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Protein

Tyrosine recombinase XerD

Gene

xerD

Organism
Escherichia coli (strain K12)
Status
Reviewed-Annotation score: -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)DescriptionActionsGraphical viewLength
Active sitei1481
Active sitei1721
Active sitei2441
Active sitei2471
Active sitei2701
Active sitei279O-(3'-phospho-DNA)-tyrosine intermediate1

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-KW
  • plasmid maintenance Source: EcoliWiki
  • resolution of recombination intermediates Source: EcoliWiki
  • response to radiation Source: EcoCyc

Keywordsi

Molecular functionDNA-binding
Biological processCell cycle, Cell division, Chromosome partition, DNA integration, DNA recombination

Enzyme and pathway databases

BioCyciEcoCyc:EG11071-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 lineageiBacteriaProteobacteriaGammaproteobacteriaEnterobacteralesEnterobacteriaceaeEscherichia
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

Keywords - Cellular componenti

Cytoplasm

Pathology & Biotechi

Mutagenesis

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Mutagenesisi148R → K: Abolishes DNA cleavage activity. 1 Publication1
Mutagenesisi244H → L: Abolishes DNA religation activity. 1 Publication1
Mutagenesisi247R → Q: Abolishes DNA cleavage activity. 2 Publications1
Mutagenesisi256 – 258NHG → ESS: Abolishes plasmid resolution but not chromosomal recombination. 1 Publication3
Mutagenesisi279Y → F: Abolishes DNA cleavage activity. 2 Publications1
Mutagenesisi294H → Q or E: Abolishes DNA recombination (in vitro). 1 Publication1
Mutagenesisi295H → E: Abolishes DNA recombination (in vitro). 1 Publication1
Mutagenesisi297R → E: Abolishes DNA recombination (in vitro). 1 Publication1
Mutagenesisi298A → Q: Reduces chromosomal recombination but not plasmid resolution. 1 Publication1

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_00000953861 – 298Tyrosine recombinase XerDAdd BLAST298

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, 485 interactors
DIPiDIP-48125N
IntActiP0A8P8, 7 interactors
STRINGi316385.ECDH10B_3068

Structurei

Secondary structure

1298
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details
Feature keyPosition(s)DescriptionActionsGraphical viewLength
Helixi4 – 17Combined sources14
Helixi23 – 42Combined sources20
Turni47 – 49Combined sources3
Helixi52 – 60Combined sources9
Helixi72 – 88Combined sources17
Beta strandi91 – 94Combined sources4
Helixi115 – 123Combined sources9
Helixi130 – 145Combined sources16
Helixi149 – 152Combined sources4
Helixi157 – 159Combined sources3
Turni162 – 165Combined sources4
Beta strandi166 – 170Combined sources5
Beta strandi172 – 174Combined sources3
Beta strandi176 – 180Combined sources5
Helixi183 – 195Combined sources13
Helixi197 – 201Combined sources5
Beta strandi208 – 211Combined sources4
Beta strandi215 – 217Combined sources3
Helixi220 – 233Combined sources14
Helixi238 – 240Combined sources3
Helixi243 – 257Combined sources15
Helixi262 – 264Combined sources3
Helixi275 – 291Combined sources17

3D structure databases

ProteinModelPortaliP0A8P8
SMRiP0A8P8
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiP0A8P8

Family & Domainsi

Sequence similaritiesi

Phylogenomic databases

eggNOGiENOG4105C13 Bacteria
COG4974 LUCA
HOGENOMiHOG000045296
InParanoidiP0A8P8
KOiK04763
OMAiTRQAFWY
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
InterProiView protein in InterPro
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
PfamiView protein in Pfam
PF02899 Phage_int_SAM_1, 1 hit
PF00589 Phage_integrase, 1 hit
SUPFAMiSSF56349 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
PATRICifig|1411691.4.peg.3839

Similar proteinsi

Entry informationi

Entry nameiXERD_ECOLI
AccessioniPrimary (citable) accession number: P0A8P8
Secondary accession number(s): P21891, Q2M9U7
Entry historyiIntegrated into UniProtKB/Swiss-Prot: June 7, 2005
Last sequence update: June 7, 2005
Last modified: March 28, 2018
This is version 112 of the entry and version 1 of the sequence. See 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

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