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Protein

Tyrosine recombinase XerD

Gene

xerD

Organism
Escherichia coli (strain K12)
Status
Reviewed-Annotation score: Annotation score: 5 out of 5-Experimental evidence at protein leveli

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

Enzyme 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 keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Active sitei148 – 1481
Active sitei172 – 1721
Active sitei244 – 2441
Active sitei247 – 2471
Active sitei270 – 2701
Active sitei279 – 2791O-(3'-phospho-DNA)-tyrosine intermediate

GO - Molecular functioni

  • DNA binding Source: UniProtKB-KW
  • 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-HAMAP
  • plasmid maintenance Source: EcoliWiki
  • resolution of recombination intermediates Source: EcoliWiki
  • transposition, DNA-mediated Source: UniProtKB-HAMAP
Complete GO annotation...

Keywords - Biological processi

Cell cycle, Cell division, Chromosome partition, DNA integration, DNA recombination

Keywords - Ligandi

DNA-binding

Enzyme and pathway databases

BioCyciEcoCyc:EG11071-MONOMER.
ECOL316407:JW2862-MONOMER.

Names & Taxonomyi

Protein namesi
Recommended name:
Tyrosine recombinase XerD
Gene namesi
Name:xerD
Synonyms:xprB
Ordered Locus Names:b2894, JW2862
OrganismiEscherichia coli (strain K12)
Taxonomic identifieri83333 [NCBI]
Taxonomic lineageiBacteriaProteobacteriaGammaproteobacteriaEnterobacterialesEnterobacteriaceaeEscherichia
Proteomesi
  • UP000000318 Componenti: Chromosome
  • UP000000625 Componenti: Chromosome

Organism-specific databases

EcoGeneiEG11071. xerD.

Subcellular locationi

GO - Cellular componenti

  • cytoplasm Source: UniProtKB-SubCell
  • Holliday junction resolvase complex Source: EcoliWiki
Complete GO annotation...

Keywords - Cellular componenti

Cytoplasm

Pathology & Biotechi

Mutagenesis

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Mutagenesisi148 – 1481R → K: Abolishes DNA cleavage activity. 1 Publication
Mutagenesisi244 – 2441H → L: Abolishes DNA religation activity. 1 Publication
Mutagenesisi247 – 2471R → Q: Abolishes DNA cleavage activity. 2 Publications
Mutagenesisi256 – 2583NHG → ESS: Abolishes plasmid resolution but not chromosomal recombination. 1 Publication
Mutagenesisi279 – 2791Y → F: Abolishes DNA cleavage activity. 2 Publications
Mutagenesisi294 – 2941H → Q or E: Abolishes DNA recombination (in vitro). 1 Publication
Mutagenesisi295 – 2951H → E: Abolishes DNA recombination (in vitro). 1 Publication
Mutagenesisi297 – 2971R → E: Abolishes DNA recombination (in vitro). 1 Publication
Mutagenesisi298 – 2981A → Q: Reduces chromosomal recombination but not plasmid resolution. 1 Publication

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 298298Tyrosine recombinase XerDPRO_0000095386Add
BLAST

Proteomic databases

PaxDbiP0A8P8.
PRIDEiP0A8P8.

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 Publication

Protein-protein interaction databases

BioGridi4262339. 483 interactions.
DIPiDIP-48125N.
IntActiP0A8P8. 7 interactions.
MINTiMINT-1282534.
STRINGi511145.b2894.

Structurei

Secondary structure

1
298
Legend: HelixTurnBeta strand
Show more details
Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Helixi4 – 1714Combined sources
Helixi23 – 4220Combined sources
Turni47 – 493Combined sources
Helixi52 – 609Combined sources
Helixi72 – 8817Combined sources
Beta strandi91 – 944Combined sources
Helixi115 – 1239Combined sources
Helixi130 – 14516Combined sources
Helixi149 – 1524Combined sources
Helixi157 – 1593Combined sources
Turni162 – 1654Combined sources
Beta strandi166 – 1705Combined sources
Beta strandi172 – 1743Combined sources
Beta strandi176 – 1805Combined sources
Helixi183 – 19513Combined sources
Helixi197 – 2015Combined sources
Beta strandi208 – 2114Combined sources
Beta strandi215 – 2173Combined sources
Helixi220 – 23314Combined sources
Helixi238 – 2403Combined sources
Helixi243 – 25715Combined sources
Helixi262 – 2643Combined sources
Helixi275 – 29117Combined sources

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
1A0PX-ray2.50A3-292[»]
ProteinModelPortaliP0A8P8.
SMRiP0A8P8. Positions 3-292.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiP0A8P8.

Family & Domainsi

Sequence similaritiesi

Phylogenomic databases

eggNOGiENOG4105C13. Bacteria.
COG4974. LUCA.
HOGENOMiHOG000045296.
InParanoidiP0A8P8.
KOiK04763.
OMAiAIWQMIK.
PhylomeDBiP0A8P8.

