Escherichia coli K-12 substr. MG1655 Polypeptide: site-specific recombinase

Gene: xerD Accession Numbers: EG11071 (EcoCyc), b2894, ECK2889

Synonyms: xprB

Regulation Summary Diagram: ?

Regulation summary diagram for xerD

Component of: Xer site-specific recombination system (extended summary available)

XerD is part of the Xer site-specific recombination system [Blakely93].

Gene Citations: [Nonaka06]

Locations: cytosol

Map Position: [3,036,869 <- 3,037,765] (65.45 centisomes, 236°)
Length: 897 bp / 298 aa

Molecular Weight of Polypeptide: 34.246 kD (from nucleotide sequence)

Unification Links: ASAP:ABE-0009500 , CGSC:30201 , DIP:DIP-48125N , EchoBASE:EB1064 , EcoGene:EG11071 , EcoliWiki:b2894 , Mint:MINT-1282534 , ModBase:P0A8P8 , OU-Microarray:b2894 , PortEco:xerD , PR:PRO_000024235 , Pride:P0A8P8 , Protein Model Portal:P0A8P8 , RefSeq:NP_417370 , RegulonDB:EG11071 , SMR:P0A8P8 , String:511145.b2894 , UniProt:P0A8P8

Relationship Links: InterPro:IN-FAMILY:IPR002104 , InterPro:IN-FAMILY:IPR004107 , InterPro:IN-FAMILY:IPR010998 , InterPro:IN-FAMILY:IPR011010 , InterPro:IN-FAMILY:IPR011932 , InterPro:IN-FAMILY:IPR013762 , InterPro:IN-FAMILY:IPR023009 , InterPro:IN-FAMILY:IPR023109 , PDB:Structure:1A0P , Pfam:IN-FAMILY:PF00589 , Pfam:IN-FAMILY:PF02899

In Paralogous Gene Group: 470 (4 members)

Gene-Reaction Schematic: ?

Gene-Reaction Schematic

Genetic Regulation Schematic: ?

Genetic regulation schematic for xerD

GO Terms:

Biological Process: GO:0006276 - plasmid maintenance Inferred from experiment [Cornet94]
GO:0071139 - resolution of recombination intermediates Inferred from experiment [Sherratt95]
GO:0006310 - DNA recombination Inferred by computational analysis [UniProtGOA11, GOA01]
GO:0006313 - transposition, DNA-mediated Inferred by computational analysis [GOA06]
GO:0007049 - cell cycle Inferred by computational analysis [UniProtGOA11, GOA01]
GO:0007059 - chromosome segregation Inferred by computational analysis [UniProtGOA11, GOA06, GOA01]
GO:0015074 - DNA integration Inferred by computational analysis [UniProtGOA11, GOA01]
GO:0051301 - cell division Inferred by computational analysis [UniProtGOA11, GOA01]
Molecular Function: GO:0009009 - site-specific recombinase activity Inferred from experiment [Blakely93, Barre00]
GO:0009037 - tyrosine-based site-specific recombinase activity Inferred from experiment Inferred by computational analysis [GOA06, Blakely93]
GO:0003677 - DNA binding Inferred by computational analysis [UniProtGOA11, GOA01]
Cellular Component: GO:0048476 - Holliday junction resolvase complex Inferred from experiment [Sherratt95, Barre00]
GO:0005737 - cytoplasm Inferred by computational analysis [UniProtGOA11a, UniProtGOA11, GOA06]
GO:0005829 - cytosol Inferred by computational analysis [DiazMejia09]

MultiFun Terms: information transfer DNA related DNA recombination

Essentiality data for xerD knockouts: ?

Growth Medium Growth? T (°C) O2 pH Osm/L Growth Observations
LB Lennox Yes 37 Aerobic 7   Yes [Baba06, Comment 1]
M9 medium with 1% glycerol Yes 37 Aerobic 7.2 0.35 Yes [Joyce06, Comment 2]
MOPS medium with 0.4% glucose Yes 37 Aerobic 7.2 0.22 Yes [Baba06, Comment 1]

Subunit of: Xer site-specific recombination system

Subunit composition of Xer site-specific recombination system = [XerC][XerD]
         site-specific tyrosine recombinase = XerC (summary available)
         site-specific recombinase = XerD (summary available)

The Xer site-specific recombination system includes XerC and XerD, which are two lambda integrase family recombinases and are involved in converting chromosome dimers formed due to homologous recombination into monomers so that segregation of the chromosomes can occur during cell division. XerC and XerD act by binding cooperatively to different halves of a specific site called dif in the replication terminus and catalyze the recombination reactions required to separate the two chromosomes. XerC performs the first step in recombination creating a Holliday junction. XerD performs the second recombination step, separating the chromosomes. XerC and XerD activities require the C-terminal, cytoplasmic domain of FtsK.

