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Conserved domains on  [gi|553319362|gb|ESA47829|]
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phage integrase, N-terminal SAM domain protein, partial [Streptococcus pyogenes GA41039]

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

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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 ...
 1-225 2.04e-125

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 PRK05084:

Pssm-ID: 469662 [Multi-domain]  Cd Length: 357  Bit Score: 358.85  E-value: 2.04e-125
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 553319362   1 MRRELLLEKIETYKAIMPWYVLDYYQSKLAVPYSFTTLYEYLKEYKRFFDWLMDADLTQAPKIADIDLSTLEHLTKKDLE 80
Cdd:PRK05084   1 MEKEKYLKLIDKLKAKMPWYVQEYYQSKLATPYSPTTLYEYLTEYRRFFNWLISEGLSDASKIKDIPLSTLENLTKKDVE 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 553319362  81 AFVLYLRERPSLNTYSTKEGLSQTTINRTLSALSSLYKYLTEEVENDQGEPYFYRNVMKKVSTKKKKETLASRAENIKQK 160
Cdd:PRK05084  81 AFILYLRERPLLNGHSTKKGNSQTTINRTLSALKSLFKYLTEEAENEDGEPYFYRNVMKKIELKKKKETLAARAHNLKQK 160

                        170       180       190       200       210       220
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 553319362 161 LFLGDETLAFLDYVDKEYEQKLSNRAKSSFRKNKERDLAIISLLLASGVRLSEAVNLDLKDVNLN 225
Cdd:PRK05084 161 LFLGDEDYEFLDFIDNEYEQKLSNRALSSFKKNKERDLAIIALILGSGLRVSELVNLDLSDLNLK 225
 
Name Accession Description Interval E-value
xerS PRK05084
site-specific tyrosine recombinase XerS; Reviewed
 1-225 2.04e-125

site-specific tyrosine recombinase XerS; Reviewed


Pssm-ID: 235339 [Multi-domain]  Cd Length: 357  Bit Score: 358.85  E-value: 2.04e-125
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 553319362   1 MRRELLLEKIETYKAIMPWYVLDYYQSKLAVPYSFTTLYEYLKEYKRFFDWLMDADLTQAPKIADIDLSTLEHLTKKDLE 80
Cdd:PRK05084   1 MEKEKYLKLIDKLKAKMPWYVQEYYQSKLATPYSPTTLYEYLTEYRRFFNWLISEGLSDASKIKDIPLSTLENLTKKDVE 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 553319362  81 AFVLYLRERPSLNTYSTKEGLSQTTINRTLSALSSLYKYLTEEVENDQGEPYFYRNVMKKVSTKKKKETLASRAENIKQK 160
Cdd:PRK05084  81 AFILYLRERPLLNGHSTKKGNSQTTINRTLSALKSLFKYLTEEAENEDGEPYFYRNVMKKIELKKKKETLAARAHNLKQK 160

                        170       180       190       200       210       220
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 553319362 161 LFLGDETLAFLDYVDKEYEQKLSNRAKSSFRKNKERDLAIISLLLASGVRLSEAVNLDLKDVNLN 225
Cdd:PRK05084 161 LFLGDEDYEFLDFIDNEYEQKLSNRALSSFKKNKERDLAIIALILGSGLRVSELVNLDLSDLNLK 225
XerD COG4974
Site-specific recombinase XerD [Replication, recombination and repair];
22-225 1.02e-17

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


Pssm-ID: 443999 [Multi-domain]  Cd Length: 291  Bit Score: 79.65  E-value: 1.02e-17
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 553319362  22 LDYYQSKLAvpYSFTTLYEYLKEYKRFFDWLmdadltqapkiADIDLSTLEHLTKKDLEAFVLYLRERpslntystkeGL 101
Cdd:COG4974   11 LEELKREKG--LSPNTIKAYRRDLRRFLRFL-----------EELGKIPLAEITPEDIRAYLNYLRER----------GL 67

