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Conserved domains on  [gi|446454992|ref|WP_000532847|]
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MULTISPECIES: tyrosine-type recombinase/integrase [Salmonella]

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
SCOP:  4002347

Graphical summary

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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 ...
167-320 1.08e-48

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 cd00800:

Pssm-ID: 469662 [Multi-domain]  Cd Length: 161  Bit Score: 160.59  E-value: 1.08e-48
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446454992 167 EEYRAIYNNATPAVRAAMEIAYLCAARVSDVLKMNWNQILEKGIFIQQGKTGVKQIKSWTDRLRDAVEICREWGEEGP-- 244
Cdd:cd00800    1 AEYAAIYAEAPPLLRLAMELALLTGQRQGDLLRLKWSDITDGGLLVEQSKTGKKLLIPWTPSLRALVDRIRALPRKRSey 80
                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 446454992 245 VIRTMYGERYSYKGFNEAWRKARKAAGDDlGRPLDCTFHDLKAKGISDYE--GTAKDKQKYSGHKTESQVLVYDRKVK 320
Cdd:cd00800   81 LINSRKGGPLSYDTLKSAWRRARKAAGLK-GETEGFTFHDLRAKAATDYAeqGGSTDAQALLGHKSDAMTERYTRKRG 157
 
Name Accession Description Interval E-value
INT_Lambda_C cd00800
C-terminal catalytic domain of Lambda integrase, a tyrosine-based site-specific recombinase; ...
167-320 1.08e-48

C-terminal catalytic domain of Lambda integrase, a tyrosine-based site-specific recombinase; Lambda-type integrases catalyze site-specific integration and excision of temperate bacteriophages and other mobile genetic elements to and from the bacterial host chromosome. They are tyrosine-based site-specific recombinase and belong to the superfamily of DNA breaking-rejoining enzymes, which share the same fold in their catalytic domain and the overall reaction mechanism. The phage lambda integrase can bridge two different and well-separated DNA sequences called arm- and core-sites. The C-terminal domain binds, cleaves and re-ligates DNA strands at the core-sites, while the N-terminal domain is largely responsible for high-affinity binding to the arm-type sites.


Pssm-ID: 271181 [Multi-domain]  Cd Length: 161  Bit Score: 160.59  E-value: 1.08e-48
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446454992 167 EEYRAIYNNATPAVRAAMEIAYLCAARVSDVLKMNWNQILEKGIFIQQGKTGVKQIKSWTDRLRDAVEICREWGEEGP-- 244
Cdd:cd00800    1 AEYAAIYAEAPPLLRLAMELALLTGQRQGDLLRLKWSDITDGGLLVEQSKTGKKLLIPWTPSLRALVDRIRALPRKRSey 80
                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 446454992 245 VIRTMYGERYSYKGFNEAWRKARKAAGDDlGRPLDCTFHDLKAKGISDYE--GTAKDKQKYSGHKTESQVLVYDRKVK 320
Cdd:cd00800   81 LINSRKGGPLSYDTLKSAWRRARKAAGLK-GETEGFTFHDLRAKAATDYAeqGGSTDAQALLGHKSDAMTERYTRKRG 157
XerC COG4973
Site-specific recombinase XerC [Replication, recombination and repair];
58-317 1.24e-34

