential mating partners. The family belongs to the superfamily of DNA breaking-rejoining enzymes, which share the same fold in their catalytic domain and the overall reaction mechanism. The catalytic domain contains six conserved active site residues. Their overall reaction mechanism 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.


Pssm-ID: 271189 [Multi-domain]  Cd Length: 147  Bit Score: 61.04  E-value: 1.79e-13
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|...
gi 1772356063  23 DYMTPHDLRHTAVSLAIHAGVNPKLVQRIAGHHTFAQTMETYA 65
Cdd:cd01189   104 PRITPHDLRHTFASLLLEAGVPLKVIAERLGHSDISTTLDVYA 146
XerD COG4974
Site-specific recombinase XerD [Replication, recombination and repair];
20-74 9.31e-11

Site-specific recombinase XerD [Replication, recombination and repair];


Pssm-ID: 443999 [Multi-domain]  Cd Length: 291  Bit Score: 55.77  E-value: 9.31e-11
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 1772356063  20 GVPDYMTPHDLRHTAVSLAIHAGVNPKLVQRIAGHHTfAQTMETYADLYDSDLDE 74
Cdd:COG4974   231 GIPKRVTPHSLRHTFATHLLEAGVDLRTVQELLGHSS-ISTTQIYTHVSDEELRE 284
XerC COG4973
Site-specific recombinase XerC [Replication, recombination and repair];
20-74 4.86e-10

Site-specific recombinase XerC [Replication, recombination and repair];


Pssm-ID: 443998 [Multi-domain]  Cd Length: 287  Bit Score: 53.81  E-value: 4.86e-10
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 1772356063  20 GVPDYMTPHDLRHTAVSLAIHAGVNPKLVQRIAGHHTfAQTMETYADLYDSDLDE 74
Cdd:COG4973   231 GLPKHVHPHDLRHSFATHLLESGGDLRAVQELLGHAS-ISTTQIYTHLDFQHLAE 284
INT_Rci_Hp1_C cd00796
Shufflon-specific DNA recombinase Rci and Bacteriophage Hp1_like integrase, C-terminal ...
 17-65 3.29e-09

Shufflon-specific DNA recombinase Rci and Bacteriophage Hp1_like integrase, C-terminal catalytic domain; Rci protein is a tyrosine recombinase specifically involved in Shufflon type of DNA rearrangement in bacteria. The shufflon of plasmid R64 consists of four invertible DNA segments which are separated and flanked by seven 19-bp repeat sequences. RCI recombinase facilitates the site-specific recombination between any inverted repeats results in an inversion of the DNA segment(s) either independently or in groups. HP1 integrase promotes site-specific recombination of the HP1 genome into that of Haemophilus influenza. Bacteriophage Hp1_like integrases are tyrosine based site specific recombinases. They belong to the superfamily of DNA breaking-rejoining enzymes, which share the same fold in their catalytic domain and the overall reaction mechanism. The catalytic domain contains six conserved active site residues. 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.


Pssm-ID: 271177 [Multi-domain]  Cd Length: 162  Bit Score: 50.40  E-value: 3.29e-09
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*....
gi 1772356063  17 KTEGVPDyMTPHDLRHTAVSLAIHAGVNPKLVQRIAGHHTFAQTMeTYA 65
Cdd:cd00796   115 KRAGLED-LRFHDLRHTFASRLVQAGVPIKTVAKILGHSSIKMTM-RYA 161
DNA_BRE_C cd00397
DNA breaking-rejoining enzymes, C-terminal catalytic domain; The DNA breaking-rejoining enzyme ...
 26-65 4.62e-09

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 [Multi-domain]  Cd Length: 167  Bit Score: 50.17  E-value: 4.62e-09
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|
gi 1772356063  26 TPHDLRHTAVSLAIHAGVNPKLVQRIAGHHTfAQTMETYA 65
Cdd:cd00397   129 TPHSLRHTFATNLLENGVDIKVVQKLLGHSS-ISTTQRYL 167
INT_tnpA_C_Tn554 cd01186
Putative Transposase A from transposon Tn554, C-terminal catalytic domain; This family ...
 26-74 2.37e-07

Putative Transposase A from transposon Tn554, C-terminal catalytic domain; This family includes putative Transposase A from transposon Tn554. It belongs to a DNA breaking-rejoining enzyme superfamily. The catalytic domain contains six conserved active site residues. The recombination reaction 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. Many DNA breaking-rejoining enzymes also have N-terminal domains, which show little sequence or structure similarity.


