Metabolic Modeling Tutorial
discounted EARLY registration ends Dec 31, 2014
Metabolic Modeling Tutorial
discounted EARLY registration ends Dec 31, 2014
Metabolic Modeling Tutorial
discounted EARLY registration ends Dec 31, 2014
Metabolic Modeling Tutorial
discounted EARLY registration ends Dec 31, 2014
Metabolic Modeling Tutorial
discounted EARLY registration ends Dec 31, 2014
twitter

Escherichia coli K-12 substr. MG1655 Polypeptide: excision nuclease subunit A



Gene: uvrA Accession Numbers: EG11061 (EcoCyc), b4058, ECK4050

Synonyms: dar, dinE

Regulation Summary Diagram: ?

Component of: UvrABC Nucleotide Excision Repair Complex (extended summary available)

Summary:
UvrA is a subunit of the UvrABC nucleotide excision repair (NER) generalized DNA repair process. UvrA forms homodimers in the presence of ATP [Sancar88], and at physiological concentrations UvrA associaties with UvrB to form a UvrA2B complex in an ATP-dependent interaction [Orren89]. UvrA binds DNA as a dimer with a strong preference for DNA ends [Wagner09a]. Regulation has been described [Van01a]. Transcription is induced by nalidixic acid [Van01a]. UvrA is one of a series of genes known as SOS genes which, in the event of DNA damage and other stresses, are induced to increased transcription levels.

uvrA insertion mutants were identified in a genetic screen for genes that are important for survival of exposure to ionizing radiation (IR). A uvrA deletion mutant has a substantial decrease in IR survival [Byrne14].

Gene Citations: [Kenyon81]

Locations: cytosol

Map Position: [4,269,072 <- 4,271,894] (92.01 centisomes)
Length: 2823 bp / 940 aa

Molecular Weight of Polypeptide: 103.87 kD (from nucleotide sequence)

Unification Links: ASAP:ABE-0013290 , CGSC:21 , DIP:DIP-35876N , EchoBASE:EB1054 , EcoGene:EG11061 , EcoliWiki:b4058 , Mint:MINT-1257037 , ModBase:P0A698 , OU-Microarray:b4058 , PortEco:uvrA , PR:PRO_000024198 , Pride:P0A698 , Protein Model Portal:P0A698 , RefSeq:NP_418482 , RegulonDB:EG11061 , SMR:P0A698 , String:511145.b4058 , UniProt:P0A698

Relationship Links: InterPro:IN-FAMILY:IPR003439 , InterPro:IN-FAMILY:IPR004602 , InterPro:IN-FAMILY:IPR013815 , InterPro:IN-FAMILY:IPR017871 , InterPro:IN-FAMILY:IPR027417 , PDB:Structure:4DFC , Pfam:IN-FAMILY:PF00005 , Prosite:IN-FAMILY:PS00211 , Prosite:IN-FAMILY:PS50893

Gene-Reaction Schematic: ?

Genetic Regulation Schematic: ?

GO Terms:

Biological Process: GO:0006200 - ATP catabolic process Inferred by computational analysis Inferred from experiment [Wagner09a, GOA01]
GO:0006281 - DNA repair Inferred from experiment Inferred by computational analysis [UniProtGOA11a, Lin89]
GO:0000737 - DNA catabolic process, endonucleolytic Inferred by computational analysis [GOA06, GOA01]
GO:0006289 - nucleotide-excision repair Inferred by computational analysis [GOA06, GOA01]
GO:0006974 - cellular response to DNA damage stimulus Inferred by computational analysis [UniProtGOA11a]
GO:0009432 - SOS response Inferred by computational analysis [UniProtGOA11a, GOA06]
GO:0090305 - nucleic acid phosphodiester bond hydrolysis Inferred by computational analysis [UniProtGOA11a]
Molecular Function: GO:0003677 - DNA binding Inferred from experiment Inferred by computational analysis [UniProtGOA11a, GOA06, Wagner09a]
GO:0005515 - protein binding Inferred from experiment [Deaconescu12]
GO:0016887 - ATPase activity Inferred from experiment Inferred by computational analysis [GOA01, Wagner09a]
GO:0000166 - nucleotide binding Inferred by computational analysis [UniProtGOA11a]
GO:0003824 - catalytic activity Inferred by computational analysis [GOA01]
GO:0004518 - nuclease activity Inferred by computational analysis [UniProtGOA11a]
GO:0005524 - ATP binding Inferred by computational analysis [UniProtGOA11a, GOA06, GOA01]
GO:0008270 - zinc ion binding Inferred by computational analysis [GOA06]
GO:0009381 - excinuclease ABC activity Inferred by computational analysis [GOA06, GOA01]
GO:0046872 - metal ion binding Inferred by computational analysis [UniProtGOA11a]
Cellular Component: GO:0005829 - cytosol Inferred from experiment Inferred by computational analysis [DiazMejia09, Ishihama08, Zhang07]
GO:0005737 - cytoplasm Inferred by computational analysis [UniProtGOA11, UniProtGOA11a, GOA06]
GO:0009380 - excinuclease repair complex Inferred by computational analysis [GOA01]

