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Escherichia coli K-12 substr. MG1655 Enzyme: exonuclease III



Gene: xthA Accession Numbers: EG11073 (EcoCyc), b1749, ECK1747

Synonyms: xth

Regulation Summary Diagram: ?

Summary:
Exonuclease III (XthA) is one of two 5' apurinic/apyrimidinic (AP) endonucleases (along with endonuclease IV) in Escherichia coli which function in the repair of DNA at sites where damaged bases have been removed by the activity of DNA glycosylases or where bases have been spontaneously lost.

AP endonucleases catalyze the incision of DNA exclusively at apurinic/apyrimidinic (AP) sites, preparing the DNA for subsequent excision, repair synthesis and DNA ligation. XthA has several other catalytic functions including 3'to 5' exonuclease with an associated phophatase activity, an RNase H-like activity, and a 3'-phosphodiesterase activity [Demple86]. XthA catalyzes the hydrolysis of double-stranded AP DNA 5' to the site of base loss resulting in 3'-OH and 5'-phosphate termini [Gossard78]. XthA recognizes AP sites based on the intercalation of Trp-212 into the DNA pocket formed at the AP site [Kaneda06].

XthA has been shown to be regulated by the katF gene product as katF deletion mutants show little measurable exonuclease III activity and are subsequently hypersensitive to H202 and near UV radiation damage to their DNA [Sak89].

Locations: cytosol

Map Position: [1,830,452 -> 1,831,258] (39.45 centisomes)
Length: 807 bp / 268 aa

Molecular Weight of Polypeptide: 30.969 kD (from nucleotide sequence)

Unification Links: ASAP:ABE-0005829 , CGSC:7 , DIP:DIP-11148N , EchoBASE:EB1066 , EcoGene:EG11073 , EcoliWiki:b1749 , Mint:MINT-1243969 , ModBase:P09030 , OU-Microarray:b1749 , PortEco:xthA , PR:PRO_000024239 , Pride:P09030 , Protein Model Portal:P09030 , RefSeq:NP_416263 , RegulonDB:EG11073 , SMR:P09030 , String:511145.b1749 , UniProt:P09030

Relationship Links: InterPro:IN-FAMILY:IPR004808 , InterPro:IN-FAMILY:IPR005135 , InterPro:IN-FAMILY:IPR020847 , InterPro:IN-FAMILY:IPR020848 , Panther:IN-FAMILY:PTHR22748 , PDB:Structure:1AKO , Pfam:IN-FAMILY:PF03372 , Prosite:IN-FAMILY:PS00726 , Prosite:IN-FAMILY:PS00727 , Prosite:IN-FAMILY:PS00728 , Prosite:IN-FAMILY:PS51435

Gene-Reaction Schematic: ?

GO Terms:

Biological Process: GO:0000738 - DNA catabolic process, exonucleolytic Inferred by computational analysis Inferred from experiment [Gossard78, Gaudet10, GOA01a]
GO:0006974 - cellular response to DNA damage stimulus Inferred from experiment Inferred by computational analysis [UniProtGOA11, Demple86]
GO:0090305 - nucleic acid phosphodiester bond hydrolysis Inferred by computational analysis Inferred from experiment [Demple86, UniProtGOA11, GOA01]
GO:0000737 - DNA catabolic process, endonucleolytic Inferred by computational analysis [Gaudet10]
GO:0006281 - DNA repair Inferred by computational analysis [UniProtGOA11, GOA01]
GO:0006284 - base-excision repair Inferred by computational analysis [Gaudet10]
Molecular Function: GO:0004527 - exonuclease activity Inferred from experiment Inferred by computational analysis [UniProtGOA11, Demple86]
GO:0008853 - exodeoxyribonuclease III activity Inferred from experiment Inferred by computational analysis [GOA01a, Gossard78]
GO:0003677 - DNA binding Inferred by computational analysis [GOA01]
GO:0003906 - DNA-(apurinic or apyrimidinic site) lyase activity Inferred by computational analysis [Gaudet10]
GO:0004518 - nuclease activity Inferred by computational analysis [UniProtGOA11, GOA01]
GO:0004519 - endonuclease activity Inferred by computational analysis [GOA01]
GO:0008311 - double-stranded DNA 3'-5' exodeoxyribonuclease activity Inferred by computational analysis [Gaudet10]
GO:0016787 - hydrolase activity Inferred by computational analysis [UniProtGOA11]
GO:0046872 - metal ion binding Inferred by computational analysis [UniProtGOA11]
Cellular Component: GO:0005829 - cytosol Inferred from experiment Inferred by computational analysis [DiazMejia09, Ishihama08, LopezCampistrou05]
GO:0005622 - intracellular Inferred by computational analysis [GOA01]

MultiFun Terms: cell processes protection radiation
information transfer DNA related DNA degradation
metabolism degradation of macromolecules DNA

Essentiality data for xthA 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]

Enzymatic reaction of: exodeoxyribonuclease III (exonuclease III)

EC Number: 3.1.11.2

(deoxynucleotides)(n) + H2O <=> (deoxynucleotides)(n-1) + a nucleoside 5'-monophosphate

The reaction direction shown, that is, A + B ↔ C + D versus C + D ↔ A + B, is in accordance with the Enzyme Commission system.

The reaction is physiologically favored in the direction shown.

