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Entry version 125 (17 Jun 2020)
Sequence version 1 (07 Jun 2005)
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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

<p>The annotation score provides a heuristic measure of the annotation content of a UniProtKB entry or proteome. This score <strong>cannot</strong> be used as a measure of the accuracy of the annotation as we cannot define the 'correct annotation' for any given protein.<p><a href='/help/annotation_score' target='_top'>More...</a></p>
-Experimental evidence at protein leveli <p>This indicates the type of evidence that supports the existence of the protein. Note that the 'protein existence' evidence does not give information on the accuracy or correctness of the sequence(s) displayed.<p><a href='/help/protein_existence' target='_top'>More...</a></p>

<p>This section provides any useful information about the protein, mostly biological knowledge.<p><a href='/help/function_section' target='_top'>More...</a></p>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

<p>This subsection of the <a href="http://www.uniprot.org/help/function%5Fsection">Function</a> section describes regulatory mechanisms for enzymes, transporters or microbial transcription factors, and reports the components which regulate (by activation or inhibition) the reaction.<p><a href='/help/activity_regulation' target='_top'>More...</a></p>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 keyPosition(s)DescriptionActionsGraphical viewLength
<p>This subsection of the <a href="http://www.uniprot.org/help/function%5Fsection">Function</a> section is used for enzymes and indicates the residues directly involved in catalysis.<p><a href='/help/act_site' target='_top'>More...</a></p>Active sitei148PROSITE-ProRule annotation1
Active sitei172PROSITE-ProRule annotation1
Active sitei244PROSITE-ProRule annotation1
Active sitei247PROSITE-ProRule annotation1
Active sitei270PROSITE-ProRule annotation1
Active sitei279O-(3'-phospho-DNA)-tyrosine intermediatePROSITE-ProRule annotation1

<p>The <a href="http://www.geneontology.org/">Gene Ontology (GO)</a> project provides a set of hierarchical controlled vocabulary split into 3 categories:<p><a href='/help/gene_ontology' target='_top'>More...</a></p>GO - Molecular functioni

GO - Biological processi

<p>UniProtKB Keywords constitute a <a href="http://www.uniprot.org/keywords">controlled vocabulary</a> with a hierarchical structure. Keywords summarise the content of a UniProtKB entry and facilitate the search for proteins of interest.<p><a href='/help/keywords' target='_top'>More...</a></p>Keywordsi

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

Enzyme and pathway databases

BioCyc Collection of Pathway/Genome Databases

More...
BioCyci
EcoCyc:EG11071-MONOMER
ECOL316407:JW2862-MONOMER

<p>This section provides information about the protein and gene name(s) and synonym(s) and about the organism that is the source of the protein sequence.<p><a href='/help/names_and_taxonomy_section' target='_top'>More...</a></p>Names & Taxonomyi

<p>This subsection of the <a href="http://www.uniprot.org/help/names%5Fand%5Ftaxonomy%5Fsection">Names and taxonomy</a> section provides an exhaustive list of all names of the protein, from commonly used to obsolete, to allow unambiguous identification of a protein.<p><a href='/help/protein_names' target='_top'>More...</a></p>Protein namesi
Recommended name:
Tyrosine recombinase XerD
<p>This subsection of the <a href="http://www.uniprot.org/help/names%5Fand%5Ftaxonomy%5Fsection">Names and taxonomy</a> section indicates the name(s) of the gene(s) that code for the protein sequence(s) described in the entry. Four distinct tokens exist: 'Name', 'Synonyms', 'Ordered locus names' and 'ORF names'.<p><a href='/help/gene_name' target='_top'>More...</a></p>Gene namesi
Name:xerD
Synonyms:xprB
Ordered Locus Names:b2894, JW2862
<p>This subsection of the <a href="http://www.uniprot.org/help/names%5Fand%5Ftaxonomy%5Fsection">Names and taxonomy</a> section provides information on the name(s) of the organism that is the source of the protein sequence.<p><a href='/help/organism-name' target='_top'>More...</a></p>OrganismiEscherichia coli (strain K12)
<p>This subsection of the <a href="http://www.uniprot.org/help/names%5Fand%5Ftaxonomy%5Fsection">Names and taxonomy</a> section shows the unique identifier assigned by the NCBI to the source organism of the protein. This is known as the 'taxonomic identifier' or 'taxid'.<p><a href='/help/taxonomic_identifier' target='_top'>More...</a></p>Taxonomic identifieri83333 [NCBI]
<p>This subsection of the <a href="http://www.uniprot.org/help/names%5Fand%5Ftaxonomy%5Fsection">Names and taxonomy</a> section contains the taxonomic hierarchical classification lineage of the source organism. It lists the nodes as they appear top-down in the taxonomic tree, with the more general grouping listed first.<p><a href='/help/taxonomic_lineage' target='_top'>More...</a></p>Taxonomic lineageiBacteriaProteobacteriaGammaproteobacteriaEnterobacteralesEnterobacteriaceaeEscherichia
<p>This subsection of the <a href="http://www.uniprot.org/help/names%5Fand%5Ftaxonomy%5Fsection">Names and taxonomy</a> section is present for entries that are part of a <a href="http://www.uniprot.org/proteomes">proteome</a>, i.e. of a set of proteins thought to be expressed by organisms whose genomes have been completely sequenced.<p><a href='/help/proteomes_manual' target='_top'>More...</a></p>Proteomesi
  • UP000000318 <p>A UniProt <a href="http://www.uniprot.org/manual/proteomes%5Fmanual">proteome</a> can consist of several components.<br></br>The component name refers to the genomic component encoding a set of proteins.<p><a href='/help/proteome_component' target='_top'>More...</a></p> Componenti: Chromosome
  • UP000000625 Componenti: Chromosome