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


Pssm-ID: 443998 [Multi-domain]  Cd Length: 287  Bit Score: 127.77  E-value: 1.24e-34
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446454992  58 RITFTQLWRKFLASADYADLAPRTQKDYLAHEKYILAVFGDAEAK--AIKPEHIRRYMD---ARGQKSRVqANHEHSSMS 132
Cdd:COG4973    1 KLTLAEALEAYLEHLRERRLSPKTLEAYRRDLRRLIPLLGDADLPleELTPADVRRFLArlhRRGLSPRT-LNRRLSALR 79
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446454992 133 RVFRWSYQRGYVPGNPCVGVdKFPKPQR--DRYITDEEYRAI--YNNATPA---VRAAMEIAYLCAARVSDVLKMNWNQI 205
Cdd:COG4973   80 SFFNWAVREGLLEANPAAGV-KAPKAPRklPRALTVDELAQLldALADDPLavrDRAIVELLYSTGLRLGELVGLDWEDV 158
                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446454992 206 -LEKGIFIQQGKTGVKQIKSWTDRLRDAVEICRE------WGEEGPVIRTMYGERYSYKGFNEAWRKARKAAGddLGRPL 278
Cdd:COG4973  159 dLDAGEVRVRGKTGKSRTVPLGPKALAALREWLAvrpelaAPDEGALFPSRRGTRLSPRNVQKRLRRLAKKAG--LPKHV 236
                        250       260       270       280
                 ....*....|....*....|....*....|....*....|..
gi 446454992 279 dcTFHDLKAKGIS---DYEGTAKDKQKYSGHKTESQVLVYDR 317
Cdd:COG4973  237 --HPHDLRHSFAThllESGGDLRAVQELLGHASISTTQIYTH 276
Phage_integrase pfam00589
Phage integrase family; Members of this family cleave DNA substrates by a series of staggered ...
163-315 6.80e-12

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: 63.11  E-value: 6.80e-12
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446454992  163 YITDEEYRAIYNNATPAV-----RAAMEIAYLCAARVSDVLKMNWNQI-LEKG-IFIQQGKTGVKQIKSWTDRLRDAVei 235
Cdd:pfam00589   1 RLTEDEVERLLDAAETGPlsirdKALLELLYATGLRISELCSLRWSDIdFENGvIRVHRGKGNKERTVPLSDAALELL-- 78
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446454992  236 cREW----GEEGPVIRTMY----GERYSYKGFNEAWRKARKAAGDDlgrpLDCTFHDLKA--------KGISDyegtaKD 299
Cdd:pfam00589  79 -KEWlskrLLEAPKSDYLFaskrGKPLSRQTVRKIFKRAGKEAGLE----LPLHPHMLRHsfathlleAGVDL-----RV 148
                         170
                  ....*....|....*.
gi 446454992  300 KQKYSGHKTESQVLVY 315
Cdd:pfam00589 149 VQKLLGHSSISTTQIY 164
 
Name Accession Description Interval E-value
INT_Lambda_C cd00800
C-terminal catalytic domain of Lambda integrase, a tyrosine-based site-specific recombinase; ...
167-320 1.08e-48

C-terminal catalytic domain of Lambda integrase, a tyrosine-based site-specific recombinase; Lambda-type integrases catalyze site-specific integration and excision of temperate bacteriophages and other mobile genetic elements to and from the bacterial host chromosome. They are tyrosine-based site-specific recombinase and belong to the superfamily of DNA breaking-rejoining enzymes, which share the same fold in their catalytic domain and the overall reaction mechanism. The phage lambda integrase can bridge two different and well-separated DNA sequences called arm- and core-sites. The C-terminal domain binds, cleaves and re-ligates DNA strands at the core-sites, while the N-terminal domain is largely responsible for high-affinity binding to the arm-type sites.


Pssm-ID: 271181 [Multi-domain]  Cd Length: 161  Bit Score: 160.59  E-value: 1.08e-48
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446454992 167 EEYRAIYNNATPAVRAAMEIAYLCAARVSDVLKMNWNQILEKGIFIQQGKTGVKQIKSWTDRLRDAVEICREWGEEGP-- 244
Cdd:cd00800    1 AEYAAIYAEAPPLLRLAMELALLTGQRQGDLLRLKWSDITDGGLLVEQSKTGKKLLIPWTPSLRALVDRIRALPRKRSey 80
                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 446454992 245 VIRTMYGERYSYKGFNEAWRKARKAAGDDlGRPLDCTFHDLKAKGISDYE--GTAKDKQKYSGHKTESQVLVYDRKVK 320
Cdd:cd00800   81 LINSRKGGPLSYDTLKSAWRRARKAAGLK-GETEGFTFHDLRAKAATDYAeqGGSTDAQALLGHKSDAMTERYTRKRG 157
XerC COG4973
Site-specific recombinase XerC [Replication, recombination and repair];
58-317 1.24e-34

