|Gene:||tatD||Accession Numbers: EG11481 (EcoCyc), b4483, ECK3833|
Synonyms: b3841 (obsolete), yigX, b3840 (obsolete), mttC, yigW, ExoXI, exonuclease XI
TatD is a magnesium dependent 3' - 5' exonuclease with a preference for single strand DNA and RNA. A tatD knockout mutant is more sensitive to H2O2 than wild type. Purified TatD has efficient exonuclease activity on ssDNA containing a 3' terminal deaminated base (uracil or hypoxanthine). TatD may be involved in the repair of H2O2 induced DNA damage [Chen14].
Purified, crystallised TatD has a TIM barrel fold (an eight stranded α β barrel). The conserved residues Glu91, Glu201 and Asp 203 are involved in metal binding at the active site [Chen14].
Deletion of tatD has very little effect on growth [Sambasivarao01]. A tatD ycfH yjjV triple mutant does not exhibit phenotypes that would suggest involvement of the corresponding proteins in the Sec-independent Tat protein export system. Like a tatD deletion, TatD overproduction does not cause transport phenotypes [Wexler00]. In a tatD mutant, mutant forms of Tat export system substrates were seen to accumulate instead of being degraded rapidly [Matos09]; however, this result may have been due to inadvertent overexpression of the Tat export substrates [Lindenstrauss10]. A tatD deletion mutant is more sensitive to kasugamycin than wild type [Skunca13].
tatD appears to be transcribed at lower levels than tatABC [Wexler00].
MttC: "membrane targeting and translocation" [Weiner98]
TatD: "twin arginine translocation" [Sargent98]
Gene Citations: [Lindenstrauss06]
|Map Position: [4,021,577 -> 4,022,359] (86.68 centisomes)||Length: 783 bp / 260 aa|
Molecular Weight of Polypeptide: 28.974 kD (from nucleotide sequence), 33.8 kD (experimental) [Sargent98 ]
Unification Links: ASAP:ABE-0174116 , DIP:DIP-10961N , EchoBASE:EB1446 , EcoGene:EG11481 , EcoliWiki:b4483 , ModBase:P27859 , OU-Microarray:b3840 , PortEco:tatD , PR:PRO_000024031 , Pride:P27859 , Protein Model Portal:P27859 , RefSeq:YP_026271 , RegulonDB:EG11481 , SMR:P27859 , String:511145.b4483 , UniProt:P27859
Relationship Links: InterPro:IN-FAMILY:IPR001130 , InterPro:IN-FAMILY:IPR018228 , InterPro:IN-FAMILY:IPR024918 , Panther:IN-FAMILY:PTHR10060 , PDB:Structure:1XWY , PDB:Structure:4P5U , PDB:Structure:4PE8 , Pfam:IN-FAMILY:PF01026 , Prosite:IN-FAMILY:PS01090 , Prosite:IN-FAMILY:PS01091 , Prosite:IN-FAMILY:PS01137
In Paralogous Gene Group: 255 (4 members)
|Biological Process:||GO:0000738 - DNA catabolic process, exonucleolytic
GO:0042542 - response to hydrogen peroxide [Chen14]
GO:0090501 - RNA phosphodiester bond hydrolysis [Chen14]
GO:0000737 - DNA catabolic process, endonucleolytic [GOA01]
GO:0006308 - DNA catabolic process [Gaudet10]
GO:0006515 - misfolded or incompletely synthesized protein catabolic process [GOA06]
GO:0090305 - nucleic acid phosphodiester bond hydrolysis [UniProtGOA11]
|Molecular Function:||GO:0000175 - 3'-5'-exoribonuclease activity
GO:0004536 - deoxyribonuclease activity [GOA06, Wexler00]
GO:0008310 - single-stranded DNA 3'-5' exodeoxyribonuclease activity [Chen14]
GO:0046872 - metal ion binding [Chen14, UniProtGOA11, GOA06, Wexler00]
GO:0004518 - nuclease activity [UniProtGOA11]
GO:0016787 - hydrolase activity [UniProtGOA11]
GO:0016888 - endodeoxyribonuclease activity, producing 5'-phosphomonoesters [GOA01]
|Cellular Component:||GO:0005829 - cytosol
[Wexler00, Chen14, DiazMejia09]
GO:0005737 - cytoplasm [UniProtGOA11a, UniProtGOA11, GOA06]
|MultiFun Terms:||information transfer → DNA related → DNA degradation|
|information transfer → protein related → turnover, degradation|
|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: 3' → 5' RNA exonuclease (ssDNA/RNA exonuclease, 3' → 5' specific)
EC Number: 3.1.13.-
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.
