XERD_ECOLI
ID XERD_ECOLI Reviewed; 298 AA.
AC P0A8P8; P21891; Q2M9U7;
DT 07-JUN-2005, integrated into UniProtKB/Swiss-Prot.
DT 07-JUN-2005, sequence version 1.
DT 03-AUG-2022, entry version 134.
DE RecName: Full=Tyrosine recombinase XerD;
GN Name=xerD; Synonyms=xprB; OrderedLocusNames=b2894, JW2862;
OS Escherichia coli (strain K12).
OC Bacteria; Proteobacteria; Gammaproteobacteria; Enterobacterales;
OC Enterobacteriaceae; Escherichia.
OX NCBI_TaxID=83333;
RN [1]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA].
RC STRAIN=K12;
RX PubMed=1987126; DOI=10.1128/jb.173.1.353-364.1991;
RA Lovett S.T., Kolodner R.D.;
RT "Nucleotide sequence of the Escherichia coli recJ chromosomal region and
RT construction of recJ-overexpression plasmids.";
RL J. Bacteriol. 173:353-364(1991).
RN [2]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=K12 / MG1655 / ATCC 47076;
RX PubMed=9278503; DOI=10.1126/science.277.5331.1453;
RA Blattner F.R., Plunkett G. III, Bloch C.A., Perna N.T., Burland V.,
RA Riley M., Collado-Vides J., Glasner J.D., Rode C.K., Mayhew G.F.,
RA Gregor J., Davis N.W., Kirkpatrick H.A., Goeden M.A., Rose D.J., Mau B.,
RA Shao Y.;
RT "The complete genome sequence of Escherichia coli K-12.";
RL Science 277:1453-1462(1997).
RN [3]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=K12 / W3110 / ATCC 27325 / DSM 5911;
RX PubMed=16738553; DOI=10.1038/msb4100049;
RA Hayashi K., Morooka N., Yamamoto Y., Fujita K., Isono K., Choi S.,
RA Ohtsubo E., Baba T., Wanner B.L., Mori H., Horiuchi T.;
RT "Highly accurate genome sequences of Escherichia coli K-12 strains MG1655
RT and W3110.";
RL Mol. Syst. Biol. 2:E1-E5(2006).
RN [4]
RP PROTEIN SEQUENCE OF 1-29, CHARACTERIZATION, AND MUTAGENESIS OF ARG-247.
RC STRAIN=K12 / DS941;
RX PubMed=8402918; DOI=10.1016/0092-8674(93)80076-q;
RA Blakely G., May G., McCulloch R., Arciszewska L.K., Burke M., Lovett S.T.,
RA Sherratt D.J.;
RT "Two related recombinases are required for site-specific recombination at
RT dif and cer in E. coli K12.";
RL Cell 75:351-361(1993).
RN [5]
RP FUNCTION, AND MUTAGENESIS OF TYR-279.
RC STRAIN=K12 / DS941;
RX PubMed=7744017; DOI=10.1002/j.1460-2075.1995.tb07203.x;
RA Arciszewska L.K., Sherratt D.J.;
RT "Xer site-specific recombination in vitro.";
RL EMBO J. 14:2112-2120(1995).
RN [6]
RP FUNCTION, AND MUTAGENESIS OF ARG-148; HIS-244; ARG-247 AND TYR-279.
RX PubMed=9268326; DOI=10.1074/jbc.272.35.21927;
RA Cornet F., Hallet B., Sherratt D.J.;
RT "Xer recombination in Escherichia coli. Site-specific DNA topoisomerase
RT activity of the XerC and XerD recombinases.";
RL J. Biol. Chem. 272:21927-21931(1997).
RN [7]
RP INTERACTION WITH XERC, AND MUTAGENESIS OF HIS-294; HIS-295; ARG-297 AND
RP ALA-298.
RC STRAIN=K12 / DS941;
RX PubMed=10361305; DOI=10.1046/j.1365-2958.1999.01418.x;
RA Spiers A.J., Sherratt D.J.;
RT "C-terminal interactions between the XerC and XerD site-specific
RT recombinases.";
RL Mol. Microbiol. 32:1031-1042(1999).
RN [8]
RP ACTIVITY REGULATION, AND MUTAGENESIS OF 256-ASN--GLY-258.