Mutation of xerC, xerD, or dif resulted in a fraction of cells becoming filamentous and unable to divide, and having aberrant nucleoids [Blakely91, Kuempel91, Blakely93]. XerC and XerD act catalytically in recombination and bind cooperatively to different sides of the recombination site [Blakely93, Blakely94, Leslie95]. XerC is responsible for the exchange of the first pair of strands to create the Holliday junction intermediate [Arciszewska95]. XerC and XerD are required for site-specific recombination of plasmid ColE1 dimers at the cer site [Colloms90, Blakely93]. Recombination of the ColE1 plasmid at cer also requires two accessory proteins--ArgR and PepA [McCulloch94a]. The C-terminal portion of FtsK is required for XerC and XerD resolution of chromosome dimers at dif, though not for resolution of plasmid dimers at cer or psi [Steiner99, Recchia99]. A 62 amino acid fragment of FtsK interacts directly with XerD and stimulates substrate cleavage [Yates06].

Created 05-Apr-2006 by Johnson A , TIGR

Sequence Features

Protein sequence of site-specific recombinase with features indicated

Feature Class Location Citations Comment
Active-Site 148
Mutagenesis-Variant 148
[Cornet97, UniProt11]
UniProt: Abolishes DNA cleavage activity.
Active-Site 172
Active-Site 244
Mutagenesis-Variant 244
[Cornet97, UniProt11]
UniProt: Abolishes DNA religation activity.
Active-Site 247
Mutagenesis-Variant 247
[Cornet97, Blakely93, UniProt11]
UniProt: Abolishes DNA cleavage activity.
Mutagenesis-Variant 256 -> 258
[Hallet99, UniProt11]
UniProt: Abolishes plasmid resolution but not chromosomal recombination.
Active-Site 270
Active-Site 279
UniProt: O-(3'-phospho-DNA)-tyrosine intermediate.
Mutagenesis-Variant 279
[Cornet97, Arciszewska95, UniProt11]
UniProt: Abolishes DNA cleavage activity.
Mutagenesis-Variant 294
[Spiers99, UniProt11]
H → E or Q: Abolishes DNA recombination (in vitro).
Mutagenesis-Variant 295
[Spiers99, UniProt11]
UniProt: Abolishes DNA recombination (in vitro).
Mutagenesis-Variant 297
[Spiers99, UniProt11]
UniProt: Abolishes DNA recombination (in vitro).
Mutagenesis-Variant 298
[Spiers99, UniProt11]
UniProt: Reduces chromosomal recombination but not plasmid resolution.

Gene Local Context (not to scale): ?

Gene local context diagram

Transcription Units:

Transcription-unit diagram

Transcription-unit diagram

Transcription-unit diagram

Transcription-unit diagram

Transcription-unit diagram


10/20/97 Gene b2894 from Blattner lab Genbank (v. M52) entry merged into EcoCyc gene EG11071; confirmed by SwissProt match.


Arciszewska95: Arciszewska LK, Sherratt DJ (1995). "Xer site-specific recombination in vitro." EMBO J 14(9);2112-20. PMID: 7744017

Baba06: Baba T, Ara T, Hasegawa M, Takai Y, Okumura Y, Baba M, Datsenko KA, Tomita M, Wanner BL, Mori H (2006). "Construction of Escherichia coli K-12 in-frame, single-gene knockout mutants: the Keio collection." Mol Syst Biol 2;2006.0008. PMID: 16738554

Barre00: Barre FX, Aroyo M, Colloms SD, Helfrich A, Cornet F, Sherratt DJ (2000). "FtsK functions in the processing of a Holliday junction intermediate during bacterial chromosome segregation." Genes Dev 14(23);2976-88. PMID: 11114887

Blakely91: Blakely G, Colloms S, May G, Burke M, Sherratt D (1991). "Escherichia coli XerC recombinase is required for chromosomal segregation at cell division." New Biol 3(8);789-98. PMID: 1931824

Blakely93: Blakely G, May G, McCulloch R, Arciszewska LK, Burke M, Lovett ST, Sherratt DJ (1993). "Two related recombinases are required for site-specific recombination at dif and cer in E. coli K12." Cell 75(2);351-61. PMID: 8402918

Blakely94: Blakely GW, Sherratt DJ (1994). "Interactions of the site-specific recombinases XerC and XerD with the recombination site dif." Nucleic Acids Res 22(25);5613-20. PMID: 7838714

Colloms90: Colloms SD, Sykora P, Szatmari G, Sherratt DJ (1990). "Recombination at ColE1 cer requires the Escherichia coli xerC gene product, a member of the lambda integrase family of site-specific recombinases." J Bacteriol 172(12);6973-80. PMID: 2254268

