UniProtKB - P0A8P8 (XERD_ECOLI)
Protein
Tyrosine recombinase XerD
Gene
xerD
Organism
Escherichia coli (strain K12)
Status
Functioni
Site-specific tyrosine recombinase, which acts by catalyzing the cutting and rejoining of the recombining DNA molecules. Binds cooperatively to specific DNA consensus sequences that are separated from XerC binding sites by a short central region, forming the heterotetrameric XerC-XerD complex that recombines DNA substrates. The complex is essential to convert dimers of the bacterial chromosome into monomers to permit their segregation at cell division. It also contributes to the segregational stability of plasmids at ColE1 xer (or cer) and pSC101 (or psi) sites. In the complex XerD specifically exchanges the bottom DNA strands (By similarity).By similarity2 Publications
Activity regulationi
During recombination, the heterotetrameric complex catalyzes two consecutive pairs of strand exchanges, implying that specific pairs of active sites are sequentially switched on and off in the recombinase tetramer to ensure that appropriate DNA strands will be exchanged at both reaction steps. FtsK plays a central role in this catalytic state switch that turns recombinase on and off reciprocally. The reciprocal C-terminal interaction between XerC and XerD may also participate in the enzymatic switch process.2 Publications
Sites
Feature key | Position(s) | DescriptionActions | Graphical view | Length |
---|---|---|---|---|
Active sitei | 148 | PROSITE-ProRule annotation | 1 | |
Active sitei | 172 | PROSITE-ProRule annotation | 1 | |
Active sitei | 244 | PROSITE-ProRule annotation | 1 | |
Active sitei | 247 | PROSITE-ProRule annotation | 1 | |
Active sitei | 270 | PROSITE-ProRule annotation | 1 | |
Active sitei | 279 | O-(3'-phospho-DNA)-tyrosine intermediatePROSITE-ProRule annotation | 1 |
GO - Molecular functioni
- DNA binding Source: EcoliWiki
- site-specific recombinase activity Source: EcoliWiki
- tyrosine-based site-specific recombinase activity Source: EcoliWiki
GO - Biological processi
- cell cycle Source: UniProtKB-KW
- cell division Source: UniProtKB-KW
- chromosome segregation Source: UniProtKB-UniRule
- plasmid maintenance Source: EcoliWiki
- resolution of recombination intermediates Source: EcoliWiki
- response to radiation Source: EcoCyc
- transposition, DNA-mediated Source: UniProtKB-UniRule
Keywordsi
Molecular function | DNA-binding |
Biological process | Cell cycle, Cell division, Chromosome partition, DNA integration, DNA recombination |
Enzyme and pathway databases
BioCyci | EcoCyc:EG11071-MONOMER |
Names & Taxonomyi
Protein namesi | Recommended name: Tyrosine recombinase XerD |
Gene namesi | Name:xerD Synonyms:xprB Ordered Locus Names:b2894, JW2862 |
Organismi | Escherichia coli (strain K12) |
Taxonomic identifieri | 83333 [NCBI] |
Taxonomic lineagei | Bacteria › Proteobacteria › Gammaproteobacteria › Enterobacterales › Enterobacteriaceae › Escherichia › |
Proteomesi |
|
Subcellular locationi
- Cytoplasm By similarity
GO - Cellular componenti
- cytoplasm Source: UniProtKB-SubCell
- Holliday junction resolvase complex Source: EcoliWiki
Keywords - Cellular componenti
CytoplasmPathology & Biotechi
Mutagenesis
Feature key | Position(s) | DescriptionActions | Graphical view | Length |
---|---|---|---|---|
Mutagenesisi | 148 | R → K: Abolishes DNA cleavage activity. 1 Publication | 1 | |
Mutagenesisi | 244 | H → L: Abolishes DNA religation activity. 1 Publication | 1 | |
Mutagenesisi | 247 | R → Q: Abolishes DNA cleavage activity. 2 Publications | 1 | |
Mutagenesisi | 256 – 258 | NHG → ESS: Abolishes plasmid resolution but not chromosomal recombination. 1 Publication | 3 | |
Mutagenesisi | 279 | Y → F: Abolishes DNA cleavage activity. 2 Publications | 1 | |
Mutagenesisi | 294 | H → Q or E: Abolishes DNA recombination (in vitro). 1 Publication | 1 | |
Mutagenesisi | 295 | H → E: Abolishes DNA recombination (in vitro). 1 Publication | 1 | |
Mutagenesisi | 297 | R → E: Abolishes DNA recombination (in vitro). 1 Publication | 1 | |
Mutagenesisi | 298 | A → Q: Reduces chromosomal recombination but not plasmid resolution. 1 Publication | 1 |
PTM / Processingi
Molecule processing
Feature key | Position(s) | DescriptionActions | Graphical view | Length |
---|---|---|---|---|
ChainiPRO_0000095386 | 1 – 298 | Tyrosine recombinase XerDAdd BLAST | 298 |
Proteomic databases
PaxDbi | P0A8P8 |
PRIDEi | P0A8P8 |
Interactioni
Subunit structurei
Forms a cyclic heterotetrameric complex composed of two molecules of XerC and two molecules of XerD, in which XerC interacts with XerD via its C-terminal region, XerD interacts with XerC via its C-terminal region and so on.