RC STRAIN=K12 / DS941;
RX PubMed=10635320; DOI=10.1016/s1097-2765(00)80224-5;
RA Hallet B., Arciszewska L.K., Sherratt D.J.;
RT "Reciprocal control of catalysis by the tyrosine recombinases XerC and
RT XerD: an enzymatic switch in site-specific recombination.";
RL Mol. Cell 4:949-959(1999).
RN [9]
RP ACTIVITY REGULATION BY FTSK.
RX PubMed=11832210; DOI=10.1016/s0092-8674(02)00624-4;
RA Aussel L., Barre F.-X., Aroyo M., Stasiak A., Stasiak A.Z., Sherratt D.J.;
RT "FtsK is a DNA motor protein that activates chromosome dimer resolution by
RT switching the catalytic state of the XerC and XerD recombinases.";
RL Cell 108:195-205(2002).
RN [10]
RP X-RAY CRYSTALLOGRAPHY (2.5 ANGSTROMS).
RX PubMed=9311978; DOI=10.1093/emboj/16.17.5178;
RA Subramanya H.S., Arciszewska L.K., Baker R.A., Bird L.E., Sherratt D.J.,
RA Wigley D.B.;
RT "Crystal structure of the site-specific recombinase, XerD.";
RL EMBO J. 16:5178-5187(1997).
CC -!- FUNCTION: Site-specific tyrosine recombinase, which acts by catalyzing
CC the cutting and rejoining of the recombining DNA molecules. Binds
CC cooperatively to specific DNA consensus sequences that are separated
CC from XerC binding sites by a short central region, forming the
CC heterotetrameric XerC-XerD complex that recombines DNA substrates. The
CC complex is essential to convert dimers of the bacterial chromosome into
CC monomers to permit their segregation at cell division. It also
CC contributes to the segregational stability of plasmids at ColE1 xer (or
CC cer) and pSC101 (or psi) sites. In the complex XerD specifically
CC exchanges the bottom DNA strands (By similarity). {ECO:0000250,
CC ECO:0000269|PubMed:7744017, ECO:0000269|PubMed:9268326}.
CC -!- ACTIVITY REGULATION: During recombination, the heterotetrameric complex
CC catalyzes two consecutive pairs of strand exchanges, implying that
CC specific pairs of active sites are sequentially switched on and off in
CC the recombinase tetramer to ensure that appropriate DNA strands will be
CC exchanged at both reaction steps. FtsK plays a central role in this
CC catalytic state switch that turns recombinase on and off reciprocally.
CC The reciprocal C-terminal interaction between XerC and XerD may also
CC participate in the enzymatic switch process.
CC {ECO:0000269|PubMed:10635320, ECO:0000269|PubMed:11832210}.
CC -!- SUBUNIT: Forms a cyclic heterotetrameric complex composed of two
CC molecules of XerC and two molecules of XerD, in which XerC interacts
CC with XerD via its C-terminal region, XerD interacts with XerC via its
CC C-terminal region and so on. {ECO:0000269|PubMed:10361305}.
CC -!- SUBCELLULAR LOCATION: Cytoplasm {ECO:0000250}.
CC -!- SIMILARITY: Belongs to the 'phage' integrase family. XerD subfamily.
CC {ECO:0000305}.
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DR EMBL; M54884; AAA62787.1; -; Genomic_DNA.
DR EMBL; U28375; AAA83075.1; -; Genomic_DNA.
DR EMBL; U00096; AAC75932.1; -; Genomic_DNA.
DR EMBL; AP009048; BAE76959.1; -; Genomic_DNA.
DR PIR; A39202; A39202.
DR RefSeq; NP_417370.1; NC_000913.3.
DR RefSeq; WP_000806638.1; NZ_STEB01000001.1.
DR PDB; 1A0P; X-ray; 2.50 A; A=3-292.
DR PDBsum; 1A0P; -.
DR AlphaFoldDB; P0A8P8; -.
DR SMR; P0A8P8; -.
DR BioGRID; 4262339; 485.
DR BioGRID; 851685; 2.
DR ComplexPortal; CPX-5123; XerCD site-specific tyrosine recombinase complex.
DR DIP; DIP-48125N; -.
DR IntAct; P0A8P8; 7.
DR STRING; 511145.b2894; -.
DR PaxDb; P0A8P8; -.
DR PRIDE; P0A8P8; -.