Pssm-ID: 271186 [Multi-domain]  Cd Length: 184  Bit Score: 45.87  E-value: 2.37e-07
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*....
gi 1772356063  26 TPHDLRHTAVSLAIHAGVNPKLVQRIAGHHTFAQTMETYADLYDSDLDE 74
Cdd:cd01186   135 TPHMFRHTHATALIRAGWSIEVVARRLGHAHVQTTLNTYGHLSEEDIRR 183
FimB COG0582
Integrase/recombinase, includes phage integrase [Replication, recombination and repair, ...
 23-65 4.39e-07

Integrase/recombinase, includes phage integrase [Replication, recombination and repair, Mobilome: prophages, transposons];


Pssm-ID: 440347 [Multi-domain]  Cd Length: 391  Bit Score: 45.41  E-value: 4.39e-07
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|...
gi 1772356063  23 DYMTPHDLRHTAVSLAIHAGVNPKLVQRIAGHHTFAQTMETYA 65
Cdd:COG0582   323 GRFTPHGFRHTASTLLNEAGFPPDVIERQLAHKDGNKVRAAYN 365
INT_C_like_4 cd01194
Uncharacterized site-specific tyrosine recombinase, C-terminal catalytic domain; Tyrosine ...
 22-61 2.14e-06

Uncharacterized site-specific tyrosine recombinase, C-terminal catalytic domain; Tyrosine recombinase (integrase) belongs to a DNA breaking-rejoining enzyme superfamily. The catalytic domain contains six conserved active site residues. The recombination reaction 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. Many DNA breaking-rejoining enzymes also have N-terminal domains, which show little sequence or structure similarity.


Pssm-ID: 271194 [Multi-domain]  Cd Length: 174  Bit Score: 43.13  E-value: 2.14e-06
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|
gi 1772356063  22 PDYMTPHDLRHTAVSLAIHAGVNPKLVQRIAGHHTFAQTM 61
Cdd:cd01194   131 DDRLTAHSLRHTAGTLALKAGKSLREVQQLLRHSDPNTTM 170
Phage_integrase pfam00589
Phage integrase family; Members of this family cleave DNA substrates by a series of staggered ...
 20-69 4.46e-06

Phage integrase family; Members of this family cleave DNA substrates by a series of staggered cuts, during which the protein becomes covalently linked to the DNA through a catalytic tyrosine residue at the carboxy end of the alignment. The catalytic site residues in CRE recombinase are Arg-173, His-289, Arg-292 and Tyr-324.


Pssm-ID: 395471 [Multi-domain]  Cd Length: 169  Bit Score: 41.92  E-value: 4.46e-06
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|
gi 1772356063  20 GVPDYMTPHDLRHTAVSLAIHAGVNPKLVQRIAGHHTFAQTMeTYADLYD 69
Cdd:pfam00589 121 GLELPLHPHMLRHSFATHLLEAGVDLRVVQKLLGHSSISTTQ-IYTHVAD 169
INT_P4_C cd00801
Bacteriophage P4 integrase, C-terminal catalytic domain; P4-like integrases are found in ...
 20-74 4.98e-05

Bacteriophage P4 integrase, C-terminal catalytic domain; P4-like integrases are found in temperate bacteriophages, integrative plasmids, pathogenicity and symbiosis islands, and other mobile genetic elements. The P4 integrase mediates integrative and excisive site-specific recombination between two sites, called attachment sites, located on the phage genome and the bacterial chromosome. The phage attachment site is often found adjacent to the integrase gene, while the host attachment sites are typically situated near tRNA genes. This family belongs to the superfamily of DNA breaking-rejoining enzymes, which share the same fold in their catalytic domain and the overall reaction mechanism. The catalytic domain contains six conserved active site residues. Their overall reaction mechanism 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.


Pssm-ID: 271182 [Multi-domain]  Cd Length: 180  Bit Score: 39.18  E-value: 4.98e-05
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 1772356063  20 GVPDYMTPHDLRHTAVSLAIHAGVNPKLVQRIAGHHTFAQTMETYaDLYDSdLDE 74
Cdd:cd00801   116 YKGKEFTPHDLRRTFSTLLNELGIDPEVIERLLNHVLGGVVRAAY-NRYDY-LEE 168
INT_C_like_5 cd01195
Uncharacterized site-specific tyrosine recombinase, C-terminal catalytic domain; Tyrosine ...
 20-66 6.75e-05

Uncharacterized site-specific tyrosine recombinase, C-terminal catalytic domain; Tyrosine recombinase (integrase) belongs to a DNA breaking-rejoining enzyme superfamily. The catalytic domain contains six conserved active site residues. The recombination reaction 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. Many DNA breaking-rejoining enzymes also have N-terminal domains, which show little sequence or structure similarity.