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


Pssm-ID: 443998 [Multi-domain]  Cd Length: 287  Bit Score: 127.77  E-value: 1.24e-34
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446454992  58 RITFTQLWRKFLASADYADLAPRTQKDYLAHEKYILAVFGDAEAK--AIKPEHIRRYMD---ARGQKSRVqANHEHSSMS 132
Cdd:COG4973    1 KLTLAEALEAYLEHLRERRLSPKTLEAYRRDLRRLIPLLGDADLPleELTPADVRRFLArlhRRGLSPRT-LNRRLSALR 79
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446454992 133 RVFRWSYQRGYVPGNPCVGVdKFPKPQR--DRYITDEEYRAI--YNNATPA---VRAAMEIAYLCAARVSDVLKMNWNQI 205
Cdd:COG4973   80 SFFNWAVREGLLEANPAAGV-KAPKAPRklPRALTVDELAQLldALADDPLavrDRAIVELLYSTGLRLGELVGLDWEDV 158
                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446454992 206 -LEKGIFIQQGKTGVKQIKSWTDRLRDAVEICRE------WGEEGPVIRTMYGERYSYKGFNEAWRKARKAAGddLGRPL 278
Cdd:COG4973  159 dLDAGEVRVRGKTGKSRTVPLGPKALAALREWLAvrpelaAPDEGALFPSRRGTRLSPRNVQKRLRRLAKKAG--LPKHV 236
                        250       260       270       280
                 ....*....|....*....|....*....|....*....|..
gi 446454992 279 dcTFHDLKAKGIS---DYEGTAKDKQKYSGHKTESQVLVYDR 317
Cdd:COG4973  237 --HPHDLRHSFAThllESGGDLRAVQELLGHASISTTQIYTH 276
XerD COG4974
Site-specific recombinase XerD [Replication, recombination and repair];
59-317 1.25e-32

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


Pssm-ID: 443999 [Multi-domain]  Cd Length: 291  Bit Score: 122.41  E-value: 1.25e-32
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446454992  59 ITFTQLWRKFLASADYAD-LAPRTQKDYLAH-EKYI--LAVFGDAEAKAIKPEHIRRYMDARGQK--SRVQANHEHSSMS 132
Cdd:COG4974    1 LTLADLLEAFLEELKREKgLSPNTIKAYRRDlRRFLrfLEELGKIPLAEITPEDIRAYLNYLRERglSPSTINRYLAALR 80
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446454992 133 RVFRWSYQRGYVPGNPCVGVdKFPKPQR--DRYITDEEYRAIYNNATPAV------RAAMEIAYLCAARVSDVLKMNWNQ 204
Cdd:COG4974   81 SFFRYAVREGLLEDNPAAKV-KLPKKPRklPRVLTEEEIEALLEALDTETpeglrdRALLLLLYATGLRVSELLGLKWSD 159
                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446454992 205 I-LEKG-IFIQQGKTGVKQIKSWTDRLRDAVEICREW---GEEGPVIRTMYGERYSYKGFNEAWRKARKAAgddlGRPLD 279
Cdd:COG4974  160 IdLDRGtIRVRRGKGGKERTVPLSPEALEALREYLEErrpRDSDYLFPTRRGRPLSRRAIRKILKRLAKRA----GIPKR 235
                        250       260       270       280
                 ....*....|....*....|....*....|....*....|....*.
gi 446454992 280 CTFHDL--------KAKGISdyegtAKDKQKYSGHKTESQVLVYDR 317
Cdd:COG4974  236 VTPHSLrhtfathlLEAGVD-----LRTVQELLGHSSISTTQIYTH 276
FimB COG0582
Integrase/recombinase, includes phage integrase [Replication, recombination and repair, ...
49-285 2.43e-21