DR EnsemblBacteria; AAC75932; AAC75932; b2894.
DR EnsemblBacteria; BAE76959; BAE76959; BAE76959.
DR GeneID; 66673232; -.
DR GeneID; 947362; -.
DR KEGG; ecj:JW2862; -.
DR KEGG; eco:b2894; -.
DR PATRIC; fig|1411691.4.peg.3839; -.
DR EchoBASE; EB1064; -.
DR eggNOG; COG4974; Bacteria.
DR HOGENOM; CLU_027562_9_0_6; -.
DR InParanoid; P0A8P8; -.
DR OMA; QAFWYLI; -.
DR PhylomeDB; P0A8P8; -.
DR BioCyc; EcoCyc:EG11071-MON; -.
DR EvolutionaryTrace; P0A8P8; -.
DR PRO; PR:P0A8P8; -.
DR Proteomes; UP000000318; Chromosome.
DR Proteomes; UP000000625; Chromosome.
DR GO; GO:0005737; C:cytoplasm; IEA:UniProtKB-SubCell.
DR GO; GO:0048476; C:Holliday junction resolvase complex; IDA:ComplexPortal.
DR GO; GO:0003677; F:DNA binding; IDA:EcoliWiki.
DR GO; GO:0009009; F:site-specific recombinase activity; IDA:EcoliWiki.
DR GO; GO:0009037; F:tyrosine-based site-specific recombinase activity; IMP:EcoliWiki.
DR GO; GO:0007049; P:cell cycle; IEA:UniProtKB-KW.
DR GO; GO:0051301; P:cell division; IEA:UniProtKB-KW.
DR GO; GO:0007059; P:chromosome segregation; IDA:ComplexPortal.
DR GO; GO:0006276; P:plasmid maintenance; IMP:EcoliWiki.
DR GO; GO:0071139; P:resolution of recombination intermediates; IDA:ComplexPortal.
DR GO; GO:0009314; P:response to radiation; IMP:EcoCyc.
DR GO; GO:0006313; P:transposition, DNA-mediated; IEA:UniProtKB-UniRule.
DR Gene3D; 1.10.150.130; -; 1.
DR Gene3D; 1.10.443.10; -; 1.
DR HAMAP; MF_01808; Recomb_XerC_XerD; 1.
DR HAMAP; MF_01807; Recomb_XerD; 1.
DR InterPro; IPR044068; CB.
DR InterPro; IPR011010; DNA_brk_join_enz.
DR InterPro; IPR013762; Integrase-like_cat_sf.
DR InterPro; IPR002104; Integrase_catalytic.
DR InterPro; IPR010998; Integrase_recombinase_N.
DR InterPro; IPR004107; Integrase_SAM-like_N.
DR InterPro; IPR011932; Recomb_XerD.
DR InterPro; IPR023009; Tyrosine_recombinase_XerC/XerD.
DR Pfam; PF02899; Phage_int_SAM_1; 1.
DR Pfam; PF00589; Phage_integrase; 1.
DR SUPFAM; SSF56349; SSF56349; 1.
DR TIGRFAMs; TIGR02225; recomb_XerD; 1.
DR PROSITE; PS51900; CB; 1.
DR PROSITE; PS51898; TYR_RECOMBINASE; 1.
PE 1: Evidence at protein level;
KW 3D-structure; Cell cycle; Cell division; Chromosome partition; Cytoplasm;
KW Direct protein sequencing; DNA integration; DNA recombination; DNA-binding;
KW Reference proteome.
FT CHAIN 1..298
FT /note="Tyrosine recombinase XerD"
FT /id="PRO_0000095386"
FT DOMAIN 2..87
FT /note="Core-binding (CB)"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU01248"
FT DOMAIN 108..292
FT /note="Tyr recombinase"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU01246"
FT ACT_SITE 148
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU01246"
FT ACT_SITE 172
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU01246"
FT ACT_SITE 244
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU01246"
FT ACT_SITE 247
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU01246"
FT ACT_SITE 270
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU01246"
FT ACT_SITE 279
FT /note="O-(3'-phospho-DNA)-tyrosine intermediate"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU01246"
FT MUTAGEN 148
FT /note="R->K: Abolishes DNA cleavage activity."
FT /evidence="ECO:0000269|PubMed:9268326"
FT MUTAGEN 244
FT /note="H->L: Abolishes DNA religation activity."