1 PublicationProtein-protein interaction databases
BioGRIDi | 4262339, 485 interactors 851685, 2 interactors |
ComplexPortali | CPX-5123, XerCD site-specific tyrosine recombinase complex |
DIPi | DIP-48125N |
IntActi | P0A8P8, 7 interactors |
STRINGi | 511145.b2894 |
Structurei
Secondary structure
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details3D structure databases
SMRi | P0A8P8 |
ModBasei | Search... |
PDBe-KBi | Search... |
Miscellaneous databases
EvolutionaryTracei | P0A8P8 |
Family & Domainsi
Domains and Repeats
Feature key | Position(s) | DescriptionActions | Graphical view | Length |
---|---|---|---|---|
Domaini | 2 – 87 | Core-binding (CB)PROSITE-ProRule annotationAdd BLAST | 86 | |
Domaini | 108 – 292 | Tyr recombinasePROSITE-ProRule annotationAdd BLAST | 185 |
Sequence similaritiesi
Phylogenomic databases
eggNOGi | COG4974, Bacteria |
HOGENOMi | CLU_027562_9_0_6 |
InParanoidi | P0A8P8 |
PhylomeDBi | P0A8P8 |
Family and domain databases
Gene3Di | 1.10.150.130, 1 hit 1.10.443.10, 1 hit |
HAMAPi | MF_01808, Recomb_XerC_XerD, 1 hit MF_01807, Recomb_XerD, 1 hit |
InterProi | View protein in InterPro IPR044068, CB IPR011010, DNA_brk_join_enz IPR013762, Integrase-like_cat_sf IPR002104, Integrase_catalytic IPR010998, Integrase_recombinase_N IPR004107, Integrase_SAM-like_N IPR011932, Recomb_XerD IPR023009, Tyrosine_recombinase_XerC/XerD |
Pfami | View protein in Pfam PF02899, Phage_int_SAM_1, 1 hit PF00589, Phage_integrase, 1 hit |
SUPFAMi | SSF56349, SSF56349, 1 hit |
TIGRFAMsi | TIGR02225, recomb_XerD, 1 hit |
PROSITEi | View protein in PROSITE PS51900, CB, 1 hit PS51898, TYR_RECOMBINASE, 1 hit |
i Sequence
Sequence statusi: Complete.