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 553319362 102 SQTTINRTLSALSSLYKYLTEEvendqgePYFYRNVMkkvstkkkkETLASRAENIKQKLFLGDETL-AFLDYVDKEyeq 180
Cdd:COG4974   68 SPSTINRYLAALRSFFRYAVRE-------GLLEDNPA---------AKVKLPKKPRKLPRVLTEEEIeALLEALDTE--- 128

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|....*
gi 553319362 181 klsnrakssfRKNKERDLAIISLLLASGVRLSEAVNLDLKDVNLN 225
Cdd:COG4974  129 ----------TPEGLRDRALLLLLYATGLRVSELLGLKWSDIDLD 163
INT_XerDC_C cd00798
XerD and XerC integrases, C-terminal catalytic domains; XerDC-like integrases are involved in ...
 196-225 3.00e-07

XerD and XerC integrases, C-terminal catalytic domains; XerDC-like integrases are involved in the site-specific integration and excision of lysogenic bacteriophage genomes, transposition of conjugative transposons, termination of chromosomal replication, and stable plasmid inheritance. They share the same fold in their catalytic domain containing six conserved active site residues and the overall reaction mechanism with the DNA breaking-rejoining enzyme superfamily. In Escherichia coli, the Xer site-specific recombination system acts to convert dimeric chromosomes, which are formed by homologous recombination to monomers. Two related recombinases, XerC and XerD, bind cooperatively to a recombination site present in the E. coli chromosome. Each recombinase catalyzes the exchange of one pair of DNA strand in a reaction that proceeds through a Holliday junction intermediate. These enzymes 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: 271179 [Multi-domain]  Cd Length: 172  Bit Score: 48.66  E-value: 3.00e-07
                         10        20        30
                 ....*....|....*....|....*....|
gi 553319362 196 RDLAIISLLLASGVRLSEAVNLDLKDVNLN 225
Cdd:cd00798   20 RDRAILELLYASGLRVSELVGLDLSDVDLD 49
Phage_int_SAM_1 pfam02899
Phage integrase, N-terminal SAM-like domain;
33-123 5.49e-06

Phage integrase, N-terminal SAM-like domain;


Pssm-ID: 427047 [Multi-domain]  Cd Length: 83  Bit Score: 43.40  E-value: 5.49e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 553319362   33 YSFTTLYEYLKEYKRFFDWLmdadltqapkiaDIDLSTLEHLTKKDLEAFVLYLRerpslntystKEGLSQTTINRTLSA 112
Cdd:pfam02899  14 LSPHTLRAYRRDLLAFLKFL------------SEGGSSLEQITTSDVRAFLAELR----------AQGLSASSLARRLSA 71

                          90
                  ....*....|.
gi 553319362  113 LSSLYKYLTEE 123
Cdd:pfam02899  72 LRSFYQFLIRE 82
 
Name Accession Description Interval E-value
xerS PRK05084
site-specific tyrosine recombinase XerS; Reviewed
 1-225 2.04e-125

site-specific tyrosine recombinase XerS; Reviewed


Pssm-ID: 235339 [Multi-domain]  Cd Length: 357  Bit Score: 358.85  E-value: 2.04e-125
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 553319362   1 MRRELLLEKIETYKAIMPWYVLDYYQSKLAVPYSFTTLYEYLKEYKRFFDWLMDADLTQAPKIADIDLSTLEHLTKKDLE 80
Cdd:PRK05084   1 MEKEKYLKLIDKLKAKMPWYVQEYYQSKLATPYSPTTLYEYLTEYRRFFNWLISEGLSDASKIKDIPLSTLENLTKKDVE 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 553319362  81 AFVLYLRERPSLNTYSTKEGLSQTTINRTLSALSSLYKYLTEEVENDQGEPYFYRNVMKKVSTKKKKETLASRAENIKQK 160
Cdd:PRK05084  81 AFILYLRERPLLNGHSTKKGNSQTTINRTLSALKSLFKYLTEEAENEDGEPYFYRNVMKKIELKKKKETLAARAHNLKQK 160