<p>This section provides information on the location and the topology of the mature protein in the cell.<p><a href='/help/subcellular_location_section' target='_top'>More...</a></p>Subcellular locationi

GO - Cellular componenti

Keywords - Cellular componenti

Cytoplasm

<p>This section provides information on the disease(s) and phenotype(s) associated with a protein.<p><a href='/help/pathology_and_biotech_section' target='_top'>More...</a></p>Pathology & Biotechi

Mutagenesis

Feature keyPosition(s)DescriptionActionsGraphical viewLength
<p>This subsection of the <a href="http://www.uniprot.org/manual/pathology%5Fand%5Fbiotech%5Fsection">'Pathology and Biotech'</a> section describes the effect of the experimental mutation of one or more amino acid(s) on the biological properties of the protein.<p><a href='/help/mutagen' target='_top'>More...</a></p>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

<p>This section describes post-translational modifications (PTMs) and/or processing events.<p><a href='/help/ptm_processing_section' target='_top'>More...</a></p>PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
<p>This subsection of the 'PTM / Processing' section describes the extent of a polypeptide chain in the mature protein following processing or proteolytic cleavage.<p><a href='/help/chain' target='_top'>More...</a></p>ChainiPRO_00000953861 – 298Tyrosine recombinase XerDAdd BLAST298

Proteomic databases

PaxDb, a database of protein abundance averages across all three domains of life

More...
PaxDbi
P0A8P8

PRoteomics IDEntifications database

More...
PRIDEi
P0A8P8

<p>This section provides information on the quaternary structure of a protein and on interaction(s) with other proteins or protein complexes.<p><a href='/help/interaction_section' target='_top'>More...</a></p>Interactioni

<p>This subsection of the <a href="http://www.uniprot.org/help/interaction%5Fsection">'Interaction'</a> section provides information about the protein quaternary structure and interaction(s) with other proteins or protein complexes (with the exception of physiological receptor-ligand interactions which are annotated in the <a href="http://www.uniprot.org/help/function%5Fsection">'Function'</a> section).<p><a href='/help/subunit_structure' target='_top'>More...</a></p>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

The Biological General Repository for Interaction Datasets (BioGRID)

More...
BioGRIDi
4262339, 485 interactors
851685, 2 interactors

ComplexPortal: manually curated resource of macromolecular complexes

More...
ComplexPortali
CPX-5123 XerCD site-specific tyrosine recombinase complex

Database of interacting proteins

More...
DIPi
DIP-48125N

Protein interaction database and analysis system

More...
IntActi
P0A8P8, 7 interactors

STRING: functional protein association networks

More...
STRINGi
511145.b2894

<p>This section provides information on the tertiary and secondary structure of a protein.<p><a href='/help/structure_section' target='_top'>More...</a></p>Structurei

Secondary structure

1298
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details

3D structure databases

SWISS-MODEL Repository - a database of annotated 3D protein structure models

More...
SMRi
P0A8P8

Database of comparative protein structure models

More...
ModBasei
Search...

Protein Data Bank in Europe - Knowledge Base

More...
PDBe-KBi
Search...