Pssm-ID: 271195 [Multi-domain]  Cd Length: 170  Bit Score: 38.99  E-value: 6.75e-05
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*...
gi 1772356063  20 GVPDYMTPHDLRHTAVSLAIHAGV-NPKLVQRIAgHHTFAQTMETYAD 66
Cdd:cd01195   121 GLGKRLSPHGLRHSAITLALDAGAgLIRKVQDFS-RHADLRTLQVYDD 167
INTN1_C_like cd01185
Integrase IntN1 of Bacteroides mobilizable transposon NBU1 and similar proteins, C-terminal ...
 25-72 2.64e-04

Integrase IntN1 of Bacteroides mobilizable transposon NBU1 and similar proteins, C-terminal catalytic domain; IntN1 is a tyrosine recombinase for the integration and excision of Bacteroides mobilizable transposon NBU1 from the host chromosome. IntN1 does not require strict homology between the recombining sites seen with other tyrosine recombinases. This family belongs to the superfamily of DNA breaking-rejoining enzymes, which share the same fold in their catalytic domain and the overall reaction mechanism. The catalytic domain contains six conserved active site residues. Their overall reaction mechanism 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.


Pssm-ID: 271185 [Multi-domain]  Cd Length: 161  Bit Score: 37.24  E-value: 2.64e-04
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*...
gi 1772356063  25 MTPHDLRHTAVSLAIHAGVNPKLVQRIAGHHTFAQTMEtYADLYDSDL 72
Cdd:cd01185   115 LTFHVARHTFATLLLLKGVDIETISKLLGHSSIKTTQI-YAKIVDSKK 161
INT_tnpB_C_Tn554 cd01187
Putative Transposase B from transposon Tn554, C-terminal catalytic domain; This family ...
 20-61 1.21e-03

Putative Transposase B from transposon Tn554, C-terminal catalytic domain; This family includes putative Transposase B from transposon Tn554. It belongs to a DNA breaking-rejoining enzyme superfamily. The catalytic domain containing six conserved active site residues. The recombination reaction 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. Many DNA breaking-rejoining enzymes also have N-terminal domains, which show little sequence or structure similarity.


Pssm-ID: 271187 [Multi-domain]  Cd Length: 142  Bit Score: 35.10  E-value: 1.21e-03
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|..
gi 1772356063  20 GVPDYMTPHDLRHTAVSLAIHAGVNPKLVQRIAGHHTFAQTM 61
Cdd:cd01187    97 GERFRFHTHRFRHTVATRLANSGMGILVLQQLLGHSSPEMTL 138
INT_C_like_1 cd01184
Uncharacterized site-specific tyrosine recombinase, C-terminal catalytic domain; Tyrosine ...
 28-54 2.09e-03

Uncharacterized site-specific tyrosine recombinase, C-terminal catalytic domain; Tyrosine recombinase (integrase) belongs to a DNA breaking-rejoining enzyme superfamily. The catalytic domain containing six conserved active site residues. The recombination reaction 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. Many DNA breaking-rejoining enzymes also have N-terminal domains, which show little sequence or structure similarity.


Pssm-ID: 271184 [Multi-domain]  Cd Length: 180  Bit Score: 34.98  E-value: 2.09e-03
                          10        20
                  ....*....|....*....|....*..
gi 1772356063  28 HDLRHTAVSLAIHAGVNPKLVQRIAGH 54
Cdd:cd01184   142 HSFRHTFITALKRAGVPEELIAQIVGH 168
 
Blast search parameters
Data Source: Precalculated data, version = cdd.v.3.21
Preset Options:Database: CDSEARCH/cdd   Low complexity filter: no  Composition Based Adjustment: yes   E-value threshold: 0.01

References:

  • Wang J et al. (2023), "The conserved domain database in 2023", Nucleic Acids Res.51(D)384-8.
  • Lu S et al. (2020), "The conserved domain database in 2020", Nucleic Acids Res.48(D)265-8.
  • Marchler-Bauer A et al. (2017), "CDD/SPARCLE: functional classification of proteins via subfamily domain architectures.", Nucleic Acids Res.45(D)200-3.
Help | Disclaimer | Write to the Help Desk
NCBI | NLM | NIH