                        170       180       190       200       210       220
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 553319362 161 LFLGDETLAFLDYVDKEYEQKLSNRAKSSFRKNKERDLAIISLLLASGVRLSEAVNLDLKDVNLN 225
Cdd:PRK05084 161 LFLGDEDYEFLDFIDNEYEQKLSNRALSSFKKNKERDLAIIALILGSGLRVSELVNLDLSDLNLK 225
XerD COG4974
Site-specific recombinase XerD [Replication, recombination and repair];
22-225 1.02e-17

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


Pssm-ID: 443999 [Multi-domain]  Cd Length: 291  Bit Score: 79.65  E-value: 1.02e-17
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 553319362  22 LDYYQSKLAvpYSFTTLYEYLKEYKRFFDWLmdadltqapkiADIDLSTLEHLTKKDLEAFVLYLRERpslntystkeGL 101
Cdd:COG4974   11 LEELKREKG--LSPNTIKAYRRDLRRFLRFL-----------EELGKIPLAEITPEDIRAYLNYLRER----------GL 67

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 553319362 102 SQTTINRTLSALSSLYKYLTEEvendqgePYFYRNVMkkvstkkkkETLASRAENIKQKLFLGDETL-AFLDYVDKEyeq 180
Cdd:COG4974   68 SPSTINRYLAALRSFFRYAVRE-------GLLEDNPA---------AKVKLPKKPRKLPRVLTEEEIeALLEALDTE--- 128

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|....*
gi 553319362 181 klsnrakssfRKNKERDLAIISLLLASGVRLSEAVNLDLKDVNLN 225
Cdd:COG4974  129 ----------TPEGLRDRALLLLLYATGLRVSELLGLKWSDIDLD 163
XerC COG4973
Site-specific recombinase XerC [Replication, recombination and repair];
17-224 5.74e-15

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


Pssm-ID: 443998 [Multi-domain]  Cd Length: 287  Bit Score: 71.92  E-value: 5.74e-15
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 553319362  17 MPWYVLDYYQSKLAVPYSFTTLYEYLKEYKRFFDWLMDADLTqapkiadidlstLEHLTKKDLEAFVLYLRerpslntys 96
Cdd:COG4973    4 LAEALEAYLEHLRERRLSPKTLEAYRRDLRRLIPLLGDADLP------------LEELTPADVRRFLARLH--------- 62

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 553319362  97 tKEGLSQTTINRTLSALSSLYKYLTEevendQGepYFYRNVMKKVStkkkketlASRAENIKQKLFLGDETLAFLDYVDK 176
Cdd:COG4973   63 -RRGLSPRTLNRRLSALRSFFNWAVR-----EG--LLEANPAAGVK--------APKAPRKLPRALTVDELAQLLDALAD 126

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|....*...
gi 553319362 177 EYEQKlsnrakssfrknkeRDLAIISLLLASGVRLSEAVNLDLKDVNL 224
Cdd:COG4973  127 DPLAV--------------RDRAIVELLYSTGLRLGELVGLDWEDVDL 160
xerC PRK00236
site-specific tyrosine recombinase XerC; Reviewed
 42-224 1.05e-11

site-specific tyrosine recombinase XerC; Reviewed


Pssm-ID: 234698 [Multi-domain]  Cd Length: 297  Bit Score: 62.86  E-value: 1.05e-11
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 553319362  42 LKEYKR----FFDWLmdadltqapkiADIDLSTLEHLTKKDLEAFVLYLRerpslntystKEGLSQTTINRTLSALSSLY 117
Cdd:PRK00236  28 LRAYRRdlraFLAFL-----------EEHGISSLQDLDAADLRSFLARRR----------RQGLSARSLARRLSALRSFY 86

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 553319362 118 KYLTEE--VENDqgepyfyrnvmkkvstkkkkETLASRAENIKQKL--FLG-DETLAFLDYVDKEyeqklsnrakssfRK 192
Cdd:PRK00236  87 RWLVRRglLKAN--------------------PAAGLRAPKIPKRLpkPLDvDQAKRLLDAIDED-------------DP 133

                        170       180       190
                 ....*....|....*....|....*....|..
gi 553319362 193 NKERDLAIISLLLASGVRLSEAVNLDLKDVNL 224
Cdd:PRK00236 134 LALRDRAILELLYGSGLRLSELVGLDIDDLDL 165
xerD PRK00283
tyrosine recombinase;
37-225 7.96e-10

tyrosine recombinase;