Enzymatic reaction of: 3' → 5' ssDNA exonuclease (ssDNA/RNA exonuclease, 3' → 5' specific)
EC Number: 18.104.22.168
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.
|Metal-Binding-Site||91, 201, 203|
10/21/2004 (paley) Merged genes G8213/tatD_2 into EG11481/tatD_1
1/26/1998 (pkarp) Merged genes G7968/yigW and EG11481/b3841
Peter D. Karp on Thu Jan 16, 2003:
Predicted gene function revised as a result of E. coli genome reannotation by Serres et al. [Serres01 ].
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
Centore08: Centore RC, Lestini R, Sandler SJ (2008). "XthA (Exonuclease III) regulates loading of RecA onto DNA substrates in log phase Escherichia coli cells." Mol Microbiol 67(1);88-101. PMID: 18034795
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
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
Lindenstrauss10: Lindenstrauss U, Matos CF, Graubner W, Robinson C, Bruser T (2010). "Malfolded recombinant Tat substrates are Tat-independently degraded in Escherichia coli." FEBS Lett 584(16);3644-8. PMID: 20659466
Matos09: Matos CF, Di Cola A, Robinson C (2009). "TatD is a central component of a Tat translocon-initiated quality control system for exported FeS proteins in Escherichia coli." EMBO Rep 10(5);474-9. PMID: 19343049
Sambasivarao01: Sambasivarao D, Dawson HA, Zhang G, Shaw G, Hu J, Weiner JH (2001). "Investigation of Escherichia coli dimethyl sulfoxide reductase assembly and processing in strains defective for the sec-independent protein translocation system membrane targeting and translocation." J Biol Chem 2001;276(23);20167-74. PMID: 11389150
Sargent98: Sargent F, Bogsch EG, Stanley NR, Wexler M, Robinson C, Berks BC, Palmer T (1998). "Overlapping functions of components of a bacterial Sec-independent protein export pathway." EMBO J 17(13);3640-50. PMID: 9649434
Skunca13: Skunca N, Bošnjak M, Kriško A, Panov P, Džeroski S, Smuc T, Supek F (2013). "Phyletic profiling with cliques of orthologs is enhanced by signatures of paralogy relationships." PLoS Comput Biol 9(1);e1002852. PMID: 23308060
Weiner98: Weiner JH, Bilous PT, Shaw GM, Lubitz SP, Frost L, Thomas GH, Cole JA, Turner RJ (1998). "A novel and ubiquitous system for membrane targeting and secretion of cofactor-containing proteins." Cell 93(1);93-101. PMID: 9546395
Wexler00: Wexler M, Sargent F, Jack RL, Stanley NR, Bogsch EG, Robinson C, Berks BC, Palmer T (2000). "TatD is a cytoplasmic protein with DNase activity. No requirement for TatD family proteins in sec-independent protein export." J Biol Chem 2000;275(22);16717-22. PMID: 10747959
Huerta03: Huerta AM, Collado-Vides J (2003). "Sigma70 promoters in Escherichia coli: specific transcription in dense regions of overlapping promoter-like signals." J Mol Biol 333(2);261-78. PMID: 14529615
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