Miscellaneous databases

Relative evolutionary importance of amino acids within a protein sequence

More...
EvolutionaryTracei
P0A8P8

<p>This section provides information on sequence similarities with other proteins and the domain(s) present in a protein.<p><a href='/help/family_and_domains_section' target='_top'>More...</a></p>Family & Domainsi

Domains and Repeats

Feature keyPosition(s)DescriptionActionsGraphical viewLength
<p>This subsection of the <a href="http://www.uniprot.org/help/family%5Fand%5Fdomains%5Fsection">Family and Domains</a> section describes the position and type of a domain, which is defined as a specific combination of secondary structures organized into a characteristic three-dimensional structure or fold.<p><a href='/help/domain' target='_top'>More...</a></p>Domaini2 – 87Core-binding (CB)PROSITE-ProRule annotationAdd BLAST86
Domaini108 – 292Tyr recombinasePROSITE-ProRule annotationAdd BLAST185

<p>This subsection of the 'Family and domains' section provides information about the sequence similarity with other proteins.<p><a href='/help/sequence_similarities' target='_top'>More...</a></p>Sequence similaritiesi

Phylogenomic databases

evolutionary genealogy of genes: Non-supervised Orthologous Groups

More...
eggNOGi
ENOG4105C13 Bacteria
COG4974 LUCA

The HOGENOM Database of Homologous Genes from Fully Sequenced Organisms

More...
HOGENOMi
CLU_027562_9_0_6

InParanoid: Eukaryotic Ortholog Groups

More...
InParanoidi
P0A8P8

KEGG Orthology (KO)

More...
KOi
K04763

Database for complete collections of gene phylogenies

More...
PhylomeDBi
P0A8P8

Family and domain databases

Gene3D Structural and Functional Annotation of Protein Families

More...
Gene3Di
1.10.150.130, 1 hit
1.10.443.10, 1 hit

HAMAP database of protein families

More...
HAMAPi
MF_01808 Recomb_XerC_XerD, 1 hit
MF_01807 Recomb_XerD, 1 hit

Integrated resource of protein families, domains and functional sites

More...
InterProi
View 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

Pfam protein domain database

More...
Pfami
View protein in Pfam
PF02899 Phage_int_SAM_1, 1 hit
PF00589 Phage_integrase, 1 hit

Superfamily database of structural and functional annotation

More...
SUPFAMi
SSF56349 SSF56349, 1 hit

TIGRFAMs; a protein family database

More...
TIGRFAMsi
TIGR02225 recomb_XerD, 1 hit

PROSITE; a protein domain and family database

More...
PROSITEi
View protein in PROSITE
PS51900 CB, 1 hit
PS51898 TYR_RECOMBINASE, 1 hit

<p>This section displays by default the canonical protein sequence and upon request all isoforms described in the entry. It also includes information pertinent to the sequence(s), including <a href="http://www.uniprot.org/help/sequence%5Flength">length</a> and <a href="http://www.uniprot.org/help/sequences">molecular weight</a>. The information is filed in different subsections. The current subsections and their content are listed below:<p><a href='/help/sequences_section' target='_top'>More...</a></p>Sequencei

<p>This subsection of the <a href="http://www.uniprot.org/help/sequences%5Fsection">Sequence</a> section indicates if the <a href="http://www.uniprot.org/help/canonical%5Fand%5Fisoforms">canonical sequence</a> displayed by default in the entry is complete or not.<p><a href='/help/sequence_status' target='_top'>More...</a></p>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
<p>The checksum is a form of redundancy check that is calculated from the sequence. It is useful for tracking sequence updates.</p> <p>It should be noted that while, in theory, two different sequences could have the same checksum value, the likelihood that this would happen is extremely low.</p> <p>However UniProtKB may contain entries with identical sequences in case of multiple genes (paralogs).</p> <p>The checksum is computed as the sequence 64-bit Cyclic Redundancy Check value (CRC64) using the generator polynomial: x<sup>64</sup> + x<sup>4</sup> + x<sup>3</sup> + x + 1. The algorithm is described in the ISO 3309 standard. </p> <p class="publication">Press W.H., Flannery B.P., Teukolsky S.A. and Vetterling W.T.<br /> <strong>Cyclic redundancy and other checksums</strong><br /> <a href="http://www.nrbook.com/b/bookcpdf.php">Numerical recipes in C 2nd ed., pp896-902, Cambridge University Press (1993)</a>)</p> Checksum:iB75DD603BEEE03E9
GO

Sequence databases

Select the link destinations:

EMBL nucleotide sequence database

More...
EMBLi

GenBank nucleotide sequence database

More...
GenBanki

DNA Data Bank of Japan; a nucleotide sequence database

More...
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

Protein sequence database of the Protein Information Resource

More...
PIRi
A39202

NCBI Reference Sequences

More...
RefSeqi
NP_417370.1, NC_000913.3
WP_000806638.1, NZ_STEB01000001.1

Genome annotation databases

Ensembl bacterial and archaeal genome annotation project

More...
EnsemblBacteriai
AAC75932; AAC75932; b2894
BAE76959; BAE76959; BAE76959

Database of genes from NCBI RefSeq genomes

More...
GeneIDi
947362

KEGG: Kyoto Encyclopedia of Genes and Genomes

More...
KEGGi
ecj:JW2862
eco:b2894

Pathosystems Resource Integration Center (PATRIC)