Family and domain databases

Gene3Di1.10.150.130. 1 hit.
1.10.443.10. 1 hit.
HAMAPiMF_01808. Recomb_XerC_XerD. 1 hit.
MF_01807. Recomb_XerD. 1 hit.
InterProiIPR011010. DNA_brk_join_enz.
IPR013762. Integrase-like_cat.
IPR002104. Integrase_catalytic.
IPR010998. Integrase_Lambda-type_N.
IPR023109. Integrase_recombinase_N.
IPR004107. Integrase_SAM-like_N.
IPR011932. Recomb_XerD.
IPR023009. Tyrosine_recombinase_XerC/XerD.
[Graphical view]
PfamiPF02899. Phage_int_SAM_1. 1 hit.
PF00589. Phage_integrase. 1 hit.
[Graphical view]
SUPFAMiSSF47823. SSF47823. 1 hit.
SSF56349. SSF56349. 1 hit.
TIGRFAMsiTIGR02225. recomb_XerD. 1 hit.

Sequencei

Sequence statusi: Complete.

P0A8P8-1 [UniParc]FASTAAdd to basket

« Hide

        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
Length:298
Mass (Da):34,246
Last modified:June 7, 2005 - v1
Checksum:iB75DD603BEEE03E9
GO

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.
PIRiA39202.
RefSeqiNP_417370.1. NC_000913.3.
WP_000806638.1. NZ_LN832404.1.

Genome annotation databases

EnsemblBacteriaiAAC75932; AAC75932; b2894.
BAE76959; BAE76959; BAE76959.
GeneIDi947362.
KEGGiecj:JW2862.
eco:b2894.
PATRICi32121200. VBIEscCol129921_2988.

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.
PIRiA39202.
RefSeqiNP_417370.1. NC_000913.3.
WP_000806638.1. NZ_LN832404.1.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
1A0PX-ray2.50A3-292[»]
ProteinModelPortaliP0A8P8.
SMRiP0A8P8. Positions 3-292.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi4262339. 483 interactions.
DIPiDIP-48125N.
IntActiP0A8P8. 7 interactions.
MINTiMINT-1282534.
STRINGi511145.b2894.

Proteomic databases

PaxDbiP0A8P8.
PRIDEiP0A8P8.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiAAC75932; AAC75932; b2894.
BAE76959; BAE76959; BAE76959.
GeneIDi947362.
KEGGiecj:JW2862.
eco:b2894.
PATRICi32121200. VBIEscCol129921_2988.

Organism-specific databases

EchoBASEiEB1064.
EcoGeneiEG11071. xerD.

Phylogenomic databases

eggNOGiENOG4105C13. Bacteria.
COG4974. LUCA.
HOGENOMiHOG000045296.
InParanoidiP0A8P8.
KOiK04763.
OMAiAIWQMIK.
PhylomeDBiP0A8P8.

Enzyme and pathway databases

BioCyciEcoCyc:EG11071-MONOMER.
ECOL316407:JW2862-MONOMER.

Miscellaneous databases

EvolutionaryTraceiP0A8P8.
PROiP0A8P8.

Family and domain databases

Gene3Di1.10.150.130. 1 hit.
1.10.443.10. 1 hit.
HAMAPiMF_01808. Recomb_XerC_XerD. 1 hit.
MF_01807. Recomb_XerD. 1 hit.
InterProiIPR011010. DNA_brk_join_enz.
IPR013762. Integrase-like_cat.
IPR002104. Integrase_catalytic.
IPR010998. Integrase_Lambda-type_N.
IPR023109. Integrase_recombinase_N.
IPR004107. Integrase_SAM-like_N.
IPR011932. Recomb_XerD.
IPR023009. Tyrosine_recombinase_XerC/XerD.
[Graphical view]
PfamiPF02899. Phage_int_SAM_1. 1 hit.
PF00589. Phage_integrase. 1 hit.
[Graphical view]
SUPFAMiSSF47823. SSF47823. 1 hit.
SSF56349. SSF56349. 1 hit.
TIGRFAMsiTIGR02225. recomb_XerD. 1 hit.
ProtoNetiSearch...

Entry informationi

Entry nameiXERD_ECOLI
AccessioniPrimary (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: September 7, 2016
This is version 101 of the entry and version 1 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programProkaryotic Protein Annotation Program

Miscellaneousi

Keywords - Technical termi

3D-structure, Complete proteome, Direct protein sequencing, Reference proteome

Documents

  1. Escherichia coli
    Escherichia coli (strain K12): entries and cross-references to EcoGene
  2. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
  3. SIMILARITY comments
    Index of protein domains and families

Similar proteinsi

Links to similar proteins from the UniProt Reference Clusters (UniRef) at 100%, 90% and 50% sequence identity:
100%UniRef100 combines identical sequences and sub-fragments with 11 or more residues from any organism into one UniRef entry.
90%UniRef90 is built by clustering UniRef100 sequences that have at least 90% sequence identity to, and 80% overlap with, the longest sequence (a.k.a seed sequence).
50%UniRef50 is built by clustering UniRef90 seed sequences that have at least 50% sequence identity to, and 80% overlap with, the longest sequence in the cluster.