MultiFun Terms: cell processes protection radiation
cell processes SOS response
information transfer DNA related DNA repair

Essentiality data for uvrA 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: UvrABC Nucleotide Excision Repair Complex

Synonyms: excinuclease ABC, UvrABC excinuclease, excinuclease UvrABC, excision nuclease ABC, UvrABC system excision endonuclease, ABC excision nuclease

Subunit composition of UvrABC Nucleotide Excision Repair Complex = [UvrB][UvrC][UvrA]
         DNA repair; excision nuclease subunit B = UvrB (summary available)
         excinuclease ABC, subunit C; repair of UV damage to DNA = UvrC (summary available)
         excision nuclease subunit A = UvrA (summary available)

Summary:
Nucleotide excision repair (NER) is a generalized DNA repair process which can repair a wide diversity of DNA lesion including UV-induced photoproducts (cyclobutane dimers, 6-4 photoproducts, thymine glycol), bulky adducts, apurininc/apyrimidinic (AP) sites and cross-links. While some of these are also repaired by other pathways, in most cases NER is the major pathway for their repair. The nucleotide excision repair pathway consists of the following steps: recognition of the damaged area; incision 3' and 5' to the damaged area; excision of the lesion-containing oligonucleotide; resynthesis of the excised strand and ligation to form a repaired duplex. The main constituents of the pathway are the products of the genes uvrA, uvrB and uvrC [Lin89].

Recognition of the damaged region is carried out in E. coli by UvrA which has been found to exist as a monomer in the absence of ATP but in the presence of ATP it forms homodimers [Sancar88]. The most stable dimer of UvrA contains a mixture of ADP and ATP which is formed upon hydrolysis [Wagner09a] although other studies have shown that UvrA dimerization is stimulated by ATP binding but not hydrolysis [Oh89]. UvrA contains two ATP binding sites and three other structural motifs-- two zinc fingers and a helix-turn-helix motif, which are thought to be required for the proper recognition of damaged DNA substrate [Wang93e]. UvrA binds DNA as a dimer with a strong preference for DNA ends [Wagner09a].

In vitro studies at physiological concentrations show that UvrA associates with UvrB to form a (UvrA2)UvrB complex in an ATP-dependent interaction [Orren89]. The complex has been shown to have a higher binding affinity for damaged DNA than for undamaged DNA [Sancar88]. Purification studies of the complex binding characteristics [Oh86] suggest that the UvrA2B complex tracks along the DNA until a damage site is located. Experimental evidence [Zou99] strongly suggests that UvrA2B complex possesses a helicase activity allowing it to unwind the double stranded DNA permitting access to the adduct by UvrB resulting in dynamic damage recognition and subsequent UvrB binding.

UvrC protein has a high affinity for the UvrB-DNA complex (the UvrA subunits having dissociated concomitant with damage site recognition and attachment). The UvrC protein is the endonucleolytic component of the nucleotide excision complex and it consists of two functional parts with the N-terminal half containing the 3' incision catalytic domain incising first after which the C-terminal half containing the 5' incision catalytic domain performs the second incision [Sancar88]. The UvrD helicase (helicase II) has been implicated in removal of the lesion-containing oligonucleotide and disassembly of the repair complex [Orren92]. An additional endonuclease (the ydjQ gene product-or Cho for UvrC Homologue) has been shown to share significant sequence homology with the N-terminal half of UvrC [Moolenaar02] and is capable of even more efficient 3' incision than UvrC.