T(opt): 22 °C [BRENDA14, Yang07c], 46 °C [BRENDA14, Hoheisel93]

pH(opt): 7.7 [BRENDA14, RICHARDSON64], 8 [BRENDA14, Yang07c]


Sequence Features

Feature Class Location Citations Comment
Metal-Binding-Site 34
[UniProt13]
UniProt: Magnesium 1; Non-Experimental Qualifier: by similarity.
Sequence-Conflict 49 -> 50
[Saporito88, UniProt10a]
Alternate sequence: KL → NV; UniProt: (in Ref. 1; AAA24767);
Active-Site 109
[UniProt13]
UniProt: Non-Experimental Qualifier: by similarity.
Metal-Binding-Site 151
[UniProt13]
UniProt: Magnesium 2; Non-Experimental Qualifier: by similarity.
Active-Site 151
[UniProt13]
UniProt: Proton donor/acceptor; Non-Experimental Qualifier: by similarity.
Metal-Binding-Site 153
[UniProt13]
UniProt: Magnesium 2; Non-Experimental Qualifier: by similarity.
Amino-Acid-Site 229
[UniProt13]
UniProt: Important for catalytic activity; Sequence Annotation Type: site; Non-Experimental Qualifier: by similarity.
Metal-Binding-Site 258
[UniProt13]
UniProt: Magnesium 1; Non-Experimental Qualifier: by similarity.
Amino-Acid-Site 259
[UniProt13]
UniProt: Interaction with DNA substrate; Sequence Annotation Type: site; Non-Experimental Qualifier: by similarity.


Gene Local Context (not to scale): ?

Transcription Unit:

Notes:

History:
10/20/97 Gene b1749 from Blattner lab Genbank (v. M52) entry merged into EcoCyc gene EG11073; confirmed by SwissProt match.


References

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." http://www.brenda-enzymes.org.

Demple86: Demple B, Johnson A, Fung D (1986). "Exonuclease III and endonuclease IV remove 3' blocks from DNA synthesis primers in H2O2-damaged Escherichia coli." Proc Natl Acad Sci U S A 83(20);7731-5. PMID: 2429316

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

Gaudet10: Gaudet P, Livstone M, Thomas P (2010). "Annotation inferences using phylogenetic trees." PMID: 19578431

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

GOA01a: GOA, MGI (2001). "Gene Ontology annotation based on Enzyme Commission mapping." Genomics 74;121-128.

Gossard78: Gossard F, Verly WG (1978). "Properties of the main endonuclease specific for apurinic sites of Escherichia coli (endonuclease VI). Mechanism of apurinic site excision from DNA." Eur J Biochem 82(2);321-32. PMID: 342234

Hoheisel93: Hoheisel JD (1993). "On the activities of Escherichia coli exonuclease III." Anal Biochem 209(2);238-46. PMID: 8470795

Ishihama08: Ishihama Y, Schmidt T, Rappsilber J, Mann M, Hartl FU, Kerner MJ, Frishman D (2008). "Protein abundance profiling of the Escherichia coli cytosol." BMC Genomics 9;102. PMID: 18304323

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

Kaneda06: Kaneda K, Sekiguchi J, Shida T (2006). "Role of the tryptophan residue in the vicinity of the catalytic center of exonuclease III family AP endonucleases: AP site recognition mechanism." Nucleic Acids Res 34(5);1552-63. PMID: 16540594

LopezCampistrou05: Lopez-Campistrous A, Semchuk P, Burke L, Palmer-Stone T, Brokx SJ, Broderick G, Bottorff D, Bolch S, Weiner JH, Ellison MJ (2005). "Localization, annotation, and comparison of the Escherichia coli K-12 proteome under two states of growth." Mol Cell Proteomics 4(8);1205-9. PMID: 15911532

RICHARDSON64: RICHARDSON CC, LEHMAN IR, KORNBERG A (1964). "A DEOXYRIBONUCLEIC ACID PHOSPHATASE-EXONUCLEASE FROM ESCHERICHIA COLI. II. CHARACTERIZATION OF THE EXONUCLEASE ACTIVITY." J Biol Chem 239;251-8. PMID: 14114851

Sak89: Sak BD, Eisenstark A, Touati D (1989). "Exonuclease III and the catalase hydroperoxidase II in Escherichia coli are both regulated by the katF gene product." Proc Natl Acad Sci U S A 86(9);3271-5. PMID: 2541439

Saporito88: Saporito SM, Smith-White BJ, Cunningham RP (1988). "Nucleotide sequence of the xth gene of Escherichia coli K-12." J Bacteriol 1988;170(10);4542-7. PMID: 3049539

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

UniProt13: UniProt Consortium (2013). "UniProt version 2013-08 released on 2013-08-01 00:00:00." Database.

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

Yang07c: Yang Z, Sismour AM, Benner SA (2007). "Nucleoside alpha-thiotriphosphates, polymerases and the exonuclease III analysis of oligonucleotides containing phosphorothioate linkages." Nucleic Acids Res 35(9);3118-27. PMID: 17452363


Report Errors or Provide Feedback
Please cite the following article in publications resulting from the use of EcoCyc: Nucleic Acids Research 41:D605-12 2013
Page generated by SRI International Pathway Tools version 18.5 on Mon Nov 24, 2014, BIOCYC13B.