Pssm-ID: 234713 [Multi-domain]  Cd Length: 299  Bit Score: 57.51  E-value: 7.96e-10
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 553319362  37 TLYEYLKEYKRFFDWLMDADLTqapkiadidlstLEHLTKKDLEAFVLYLRERpslntystkeGLSQTTINRTLSALSSL 116
Cdd:PRK00283  26 TLSSYRRDLELFAEWLAARGLS------------LAEATRDDLQAFLAELAEG----------GYKATSSARRLSALRRF 83

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 553319362 117 YKYLTEE--VENDqgePyfyrnvmkkvstkkkkeTLASRAENIKQKL--FLG-DETLAFLDYVDKEYEQKLsnrakssfr 191
Cdd:PRK00283  84 FQFLLREglREDD---P-----------------SALLDSPKLPRRLpkTLSeAQVEALLDAPDIDTPLGL--------- 134

                        170       180       190
                 ....*....|....*....|....*....|....
gi 553319362 192 knkeRDLAIISLLLASGVRLSEAVNLDLKDVNLN 225
Cdd:PRK00283 135 ----RDRAMLELLYATGLRVSELVGLTLDDVSLR 164
INT_XerDC_C cd00798
XerD and XerC integrases, C-terminal catalytic domains; XerDC-like integrases are involved in ...
 196-225 3.00e-07

XerD and XerC integrases, C-terminal catalytic domains; XerDC-like integrases are involved in the site-specific integration and excision of lysogenic bacteriophage genomes, transposition of conjugative transposons, termination of chromosomal replication, and stable plasmid inheritance. They share the same fold in their catalytic domain containing six conserved active site residues and the overall reaction mechanism with the DNA breaking-rejoining enzyme superfamily. In Escherichia coli, the Xer site-specific recombination system acts to convert dimeric chromosomes, which are formed by homologous recombination to monomers. Two related recombinases, XerC and XerD, bind cooperatively to a recombination site present in the E. coli chromosome. Each recombinase catalyzes the exchange of one pair of DNA strand in a reaction that proceeds through a Holliday junction intermediate. These enzymes 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: 271179 [Multi-domain]  Cd Length: 172  Bit Score: 48.66  E-value: 3.00e-07
                         10        20        30
                 ....*....|....*....|....*....|
gi 553319362 196 RDLAIISLLLASGVRLSEAVNLDLKDVNLN 225
Cdd:cd00798   20 RDRAILELLYASGLRVSELVGLDLSDVDLD 49
Phage_int_SAM_1 pfam02899
Phage integrase, N-terminal SAM-like domain;
33-123 5.49e-06

Phage integrase, N-terminal SAM-like domain;


Pssm-ID: 427047 [Multi-domain]  Cd Length: 83  Bit Score: 43.40  E-value: 5.49e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 553319362   33 YSFTTLYEYLKEYKRFFDWLmdadltqapkiaDIDLSTLEHLTKKDLEAFVLYLRerpslntystKEGLSQTTINRTLSA 112
Cdd:pfam02899  14 LSPHTLRAYRRDLLAFLKFL------------SEGGSSLEQITTSDVRAFLAELR----------AQGLSASSLARRLSA 71

                          90
                  ....*....|.
gi 553319362  113 LSSLYKYLTEE 123
Cdd:pfam02899  72 LRSFYQFLIRE 82
DNA_BRE_C cd00397
DNA breaking-rejoining enzymes, C-terminal catalytic domain; The DNA breaking-rejoining enzyme ...
 185-225 6.32e-05

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: 42.08  E-value: 6.32e-05
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|.
gi 553319362 185 RAKSSFRKNKERDLAIISLLLASGVRLSEAVNLDLKDVNLN 225
Cdd:cd00397    7 DAIDEDKKIDLRDRAILLLLLETGLRISELLALKVKDIDLD 47
Phage_integrase pfam00589
Phage integrase family; Members of this family cleave DNA substrates by a series of staggered ...
 162-225 9.87e-04