In E. coli, NER occurs at a higher rate on the transcribed strand of actively transcribed genes (compared to the non-transcribed strand of the same gene or non-transcribed regions of the genome). This transcription-coupled repair (TCR) activity has been ascribed to a protein called the 'transcription-repair coupling factor' which in E.coli is the product of the mfd (mutation frequency decline) gene [Selby93a]. A second pathway for TCR, involving the DNA helicase protein UvrD has also been characterised in E. coli K-12. In this pathway UvrD, in conjuction with NusA, clears lesions by forcing obstructed elongation complexes to backtrack, allowing UvrABC to gain access to damaged sites [Epshtein14]. UvrD mediated TCR facilitates NER without the loss of RNA polymerase which enables prompt resumption of transcription [Epshtein14].

UvrA is one of a series of genes known as SOS genes which, in the event of DNA damage and other stresses, are induced to increased transcription levels. UvrA is constitutively expressed in E. coli at a level of ~ 25 molecules per cell but SOS-mediated induction of its gene increases the level to ~ 250 molecules per cell. UvrB and UvrD are also inducible by DNA damage. UvrC is not induced in the SOS response, however its homolog, Cho, is.

Reviews: [Van94b, Spivak14]
Comment: [Artsimovitch14]


Enzymatic reaction of: Nucleotide excision repair (UvrABC Nucleotide Excision Repair Complex)

Synonyms: excinuclease, excision endonuclease, excision nuclease

EC Number: 3.1.25.-

DNA with lesion + H2O <=> DNA without lesion

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.


Sequence Features

Feature Class Location Citations Comment
Nucleotide-Phosphate-Binding-Region 31 -> 38
[UniProt10]
UniProt: ATP;
Mutagenesis-Variant 253
[Navaratnam89, UniProt11]
Alternate sequence: C → S; UniProt: Reduced activity.
Alternate sequence: C → H; UniProt: Reduced activity.
Alternate sequence: C → A; UniProt: Reduced activity.
Zn-Finger-Region 253 -> 280
[UniProt10]
UniProt: C4-type;
Conserved-Region 310 -> 587
[UniProt09]
UniProt: ABC transporter 1;
Conserved-Region 607 -> 937
[UniProt09]
UniProt: ABC transporter 2;
Nucleotide-Phosphate-Binding-Region 640 -> 647
[UniProt10]
UniProt: ATP;
Zn-Finger-Region 740 -> 766
[UniProt10]
UniProt: C4-type;


Gene Local Context (not to scale): ?

Transcription Units:

Notes:

History:
10/20/97 Gene b4058 from Blattner lab Genbank (v. M52) entry merged into EcoCyc gene EG11061; confirmed by SwissProt match.


References

Artsimovitch14: Artsimovitch I (2014). "Molecular biology: The tug of DNA repair." Nature 505(7483);298-9. PMID: 24402229

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

Byrne14: Byrne RT, Chen SH, Wood EA, Cabot EL, Cox MM (2014). "Surviving extreme exposure to ionizing radiation: Escherichia coli genes and pathways." J Bacteriol. PMID: 25049088

Deaconescu12: Deaconescu AM, Sevostyanova A, Artsimovitch I, Grigorieff N (2012). "Nucleotide excision repair (NER) machinery recruitment by the transcription-repair coupling factor involves unmasking of a conserved intramolecular interface." Proc Natl Acad Sci U S A 109(9);3353-8. PMID: 22331906

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

Epshtein14: Epshtein V, Kamarthapu V, McGary K, Svetlov V, Ueberheide B, Proshkin S, Mironov A, Nudler E (2014). "UvrD facilitates DNA repair by pulling RNA polymerase backwards." Nature 505(7483);372-7. PMID: 24402227

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."

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

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

Kenyon81: Kenyon CJ, Walker GC (1981). "Expression of the E. coli uvrA gene is inducible." Nature 1981;289(5800);808-10. PMID: 6780917

Lin89: Lin JJ, Sancar A (1989). "A new mechanism for repairing oxidative damage to DNA: (A)BC excinuclease removes AP sites and thymine glycols from DNA." Biochemistry 28(20);7979-84. PMID: 2690930

Moolenaar02: Moolenaar GF, van Rossum-Fikkert S, van Kesteren M, Goosen N (2002). "Cho, a second endonuclease involved in Escherichia coli nucleotide excision repair." Proc Natl Acad Sci U S A 99(3);1467-72. PMID: 11818552

