Escherichia coli K-12 substr. MG1655 Polypeptide: exonuclease VII, large subunit

Gene: xseA Accession Numbers: EG11072 (EcoCyc), b2509, ECK2505

Synonyms: xse

Regulation Summary Diagram: ?

Regulation summary diagram for xseA

Component of: exonuclease VII (extended summary available)

XseA is the large subunit of Exonuclease VII [Vales82].

Gene Citations: [Hutchings00]

Locations: cytosol

Map Position: [2,632,254 -> 2,633,624] (56.73 centisomes, 204°)
Length: 1371 bp / 456 aa

Molecular Weight of Polypeptide: 51.832 kD (from nucleotide sequence), 54 kD (experimental) [Vales82 ]

Unification Links: ASAP:ABE-0008263 , CGSC:6 , DIP:DIP-11146N , EchoBASE:EB1065 , EcoGene:EG11072 , EcoliWiki:b2509 , Mint:MINT-1272208 , OU-Microarray:b2509 , PortEco:xseA , PR:PRO_000024237 , Pride:P04994 , Protein Model Portal:P04994 , RefSeq:NP_417004 , RegulonDB:EG11072 , String:511145.b2509 , UniProt:P04994

Relationship Links: InterPro:IN-FAMILY:IPR003753 , InterPro:IN-FAMILY:IPR020579 , InterPro:IN-FAMILY:IPR025824 , Pfam:IN-FAMILY:PF02601 , Pfam:IN-FAMILY:PF13742

Gene-Reaction Schematic: ?

Gene-Reaction Schematic

Genetic Regulation Schematic: ?

Genetic regulation schematic for xseA

GO Terms:

Biological Process: GO:0006308 - DNA catabolic process Inferred by computational analysis [GOA01a]
GO:0090305 - nucleic acid phosphodiester bond hydrolysis Inferred by computational analysis [UniProtGOA11a]
Molecular Function: GO:0005515 - protein binding Inferred from experiment [Rajagopala14, Butland05]
GO:0003676 - nucleic acid binding Inferred by computational analysis [GOA01a]
GO:0004518 - nuclease activity Inferred by computational analysis [UniProtGOA11a]
GO:0004527 - exonuclease activity Inferred by computational analysis [UniProtGOA11a]
GO:0008855 - exodeoxyribonuclease VII activity Inferred by computational analysis [GOA06, GOA01, GOA01a]
GO:0016787 - hydrolase activity Inferred by computational analysis [UniProtGOA11a]
Cellular Component: GO:0005737 - cytoplasm Inferred by computational analysis [UniProtGOA11, UniProtGOA11a, GOA06]
GO:0005829 - cytosol Inferred by computational analysis [DiazMejia09]
GO:0009318 - exodeoxyribonuclease VII complex Inferred by computational analysis [GOA01a]

MultiFun Terms: information transfer DNA related DNA degradation
metabolism degradation of macromolecules DNA

Essentiality data for xseA knockouts: ?

Growth Medium Growth? T (°C) O2 pH Osm/L Growth Observations
LB enriched Yes 37 Aerobic 6.95   Yes [Gerdes03, Comment 1]
LB Lennox Yes 37 Aerobic 7   Yes [Baba06, Comment 2]
M9 medium with 1% glycerol Yes 37 Aerobic 7.2 0.35 Yes [Joyce06, Comment 3]
MOPS medium with 0.4% glucose Yes 37 Aerobic 7.2 0.22 Yes [Baba06, Comment 2]

Subunit of: exonuclease VII

Synonyms: ExoVII

Subunit composition of exonuclease VII = [XseA][XseB]4
         exonuclease VII, large subunit = XseA (summary available)
         exonuclease VII, small subunit = XseB (summary available)

Purified Exonuclease VII (ExoVII) has been shown to be specific for single-stranded, linear DNA or duplex DNA with single-stranded termini [Chase74]. ExoVII can initiate hydrolysis at either 5` or 3` ends of DNA with oligonucleotides generated as products [Chase74]. Large oligonucleotides are generated first, and these can be further degraded to smaller oligonucleotides [Chase74a]. ExoVII activity is ATP-independent [Chase74a]. ExoVII is also capable of excision of thymine dimers from duplex DNA after incision by an endonuclease specific for thymine dimers [Chase74a]. ExoVII activity remains high in the presence of EDTA, is increased by Mg2+, and is optimum at a pH of 7.9 in phosphate buffer [Chase74]. The friction coefficient of ExoVII suggests an asymmetric protein structure [Chase74].

Mutants deficient in RecJ, exonuclease I, and exonuclease VII are unusually sensitive to UV irradiation [Viswanathan99]. XseA mutants have increased frequency of recombination and sensitivity to nalidixic acid [Chase77] as well as reduced survivability at elevated temperatures in a polAex- background [Chase77a]. Exonuclease VII has been purified and was found to be composed of 1 subunit of XseA of 54 kDa and 4 subunits of XseB of 10.5 kDa [Vales82]. Overproduction of XseA reduced exonuclease VII acitivity [Chase86]. xseA transcription is repressed when the divergently transcribed guaBA is induced by the cyclic AMP receptor protein [Hutchings00].