P0A8P8-1 [UniParc]FASTAAdd to basket
10 20 30 40 50
MKQDLARIEQ FLDALWLEKN LAENTLNAYR RDLSMMVEWL HHRGLTLATA
60 70 80 90 100
QSDDLQALLA ERLEGGYKAT SSARLLSAVR RLFQYLYREK FREDDPSAHL
110 120 130 140 150
ASPKLPQRLP KDLSEAQVER LLQAPLIDQP LELRDKAMLE VLYATGLRVS
160 170 180 190 200
ELVGLTMSDI SLRQGVVRVI GKGNKERLVP LGEEAVYWLE TYLEHGRPWL
210 220 230 240 250
LNGVSIDVLF PSQRAQQMTR QTFWHRIKHY AVLAGIDSEK LSPHVLRHAF
260 270 280 290
ATHLLNHGAD LRVVQMLLGH SDLSTTQIYT HVATERLRQL HQQHHPRA
Sequence databases
Select the link destinations: EMBLi GenBanki DDBJi Links Updated | M54884 Genomic DNA Translation: AAA62787.1 U28375 Genomic DNA Translation: AAA83075.1 U00096 Genomic DNA Translation: AAC75932.1 AP009048 Genomic DNA Translation: BAE76959.1 |
PIRi | A39202 |
RefSeqi | NP_417370.1, NC_000913.3 WP_000806638.1, NZ_STEB01000001.1 |
Genome annotation databases
EnsemblBacteriai | AAC75932; AAC75932; b2894 BAE76959; BAE76959; BAE76959 |
GeneIDi | 48726198 947362 |
KEGGi | ecj:JW2862 eco:b2894 |
PATRICi | fig|1411691.4.peg.3839 |
Similar proteinsi
Cross-referencesi
Sequence databases
Select the link destinations: EMBLi GenBanki DDBJi Links Updated | M54884 Genomic DNA Translation: AAA62787.1 U28375 Genomic DNA Translation: AAA83075.1 U00096 Genomic DNA Translation: AAC75932.1 AP009048 Genomic DNA Translation: BAE76959.1 |
PIRi | A39202 |
RefSeqi | NP_417370.1, NC_000913.3 WP_000806638.1, NZ_STEB01000001.1 |
3D structure databases
Select the link destinations: PDBei RCSB PDBi PDBji Links Updated | PDB entry | Method | Resolution (Å) | Chain | Positions | PDBsum |
1A0P | X-ray | 2.50 | A | 3-292 | [»] | |
SMRi | P0A8P8 | |||||
ModBasei | Search... | |||||
PDBe-KBi | Search... |
Protein-protein interaction databases
BioGRIDi | 4262339, 485 interactors 851685, 2 interactors |
ComplexPortali | CPX-5123, XerCD site-specific tyrosine recombinase complex |
DIPi | DIP-48125N |
IntActi | P0A8P8, 7 interactors |
STRINGi | 511145.b2894 |
Proteomic databases
PaxDbi | P0A8P8 |
PRIDEi | P0A8P8 |
Genome annotation databases
EnsemblBacteriai | AAC75932; AAC75932; b2894 BAE76959; BAE76959; BAE76959 |
GeneIDi | 48726198 947362 |
KEGGi | ecj:JW2862 eco:b2894 |
PATRICi | fig|1411691.4.peg.3839 |
Organism-specific databases
EchoBASEi | EB1064 |
Phylogenomic databases
eggNOGi | COG4974, Bacteria |
HOGENOMi | CLU_027562_9_0_6 |
InParanoidi | P0A8P8 |
PhylomeDBi | P0A8P8 |
Enzyme and pathway databases
BioCyci | EcoCyc:EG11071-MONOMER |
Miscellaneous databases
EvolutionaryTracei | P0A8P8 |
PROi | PR:P0A8P8 |
Family and domain databases
Gene3Di | 1.10.150.130, 1 hit 1.10.443.10, 1 hit |
HAMAPi | MF_01808, Recomb_XerC_XerD, 1 hit MF_01807, Recomb_XerD, 1 hit |
InterProi | View protein in InterPro IPR044068, CB IPR011010, DNA_brk_join_enz IPR013762, Integrase-like_cat_sf IPR002104, Integrase_catalytic IPR010998, Integrase_recombinase_N IPR004107, Integrase_SAM-like_N IPR011932, Recomb_XerD IPR023009, Tyrosine_recombinase_XerC/XerD |
Pfami | View protein in Pfam PF02899, Phage_int_SAM_1, 1 hit PF00589, Phage_integrase, 1 hit |
SUPFAMi | SSF56349, SSF56349, 1 hit |
TIGRFAMsi | TIGR02225, recomb_XerD, 1 hit |
PROSITEi | View protein in PROSITE PS51900, CB, 1 hit PS51898, TYR_RECOMBINASE, 1 hit |
ProtoNeti | Search... |
MobiDBi | Search... |
Entry informationi
Entry namei | XERD_ECOLI | |
Accessioni | P0A8P8Primary (citable) accession number: P0A8P8 Secondary accession number(s): P21891, Q2M9U7 | |
Entry historyi | Integrated into UniProtKB/Swiss-Prot: | June 7, 2005 |
Last sequence update: | June 7, 2005 | |
Last modified: | December 2, 2020 | |
This is version 128 of the entry and version 1 of the sequence. See complete history. | ||
Entry statusi | Reviewed (UniProtKB/Swiss-Prot) | |
Annotation program | Prokaryotic Protein Annotation Program |
Miscellaneousi
Keywords - Technical termi
3D-structure, Direct protein sequencing, Reference proteomeDocuments
- PDB cross-references
Index of Protein Data Bank (PDB) cross-references - SIMILARITY comments
Index of protein domains and families