Cornet94: Cornet F, Mortier I, Patte J, Louarn JM (1994). "Plasmid pSC101 harbors a recombination site, psi, which is able to resolve plasmid multimers and to substitute for the analogous chromosomal Escherichia coli site dif." J Bacteriol 176(11);3188-95. PMID: 8195072

Cornet97: Cornet F, Hallet B, Sherratt DJ (1997). "Xer recombination in Escherichia coli. Site-specific DNA topoisomerase activity of the XerC and XerD recombinases." J Biol Chem 272(35);21927-31. PMID: 9268326

DiazMejia09: Diaz-Mejia JJ, Babu M, Emili A (2009). "Computational and experimental approaches to chart the Escherichia coli cell-envelope-associated proteome and interactome." FEMS Microbiol Rev 33(1);66-97. PMID: 19054114

GOA01: GOA, DDB, FB, MGI, ZFIN (2001). "Gene Ontology annotation through association of InterPro records with GO terms."

GOA06: GOA, SIB (2006). "Electronic Gene Ontology annotations created by transferring manual GO annotations between orthologous microbial proteins."

Hallet99: Hallet B, Arciszewska LK, Sherratt DJ (1999). "Reciprocal control of catalysis by the tyrosine recombinases XerC and XerD: an enzymatic switch in site-specific recombination." Mol Cell 4(6);949-59. PMID: 10635320

Joyce06: Joyce AR, Reed JL, White A, Edwards R, Osterman A, Baba T, Mori H, Lesely SA, Palsson BO, Agarwalla S (2006). "Experimental and computational assessment of conditionally essential genes in Escherichia coli." J Bacteriol 188(23);8259-71. PMID: 17012394

Kuempel91: Kuempel PL, Henson JM, Dircks L, Tecklenburg M, Lim DF (1991). "dif, a recA-independent recombination site in the terminus region of the chromosome of Escherichia coli." New Biol 3(8);799-811. PMID: 1657123

Leslie95: Leslie NR, Sherratt DJ (1995). "Site-specific recombination in the replication terminus region of Escherichia coli: functional replacement of dif." EMBO J 14(7);1561-70. PMID: 7729430

McCulloch94a: McCulloch R, Coggins LW, Colloms SD, Sherratt DJ (1994). "Xer-mediated site-specific recombination at cer generates Holliday junctions in vivo." EMBO J 13(8);1844-55. PMID: 8168483

Nonaka06: Nonaka G, Blankschien M, Herman C, Gross CA, Rhodius VA (2006). "Regulon and promoter analysis of the E. coli heat-shock factor, sigma32, reveals a multifaceted cellular response to heat stress." Genes Dev 20(13);1776-89. PMID: 16818608

Recchia99: Recchia GD, Aroyo M, Wolf D, Blakely G, Sherratt DJ (1999). "FtsK-dependent and -independent pathways of Xer site-specific recombination." EMBO J 18(20);5724-34. PMID: 10523315

Sherratt95: Sherratt DJ, Arciszewska LK, Blakely G, Colloms S, Grant K, Leslie N, McCulloch R (1995). "Site-specific recombination and circular chromosome segregation." Philos Trans R Soc Lond B Biol Sci 347(1319);37-42. PMID: 7746851

Spiers99: Spiers AJ, Sherratt DJ (1999). "C-terminal interactions between the XerC and XerD site-specific recombinases." Mol Microbiol 32(5);1031-42. PMID: 10361305

Steiner99: Steiner W, Liu G, Donachie WD, Kuempel P (1999). "The cytoplasmic domain of FtsK protein is required for resolution of chromosome dimers." Mol Microbiol 31(2);579-83. PMID: 10027974

UniProt11: UniProt Consortium (2011). "UniProt version 2011-06 released on 2011-06-30 00:00:00." Database.

UniProt15: UniProt Consortium (2015). "UniProt version 2015-01 released on 2015-01-16 00:00:00." Database.

UniProtGOA11: UniProt-GOA (2011). "Gene Ontology annotation based on manual assignment of UniProtKB keywords in UniProtKB/Swiss-Prot entries."

UniProtGOA11a: UniProt-GOA (2011). "Gene Ontology annotation based on the manual assignment of UniProtKB Subcellular Location terms in UniProtKB/Swiss-Prot entries."

Yates06: Yates J, Zhekov I, Baker R, Eklund B, Sherratt DJ, Arciszewska LK (2006). "Dissection of a functional interaction between the DNA translocase, FtsK, and the XerD recombinase." Mol Microbiol 59(6);1754-66. PMID: 16553881

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Please cite the following article in publications resulting from the use of EcoCyc: Nucleic Acids Research 41:D605-12 2013
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