Molecular Weight: 88 kD (experimental) [Chase74]

GO Terms:

Biological Process: GO:0000738 - DNA catabolic process, exonucleolytic Inferred from experiment [Chase74a]
Molecular Function: GO:0008297 - single-stranded DNA exodeoxyribonuclease activity Inferred from experiment [Chase74]

Enzymatic reaction of: exonuclease VII

EC Number:

a single stranded DNA + H2O <=> a ribonucleoside 5'-monophosphate + a single-stranded oligodeoxyribonucleotide

The reaction direction shown, that is, A + B ↔ C + D versus C + D ↔ A + B, is in accordance with the direction in which it was curated.

The reaction is physiologically favored in the direction shown.

T(opt): 37 °C [BRENDA14, Chase74]

pH(opt): 7.8 [BRENDA14, Chase74]

Sequence Features

Protein sequence of exonuclease VII, large subunit with features indicated

Feature Class Location Citations Comment
Sequence-Conflict 67
[Chase86, UniProt10a]
UniProt: (in Ref. 1; AAA24766);

Gene Local Context (not to scale): ?

Gene local context diagram

Transcription Units:

Transcription-unit diagram

Transcription-unit diagram


10/20/97 Gene b2509 from Blattner lab Genbank (v. M52) entry merged into EcoCyc gene EG11072; confirmed by SwissProt match.


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

BRENDA14: BRENDA team (2014). "Imported from BRENDA version existing on Aug 2014."

Butland05: Butland G, Peregrin-Alvarez JM, Li J, Yang W, Yang X, Canadien V, Starostine A, Richards D, Beattie B, Krogan N, Davey M, Parkinson J, Greenblatt J, Emili A (2005). "Interaction network containing conserved and essential protein complexes in Escherichia coli." Nature 433(7025);531-7. PMID: 15690043

Chase74: Chase JW, Richardson CC (1974). "Exonuclease VII of Escherichia coli. Purification and properties." J Biol Chem 249(14);4545-52. PMID: 4602029

Chase74a: Chase JW, Richardson CC (1974). "Exonuclease VII of Escherichia coli. Mechanism of action." J Biol Chem 249(14);4553-61. PMID: 4602030

Chase77: Chase JW, Richardson CC (1977). "Escherichia coli mutants deficient in exonuclease VII." J Bacteriol 129(2);934-47. PMID: 320198

Chase77a: Chase JW, Masker WE (1977). "Deoxyribonucleic acid repair in Escherichia coli mutants deficient in the 5'----3' exonuclease activity of deoxyribonucleic acid polymerase I and exonuclease VII." J Bacteriol 130(2);667-75. PMID: 400786

Chase86: Chase JW, Rabin BA, Murphy JB, Stone KL, Williams KR (1986). "Escherichia coli exonuclease VII. Cloning and sequencing of the gene encoding the large subunit (xseA)." J Biol Chem 261(32);14929-35. PMID: 3021756

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

Gerdes03: Gerdes SY, Scholle MD, Campbell JW, Balazsi G, Ravasz E, Daugherty MD, Somera AL, Kyrpides NC, Anderson I, Gelfand MS, Bhattacharya A, Kapatral V, D'Souza M, Baev MV, Grechkin Y, Mseeh F, Fonstein MY, Overbeek R, Barabasi AL, Oltvai ZN, Osterman AL (2003). "Experimental determination and system level analysis of essential genes in Escherichia coli MG1655." J Bacteriol 185(19);5673-84. PMID: 13129938

GOA01: GOA, MGI (2001). "Gene Ontology annotation based on Enzyme Commission mapping." Genomics 74;121-128.

GOA01a: 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."

Hutchings00: Hutchings MI, Drabble WT (2000). "Regulation of the divergent guaBA and xseA promoters of Escherichia coli by the cyclic AMP receptor protein." FEMS Microbiol Lett 187(2);115-22. PMID: 10856643

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

Rajagopala14: Rajagopala SV, Sikorski P, Kumar A, Mosca R, Vlasblom J, Arnold R, Franca-Koh J, Pakala SB, Phanse S, Ceol A, Hauser R, Siszler G, Wuchty S, Emili A, Babu M, Aloy P, Pieper R, Uetz P (2014). "The binary protein-protein interaction landscape of Escherichia coli." Nat Biotechnol 32(3);285-90. PMID: 24561554

UniProt10a: UniProt Consortium (2010). "UniProt version 2010-11 released on 2010-11-02 00:00:00." Database.

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

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

Vales82: Vales LD, Rabin BA, Chase JW (1982). "Subunit structure of Escherichia coli exonuclease VII." J Biol Chem 257(15);8799-805. PMID: 6284744

Viswanathan99: Viswanathan M, Lanjuin A, Lovett ST (1999). "Identification of RNase T as a high-copy suppressor of the UV sensitivity associated with single-strand DNA exonuclease deficiency in Escherichia coli." Genetics 151(3);929-34. PMID: 10049912

Other References Related to Gene Regulation

Davies96: Davies IJ, Drabble WT (1996). "Stringent and growth-rate-dependent control of the gua operon of Escherichia coli K-12." Microbiology 1996;142 ( Pt 9);2429-37. PMID: 8828209

Husnain09: Husnain SI, Busby SJ, Thomas MS (2009). "Downregulation of the Escherichia coli guaB promoter by upstream-bound cyclic AMP receptor protein." J Bacteriol 191(19);6094-104. PMID: 19633076

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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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