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Escherichia coli K-12 substr. MG1655 Enzyme: ssDNA/RNA exonuclease, 3' → 5' specific



Gene: tatD Accession Numbers: EG11481 (EcoCyc), b4483, ECK3833

Synonyms: b3841 (obsolete), yigX, b3840 (obsolete), mttC, yigW, ExoXI, exonuclease XI

Regulation Summary Diagram: ?

Summary:
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].

TatD exhibits magnesium-dependent DNase activity [Wexler00]. A tatD mutant shows increased RecA-GFP foci formation [Centore08].

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" [Sargent98a]

Gene Citations: [Lindenstrauss06]

Locations: cytosol

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) [Sargent98a ]

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)

Gene-Reaction Schematic: ?

GO Terms:

Biological Process: GO:0000738 - DNA catabolic process, exonucleolytic Inferred from experiment [Chen14]
GO:0042542 - response to hydrogen peroxide Inferred from experiment [Chen14]
GO:0090501 - RNA phosphodiester bond hydrolysis Inferred from experiment [Chen14]
GO:0000737 - DNA catabolic process, endonucleolytic Inferred by computational analysis [GOA01]
GO:0006308 - DNA catabolic process Inferred by computational analysis [Gaudet10]
GO:0006515 - misfolded or incompletely synthesized protein catabolic process Inferred by computational analysis [GOA06]
GO:0090305 - nucleic acid phosphodiester bond hydrolysis Inferred by computational analysis [UniProtGOA11]
Molecular Function: GO:0000175 - 3'-5'-exoribonuclease activity Inferred from experiment [Chen14]
GO:0004536 - deoxyribonuclease activity Inferred from experiment Inferred by computational analysis [GOA06, Wexler00]
GO:0008310 - single-stranded DNA 3'-5' exodeoxyribonuclease activity Inferred from experiment [Chen14]
GO:0046872 - metal ion binding Inferred by computational analysis Inferred from experiment [Chen14, UniProtGOA11, GOA06, Wexler00]
GO:0004518 - nuclease activity Inferred by computational analysis [UniProtGOA11]
GO:0016787 - hydrolase activity Inferred by computational analysis [UniProtGOA11]
GO:0016888 - endodeoxyribonuclease activity, producing 5'-phosphomonoesters Inferred by computational analysis [GOA01]
Cellular Component: GO:0005829 - cytosol Inferred by computational analysis Inferred from experiment [Wexler00, Chen14, DiazMejia09]
GO:0005737 - cytoplasm Inferred by computational analysis [UniProtGOA11a, UniProtGOA11, GOA06]

MultiFun Terms: information transfer DNA related DNA degradation
information transfer protein related turnover, degradation

Essentiality data for tatD 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]

Credits:
Curated 14-Jan-2013 by Keseler I , SRI International
Last-Curated ? 11-Sep-2014 by Mackie A , Macquarie University


Enzymatic reaction of: 3' → 5' RNA exonuclease (ssDNA/RNA exonuclease, 3' → 5' specific)

EC Number: 3.1.13.-

RNA + n H2O <=> n a nucleoside 5'-monophosphate

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: 3.1.11.1

DNAn + H2O <=> (deoxynucleotides)(n-1) + a 2'-deoxyribonucleoside 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.

Cofactors or Prosthetic Groups: Mg2+ [Chen14]


Sequence Features

Feature Class Location Citations Comment
Mutagenesis-Variant 62
[Chen14]
alternate sequence H → A, purified protein has reduced exonuclease activity
Metal-Binding-Site 91, 201, 203
[Chen14]
 
Mutagenesis-Variant 127
[Chen14]
alternate sequence H → A, purified protein retains exonuclease activity
Mutagenesis-Variant 152
[Chen14]
alternate sequence H → A, purified protein retains exonuclease activity
Metal-Binding-Site 152
[UniProt11a]
UniProt: Divalent metal cation.
Metal-Binding-Site 153
[UniProt11a]
UniProt: Divalent metal cation.
Metal-Binding-Site 201
[UniProt11a]
UniProt: Divalent metal cation.


Gene Local Context (not to scale): ?

Transcription Units:

Notes:

History:
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 ].


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

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

Chen14: Chen YC, Li CL, Hsiao YY, Duh Y, Yuan HS (2014). "Structure and function of TatD exonuclease in DNA repair." Nucleic Acids Res. PMID: 25114049

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."

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

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

Lindenstrauss06: Lindenstrauss U, Bruser T (2006). "Conservation and variation between Rhodobacter capsulatus and Escherichia coli Tat systems." J Bacteriol 188(22);7807-14. PMID: 16980457

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

Sargent98a: 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

Serres01: Serres MH, Gopal S, Nahum LA, Liang P, Gaasterland T, Riley M (2001). "A functional update of the Escherichia coli K-12 genome." Genome Biol 2(9);RESEARCH0035. PMID: 11574054

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

UniProt11a: 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 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."

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

Other References Related to Gene Regulation

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


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 Fri Nov 28, 2014, biocyc13.