FT /evidence="ECO:0000269|PubMed:9268326"
FT MUTAGEN 247
FT /note="R->Q: Abolishes DNA cleavage activity."
FT /evidence="ECO:0000269|PubMed:8402918,
FT ECO:0000269|PubMed:9268326"
FT MUTAGEN 256..258
FT /note="NHG->ESS: Abolishes plasmid resolution but not
FT chromosomal recombination."
FT /evidence="ECO:0000269|PubMed:10635320"
FT MUTAGEN 279
FT /note="Y->F: Abolishes DNA cleavage activity."
FT /evidence="ECO:0000269|PubMed:7744017,
FT ECO:0000269|PubMed:9268326"
FT MUTAGEN 294
FT /note="H->Q,E: Abolishes DNA recombination (in vitro)."
FT /evidence="ECO:0000269|PubMed:10361305"
FT MUTAGEN 295
FT /note="H->E: Abolishes DNA recombination (in vitro)."
FT /evidence="ECO:0000269|PubMed:10361305"
FT MUTAGEN 297
FT /note="R->E: Abolishes DNA recombination (in vitro)."
FT /evidence="ECO:0000269|PubMed:10361305"
FT MUTAGEN 298
FT /note="A->Q: Reduces chromosomal recombination but not
FT plasmid resolution."
FT /evidence="ECO:0000269|PubMed:10361305"
FT HELIX 4..17
FT /evidence="ECO:0007829|PDB:1A0P"
FT HELIX 23..42
FT /evidence="ECO:0007829|PDB:1A0P"
FT TURN 47..49
FT /evidence="ECO:0007829|PDB:1A0P"
FT HELIX 52..60
FT /evidence="ECO:0007829|PDB:1A0P"
FT HELIX 72..88
FT /evidence="ECO:0007829|PDB:1A0P"
FT STRAND 91..94
FT /evidence="ECO:0007829|PDB:1A0P"
FT HELIX 115..123
FT /evidence="ECO:0007829|PDB:1A0P"
FT HELIX 130..145
FT /evidence="ECO:0007829|PDB:1A0P"
FT HELIX 149..152
FT /evidence="ECO:0007829|PDB:1A0P"
FT HELIX 157..159
FT /evidence="ECO:0007829|PDB:1A0P"
FT TURN 162..165
FT /evidence="ECO:0007829|PDB:1A0P"
FT STRAND 166..170
FT /evidence="ECO:0007829|PDB:1A0P"
FT STRAND 172..174
FT /evidence="ECO:0007829|PDB:1A0P"
FT STRAND 176..180
FT /evidence="ECO:0007829|PDB:1A0P"
FT HELIX 183..195
FT /evidence="ECO:0007829|PDB:1A0P"
FT HELIX 197..201
FT /evidence="ECO:0007829|PDB:1A0P"
FT STRAND 208..211
FT /evidence="ECO:0007829|PDB:1A0P"
FT STRAND 215..217
FT /evidence="ECO:0007829|PDB:1A0P"
FT HELIX 220..233
FT /evidence="ECO:0007829|PDB:1A0P"
FT HELIX 238..240
FT /evidence="ECO:0007829|PDB:1A0P"
FT HELIX 243..257
FT /evidence="ECO:0007829|PDB:1A0P"
FT HELIX 262..264
FT /evidence="ECO:0007829|PDB:1A0P"
FT HELIX 275..291
FT /evidence="ECO:0007829|PDB:1A0P"
SQ SEQUENCE 298 AA; 34246 MW; B75DD603BEEE03E9 CRC64;
MKQDLARIEQ FLDALWLEKN LAENTLNAYR RDLSMMVEWL HHRGLTLATA QSDDLQALLA
ERLEGGYKAT SSARLLSAVR RLFQYLYREK FREDDPSAHL ASPKLPQRLP KDLSEAQVER
LLQAPLIDQP LELRDKAMLE VLYATGLRVS ELVGLTMSDI SLRQGVVRVI GKGNKERLVP
LGEEAVYWLE TYLEHGRPWL LNGVSIDVLF PSQRAQQMTR QTFWHRIKHY AVLAGIDSEK
LSPHVLRHAF ATHLLNHGAD LRVVQMLLGH SDLSTTQIYT HVATERLRQL HQQHHPRA