More...
PATRICi
fig|1411691.4.peg.3839

<p>This section provides links to proteins that are similar to the protein sequence(s) described in this entry at different levels of sequence identity thresholds (100%, 90% and 50%) based on their membership in UniProt Reference Clusters (<a href="http://www.uniprot.org/help/uniref">UniRef</a>).<p><a href='/help/similar_proteins_section' target='_top'>More...</a></p>Similar proteinsi

<p>This section is used to point to information related to entries and found in data collections other than UniProtKB.<p><a href='/help/cross_references_section' target='_top'>More...</a></p>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_STEB01000001.1

3D structure databases

Select the link destinations:

Protein Data Bank Europe

More...
PDBei

Protein Data Bank RCSB

More...
RCSB PDBi

Protein Data Bank Japan

More...
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
1A0PX-ray2.50A3-292[»]
SMRiP0A8P8
ModBaseiSearch...
PDBe-KBiSearch...

Protein-protein interaction databases

BioGRIDi4262339, 485 interactors
851685, 2 interactors
ComplexPortaliCPX-5123 XerCD site-specific tyrosine recombinase complex
DIPiDIP-48125N
IntActiP0A8P8, 7 interactors
STRINGi511145.b2894

Proteomic databases

PaxDbiP0A8P8
PRIDEiP0A8P8

Genome annotation databases

EnsemblBacteriaiAAC75932; AAC75932; b2894
BAE76959; BAE76959; BAE76959
GeneIDi947362
KEGGiecj:JW2862
eco:b2894
PATRICifig|1411691.4.peg.3839

Organism-specific databases

EchoBASE - an integrated post-genomic database for E. coli

More...
EchoBASEi
EB1064

Phylogenomic databases

eggNOGiENOG4105C13 Bacteria
COG4974 LUCA
HOGENOMiCLU_027562_9_0_6
InParanoidiP0A8P8
KOiK04763
PhylomeDBiP0A8P8

Enzyme and pathway databases

BioCyciEcoCyc:EG11071-MONOMER
ECOL316407:JW2862-MONOMER

Miscellaneous databases

EvolutionaryTraceiP0A8P8

Protein Ontology

More...
PROi
PR:P0A8P8

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
PROSITEiView protein in PROSITE
PS51900 CB, 1 hit
PS51898 TYR_RECOMBINASE, 1 hit

ProtoNet; Automatic hierarchical classification of proteins

More...
ProtoNeti
Search...

MobiDB: a database of protein disorder and mobility annotations

More...
MobiDBi
Search...

<p>This section provides general information on the entry.<p><a href='/help/entry_information_section' target='_top'>More...</a></p>Entry informationi

<p>This subsection of the 'Entry information' section provides a mnemonic identifier for a UniProtKB entry, but it is not a stable identifier. Each reviewed entry is assigned a unique entry name upon integration into UniProtKB/Swiss-Prot.<p><a href='/help/entry_name' target='_top'>More...</a></p>Entry nameiXERD_ECOLI
<p>This subsection of the 'Entry information' section provides one or more accession number(s). These are stable identifiers and should be used to cite UniProtKB entries. Upon integration into UniProtKB, each entry is assigned a unique accession number, which is called 'Primary (citable) accession number'.<p><a href='/help/accession_numbers' target='_top'>More...</a></p>AccessioniPrimary (citable) accession number: P0A8P8
Secondary accession number(s): P21891, Q2M9U7
<p>This subsection of the 'Entry information' section shows the date of integration of the entry into UniProtKB, the date of the last sequence update and the date of the last annotation modification ('Last modified'). The version number for both the entry and the <a href="http://www.uniprot.org/help/canonical%5Fand%5Fisoforms">canonical sequence</a> are also displayed.<p><a href='/help/entry_history' target='_top'>More...</a></p>Entry historyiIntegrated into UniProtKB/Swiss-Prot: June 7, 2005
Last sequence update: June 7, 2005
Last modified: June 17, 2020
This is version 125 of the entry and version 1 of the sequence. See complete history.
<p>This subsection of the 'Entry information' section indicates whether the entry has been manually annotated and reviewed by UniProtKB curators or not, in other words, if the entry belongs to the Swiss-Prot section of UniProtKB (<strong>reviewed</strong>) or to the computer-annotated TrEMBL section (<strong>unreviewed</strong>).<p><a href='/help/entry_status' target='_top'>More...</a></p>Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programProkaryotic Protein Annotation Program

<p>This section contains any relevant information that doesn't fit in any other defined sections<p><a href='/help/miscellaneous_section' target='_top'>More...</a></p>Miscellaneousi

Keywords - Technical termi

3D-structure, Direct protein sequencing, Reference proteome

Documents

  1. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
  2. SIMILARITY comments
    Index of protein domains and families
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