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


Pssm-ID: 440347 [Multi-domain]  Cd Length: 391  Bit Score: 93.56  E-value: 2.43e-21
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446454992  49 EKKVEGRKNRITFTQLWRKFLASADyADLAPRTQKDYLAH-EKYILAVFGDAEAKAIKPEHIRRYMD---ARGqkSRVQA 124
Cdd:COG0582   87 AKAAAAAAAANTFEEVAEEWLEEKK-PEWKEKTAAQVRRTlEKHIFPVLGDRPIAEITPPDLLAVLRpieARG--APETA 163
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446454992 125 NHEHSSMSRVFRWSYQRGYVPGNPCVGVDKF---PKPQRDRYITDEE----YRAIYN-NATPAVRAAMEIAYLCAARVSD 196
Cdd:COG0582  164 RRVRQRLRQVFRYAVARGLIERNPAADLKGAlpkPKVKHHPALTPEElpelLRALDAyRGSPVTRLALRLLLLTGVRPGE 243
                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446454992 197 VLKMNWNQI-LEKGI-FIQQGKTgvkqiKSWTDRL----RDAVEICREwgeegpvIRTMYGE--------RYSYKGFNE- 261
Cdd:COG0582  244 LRGARWSEIdLEAALwTIPAERM-----KTRRPHIvplsRQALEILKE-------LKPLTGDseyvfpsrRGPKKPMSEn 311
                        250       260
                 ....*....|....*....|....
gi 446454992 262 AWRKARKAAGDDlgrplDCTFHDL 285
Cdd:COG0582  312 TLNKALRRMGYG-----RFTPHGF 330
Phage_integrase pfam00589
Phage integrase family; Members of this family cleave DNA substrates by a series of staggered ...
163-315 6.80e-12

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: 63.11  E-value: 6.80e-12
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446454992  163 YITDEEYRAIYNNATPAV-----RAAMEIAYLCAARVSDVLKMNWNQI-LEKG-IFIQQGKTGVKQIKSWTDRLRDAVei 235
Cdd:pfam00589   1 RLTEDEVERLLDAAETGPlsirdKALLELLYATGLRISELCSLRWSDIdFENGvIRVHRGKGNKERTVPLSDAALELL-- 78
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446454992  236 cREW----GEEGPVIRTMY----GERYSYKGFNEAWRKARKAAGDDlgrpLDCTFHDLKA--------KGISDyegtaKD 299
Cdd:pfam00589  79 -KEWlskrLLEAPKSDYLFaskrGKPLSRQTVRKIFKRAGKEAGLE----LPLHPHMLRHsfathlleAGVDL-----RV 148
                         170
                  ....*....|....*.
gi 446454992  300 KQKYSGHKTESQVLVY 315
Cdd:pfam00589 149 VQKLLGHSSISTTQIY 164
INT_Rci_Hp1_C cd00796
Shufflon-specific DNA recombinase Rci and Bacteriophage Hp1_like integrase, C-terminal ...
160-315 2.70e-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: 55.41  E-value: 2.70e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446454992 160 RDRYITDEEYRAIYNNAT----PAVRAAMEIAYLCAARVSDVLKMNWNQI-LEKG-IFIQQGKTGVKQIKSWTDRLRDAv 233
Cdd:cd00796    1 RDRFLTEDEEARLLAALEestnPHLRLIVLLALYTGARRGEILSLRWDDIdLEVGlIVLPETKNGKPRTVPLSDEAIAI- 79
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446454992 234 eICREWGEEGPVIRTMYG--ERYSYKGFNEAWRKARKAAGDDlgrplDCTFHDLK--------AKGISDYegtakDKQKY 303
Cdd:cd00796   80 -LKELKRKRGKDGFFVDGrfFGIPIASLRRAFKKARKRAGLE-----DLRFHDLRhtfasrlvQAGVPIK-----TVAKI 148
                        170
                 ....*....|..
gi 446454992 304 SGHKTESQVLVY 315
Cdd:cd00796  149 LGHSSIKMTMRY 160
 
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.
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