xerD

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	Length
Active siteⁱ	148		1
Active siteⁱ	172		1
Active siteⁱ	244		1
Active siteⁱ	247		1
Active siteⁱ	270		1
Active siteⁱ	279	O-(3'-phospho-DNA)-tyrosine intermediate	1

GO - Molecular functionⁱ

DNA binding Source: UniProtKB-KW
site-specific recombinase activity
Source: EcoliWiki
Inferred from direct assayⁱ
- 11114887
- 8402918
tyrosine-based site-specific recombinase activity
Source: EcoliWiki
Inferred from mutant phenotypeⁱ
- 8402918

View the complete GO annotation on QuickGO ...

GO - Biological processⁱ

cell cycle Source: UniProtKB-KW
cell division Source: UniProtKB-KW
chromosome segregation Source: UniProtKB-KW
plasmid maintenance
Source: EcoliWiki
Inferred from mutant phenotypeⁱ
- 8195072
resolution of recombination intermediates
Source: EcoliWiki
Inferred from direct assayⁱ
- 7746851
response to radiation
Source: EcoCyc
Inferred from mutant phenotypeⁱ
- 27718375

View the complete GO annotation on QuickGO ...

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

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	cellular organisms › Bacteria › Proteobacteria › Gammaproteobacteria › Enterobacterales › Enterobacteriaceae › Escherichia › Escherichia coli
Proteomesⁱ	UP000000318 Componentⁱ: Chromosome UP000000625 Componentⁱ: Chromosome

Organism-specific databases

EcoGeneⁱ	EG11071 xerD

EcoGeneⁱ

EG11071 xerD

Subcellular locationⁱ

Cytoplasm By similarity

GO - Cellular componentⁱ

cytoplasm Source: UniProtKB-SubCell
Holliday junction resolvase complex
Source: EcoliWiki
Inferred from direct assayⁱ
- 11114887
- 7746851

View the complete GO annotation on QuickGO ...

Keywords - Cellular componentⁱ

Cytoplasm

Pathology & Biotechⁱ

Mutagenesis

Feature key	Position(s)	DescriptionActions	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 Publication

Protein-protein interaction databases

BioGridⁱ	4262339, 485 interactors
Database of interacting proteins More...DIPⁱ	DIP-48125N
IntActⁱ	P0A8P8, 7 interactors
STRINGⁱ	316385.ECDH10B_3068

Structureⁱ

Secondary structure

Legend: HelixTurnBeta strandPDB Structure known for this area

Feature key	Position(s)	DescriptionActions	Length
Helixⁱ	4 – 17	Combined sources	14
Helixⁱ	23 – 42	Combined sources	20
Turnⁱ	47 – 49	Combined sources	3
Helixⁱ	52 – 60	Combined sources	9
Helixⁱ	72 – 88	Combined sources	17
Beta strandⁱ	91 – 94	Combined sources	4
Helixⁱ	115 – 123	Combined sources	9
Helixⁱ	130 – 145	Combined sources	16
Helixⁱ	149 – 152	Combined sources	4
Helixⁱ	157 – 159	Combined sources	3
Turnⁱ	162 – 165	Combined sources	4
Beta strandⁱ	166 – 170	Combined sources	5
Beta strandⁱ	172 – 174	Combined sources	3
Beta strandⁱ	176 – 180	Combined sources	5
Helixⁱ	183 – 195	Combined sources	13
Helixⁱ	197 – 201	Combined sources	5
Beta strandⁱ	208 – 211	Combined sources	4
Beta strandⁱ	215 – 217	Combined sources	3
Helixⁱ	220 – 233	Combined sources	14
Helixⁱ	238 – 240	Combined sources	3
Helixⁱ	243 – 257	Combined sources	15
Helixⁱ	262 – 264	Combined sources	3
Helixⁱ	275 – 291	Combined sources	17

Show more details

3D structure databases

ProteinModelPortalⁱ	P0A8P8
SMRⁱ	P0A8P8
ModBaseⁱ	Search...
MobiDBⁱ	Search...

Miscellaneous databases

EvolutionaryTraceⁱ	P0A8P8

EvolutionaryTraceⁱ

P0A8P8

Family & Domainsⁱ

Sequence similaritiesⁱ

Belongs to the 'phage' integrase family. XerD subfamily.Curated

Phylogenomic databases

eggNOGⁱ	ENOG4105C13 Bacteria COG4974 LUCA
HOGENOMⁱ	HOG000045296
InParanoidⁱ	P0A8P8
KEGG Orthology (KO) More...KOⁱ	K04763
OMAⁱ	TRQAFWY
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 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
SUPFAMⁱ	SSF56349 SSF56349, 1 hit
TIGRFAMsⁱ	TIGR02225 recomb_XerD, 1 hit

Sequenceⁱ

Sequence statusⁱ: Complete.

P0A8P8-1 [UniParc]FASTA Add 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
PIRⁱ	A39202
NCBI Reference Sequences More...RefSeqⁱ	NP_417370.1, NC_000913.3 WP_000806638.1, NZ_LN832404.1

Genome annotation databases

EnsemblBacteriaⁱ	AAC75932; AAC75932; b2894 BAE76959; BAE76959; BAE76959
GeneIDⁱ	947362
KEGGⁱ	ecj:JW2862 eco:b2894
PATRICⁱ	fig\|1411691.4.peg.3839

Protein	Similar proteins		Species	Score	Length	Source
P0A8P8	Tyrosine recombinase XerD		ECOL6		298	UniRef100_P0A8P9
Tyrosine recombinase XerD		Escherichia coli NCCP15648		298
Site-specific tyrosine recombinase XerD		Escherichia coli O145 str. RM9872		298
Tyrosine recombinase XerD		Klebsiella pneumoniae IS22		298
Tyrosine recombinase XerD		Escherichia coli D6-113.11		298
+146

Protein	Similar proteins		Species	Score	Length	Source
P0A8P8	Tyrosine recombinase XerD		ECO57		298	UniRef90_Q8X574
Tyrosine recombinase XerD		SALTI		298
Tyrosine recombinase XerD		SALTY		298
Tyrosine recombinase XerD		SHIFL		298
Tyrosine recombinase XerD		ECOL6		298
+791

Protein	Similar proteins		Species	Score	Length	Source
P0A8P8	Tyrosine recombinase XerD		ECO57		298	UniRef50_Q8X574
Tyrosine recombinase XerD		ECOL6		298
Tyrosine recombinase XerD		SALTI		298
Tyrosine recombinase XerD		SALTY		298
Tyrosine recombinase XerD		SHIFL		298
+1692

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:	September 12, 2018
	This is version 113 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, Complete proteome, Direct protein sequencing, Reference proteome

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UniProtKB - P0A8P8 (XERD_ECOLI)

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Tyrosine recombinase XerD

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<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

Sites

<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

Enzyme and pathway databases

<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

Organism-specific databases

<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

<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

<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

Proteomic databases

<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

Protein-protein interaction databases

<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

3D structure databases

Miscellaneous databases

<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

<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

Family and domain databases

Sequence databases

Genome annotation databases

<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 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

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Functionⁱ

GO - Molecular functionⁱ

GO - Biological processⁱ

Names & Taxonomyⁱ

Subcellular locationⁱ

GO - Cellular componentⁱ

Keywords - Cellular componentⁱ

Pathology & Biotechⁱ

PTM / Processingⁱ

Interactionⁱ

Structureⁱ

Family & Domainsⁱ

Sequence similaritiesⁱ

Entry informationⁱ

Miscellaneousⁱ

Keywords - Technical termⁱ