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: 38.45  E-value: 9.87e-04
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 553319362  162 FLGDETLAFLDYVDKEyeqklsnrakssfrKNKERDLAIISLLLASGVRLSEAVNLDLKDVNLN 225
Cdd:pfam00589   2 LTEDEVERLLDAAETG--------------PLSIRDKALLELLYATGLRISELCSLRWSDIDFE 51
Phage_int_SAM_4 pfam13495
Phage integrase, N-terminal SAM-like domain;
33-123 1.40e-03

Phage integrase, N-terminal SAM-like domain;


Pssm-ID: 463898 [Multi-domain]  Cd Length: 83  Bit Score: 36.44  E-value: 1.40e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 553319362   33 YSFTTLYEYLKEYKRFFDWLmdadltqapkiadiDLSTLEHLTKKDLEAFVLYLRerpslntysTKEGLSQTTINRTLSA 112
Cdd:pfam13495  14 YAERTIKAYLRWIRRFLRFH--------------DKKHPEELTEEDIEAYLSHLA---------NERNVSASTQNQALNA 70

                          90
                  ....*....|.
gi 553319362  113 LSSLYKYLTEE 123
Cdd:pfam13495  71 LSFFYRWVLER 81
INT_RitA_C_like cd01188
C-terminal catalytic domain of recombinase RitA, a component of the recombinase trio; ...
 196-223 3.34e-03

C-terminal catalytic domain of recombinase RitA, a component of the recombinase trio; Recombinases RitA (also known as pAE1), RitB, and RitC are encoded by three adjacent and overlapping genes. Collectively they are known as the Recombinase in Trio (RIT). This RitA family includes various bacterial integrases and integrases from the deletion-prone region of plasmid pAE1 of Alcaligenes eutrophus H1. All three integrases contain a catalytic motif, suggesting that they are all active enzymes. However, their specific roles are not fully understood. All three families 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: 271188 [Multi-domain]  Cd Length: 179  Bit Score: 37.22  E-value: 3.34e-03
                         10        20
                 ....*....|....*....|....*...
gi 553319362 196 RDLAIISLLLASGVRLSEAVNLDLKDVN 223
Cdd:cd01188   21 RDYAILLLLARLGLRAGDVAGLRLDDID 48
INT_IntI_C cd01193
Integron integrase and similar protiens, C-terminal catalytic domain; Integron integrases ...
 196-223 6.39e-03

Integron integrase and similar protiens, C-terminal catalytic domain; Integron integrases mediate site-specific DNA recombination between a proximal primary site (attI) and a secondary target site (attC) found within mobile gene cassettes encoding resistance or virulence factors. Unlike other site specific recombinases, the attC sites lack sequence conservation. Integron integrase exhibits broader DNA specificity by recognizing the non-conserved attC sites. The structure shows that DNA target site recognition are not dependent on canonical DNA but on the position of two flipped-out bases that interact in cis and in trans with the integrase. Integron-integrases are present in many natural occurring mobile elements, including transposons and conjugative plasmids. Vibrio, Shewanella, Xanthomonas, and Pseudomonas species harbor chromosomal super-integrons. All integron-integrases carry large inserts unlike the TnpF ermF-like proteins also seen in this group.


Pssm-ID: 271193 [Multi-domain]  Cd Length: 176  Bit Score: 36.10  E-value: 6.39e-03
                         10        20
                 ....*....|....*....|....*...
gi 553319362 196 RDLAIISLLLASGVRLSEAVNLDLKDVN 223
Cdd:cd01193   22 RHRLILSLLYGAGLRISELLRLRVKDID 49
INT_C_like_5 cd01195
Uncharacterized site-specific tyrosine recombinase, C-terminal catalytic domain; Tyrosine ...
 196-222 8.21e-03

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: 35.91  E-value: 8.21e-03
                         10        20
                 ....*....|....*....|....*..
gi 553319362 196 RDLAIISLLLASGVRLSEAVNLDLKDV 222
Cdd:cd01195   21 RDEALVRLLLDNALRRSEAVALDVEDL 47
 
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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