Navaratnam89: Navaratnam S, Myles GM, Strange RW, Sancar A (1989). "Evidence from extended X-ray absorption fine structure and site-specific mutagenesis for zinc fingers in UvrA protein of Escherichia coli." J Biol Chem 264(27);16067-71. PMID: 2550431

Oh86: Oh EY, Grossman L (1986). "The effect of Escherichia coli Uvr protein binding on the topology of supercoiled DNA." Nucleic Acids Res 14(21);8557-71. PMID: 3024109

Oh89: Oh EY, Claassen L, Thiagalingam S, Mazur S, Grossman L (1989). "ATPase activity of the UvrA and UvrAB protein complexes of the Escherichia coli UvrABC endonuclease." Nucleic Acids Res 17(11);4145-59. PMID: 2525700

Orren89: Orren DK, Sancar A (1989). "The (A)BC excinuclease of Escherichia coli has only the UvrB and UvrC subunits in the incision complex." Proc Natl Acad Sci U S A 86(14);5237-41. PMID: 2546148

Orren92: Orren DK, Selby CP, Hearst JE, Sancar A (1992). "Post-incision steps of nucleotide excision repair in Escherichia coli. Disassembly of the UvrBC-DNA complex by helicase II and DNA polymerase I." J Biol Chem 267(2);780-8. PMID: 1530937

Sancar88: Sancar A, Sancar GB (1988). "DNA repair enzymes." Annu Rev Biochem 57;29-67. PMID: 3052275

Selby93a: Selby CP, Sancar A (1993). "Transcription-repair coupling and mutation frequency decline." J Bacteriol 175(23);7509-14. PMID: 8244919

Spivak14: Spivak G, Ganesan AK (2014). "The complex choreography of transcription-coupled repair." DNA Repair (Amst). PMID: 24751236

UniProt09: UniProt Consortium (2009). "UniProt version 15.8 released on 2009-10-01 00:00:00." Database.

UniProt10: UniProt Consortium (2010). "UniProt version 2010-11 released on 2010-11-02 00:00:00." Database.

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

Van01a: Van Dyk TK, DeRose EJ, Gonye GE (2001). "LuxArray, a high-density, genomewide transcription analysis of Escherichia coli using bioluminescent reporter strains." J Bacteriol 183(19);5496-505. PMID: 11544210

Van94b: Van Houten B, McCullough A (1994). "Nucleotide excision repair in E. coli." Ann N Y Acad Sci 726;236-51. PMID: 8092680

Wagner09a: Wagner K, Moolenaar G, van Noort J, Goosen N (2009). "Single-molecule analysis reveals two separate DNA-binding domains in the Escherichia coli UvrA dimer." Nucleic Acids Res 37(6);1962-72. PMID: 19208636

Wang93e: Wang J, Grossman L (1993). "Mutations in the helix-turn-helix motif of the Escherichia coli UvrA protein eliminate its specificity for UV-damaged DNA." J Biol Chem 268(7);5323-31. PMID: 8444906

Zhang07: Zhang N, Chen R, Young N, Wishart D, Winter P, Weiner JH, Li L (2007). "Comparison of SDS- and methanol-assisted protein solubilization and digestion methods for Escherichia coli membrane proteome analysis by 2-D LC-MS/MS." Proteomics 7(4);484-93. PMID: 17309111

Zou99: Zou Y, Van Houten B (1999). "Strand opening by the UvrA(2)B complex allows dynamic recognition of DNA damage." EMBO J 18(17);4889-901. PMID: 10469667

Other References Related to Gene Regulation

Brandsma85: Brandsma JA, Bosch D, de Ruyter M, van de Putte P (1985). "Analysis of the regulatory region of the ssb gene of Escherichia coli." Nucleic Acids Res 1985;13(14);5095-109. PMID: 2991853

Ogasawara05: Ogasawara H, Teramoto J, Yamamoto S, Hirao K, Yamamoto K, Ishihama A, Utsumi R (2005). "Negative regulation of DNA repair gene (uvrA) expression by ArcA/ArcB two-component system in Escherichia coli." FEMS Microbiol Lett 251(2);243-9. PMID: 16140472

Sancar82: Sancar A, Sancar GB, Rupp WD, Little JW, Mount DW (1982). "LexA protein inhibits transcription of the E. coli uvrA gene in vitro." Nature 1982;298(5869);96-8. PMID: 6283374


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 Thu Dec 18, 2014, biocyc13.