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discounted EARLY registration ends Dec 31, 2014
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Metabolic Modeling Tutorial
discounted EARLY registration ends Dec 31, 2014
BioCyc websites down
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for maintenance.
Metabolic Modeling Tutorial
discounted EARLY registration ends Dec 31, 2014
BioCyc websites down
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Escherichia coli K-12 substr. MG1655 Enzyme: RNase D



Gene: rnd Accession Numbers: EG10858 (EcoCyc), b1804, ECK1802

Regulation Summary Diagram: ?

Summary:
RNase D is an exonuclease involved in the 3' ribonucleolytic processing of precursor tRNA. Though RNase D appears to be a minor player in this task and is not required for viability or proper tRNA processing, it can support such processing in the absence of other exonucleases (RNase II, RNase BN, RNase T and RNase PH) [Reuven93, Kelly92a, Zaniewski84].

In vitro, RNase D cleaves tRNA nonprocessively from the 3' end to yield mononucleotides and active tRNA. Cleavage of tRNA slows at the CCA nucleotide sequence, allowing aminoacylation of the tRNA that prevents additional cleavage [Cudny80]. RNase D activity is very dependent on the structure of the 3' end of the target tRNA, with cleavage of altered tRNA proceeding much faster than cleavage of wild type, and no cleavage of tRNA bearing a 3' phosphate [Ghosh78, Cudny81]. When overexpressed in vivo, RNase D cleaves the 3' end of tRNA, eventually cleaving past the CCA sequence to yield damaged tRNA that cannot be fixed by tRNA nucleotidyltransferase [Zhang88a].

Translation of RNase D depends on a stem-loop structure followed by eight uridines upstream of the Shine-Delgarno sequence [Zhang89b, Zhang92c].

Overexpression of RNase D leads to slow growth [Zhang88b].

Citations: [Deutscher90]

Locations: cytosol

Map Position: [1,884,888 <- 1,886,015] (40.63 centisomes)
Length: 1128 bp / 375 aa

Molecular Weight of Polypeptide: 42.734 kD (from nucleotide sequence)

pI: 6.2 [Cudny81a]

Unification Links: ASAP:ABE-0006003 , CGSC:270 , DIP:DIP-10726N , EchoBASE:EB0851 , EcoGene:EG10858 , EcoliWiki:b1804 , Mint:MINT-1309170 , ModBase:P09155 , OU-Microarray:b1804 , PortEco:rnd , PR:PRO_000023788 , Pride:P09155 , Protein Model Portal:P09155 , RefSeq:NP_416318 , RegulonDB:EG10858 , SMR:P09155 , String:511145.b1804 , UniProt:P09155

Relationship Links: InterPro:IN-FAMILY:IPR002121 , InterPro:IN-FAMILY:IPR002562 , InterPro:IN-FAMILY:IPR006292 , InterPro:IN-FAMILY:IPR010997 , InterPro:IN-FAMILY:IPR012337 , PDB:Structure:1YT3 , Pfam:IN-FAMILY:PF00570 , Pfam:IN-FAMILY:PF01612 , Prosite:IN-FAMILY:PS50967 , Smart:IN-FAMILY:SM00341 , Smart:IN-FAMILY:SM00474

Gene-Reaction Schematic: ?

GO Terms:

Biological Process: GO:0008033 - tRNA processing Inferred from experiment Inferred by computational analysis [UniProtGOA11a, GOA01a, Reuven93]
GO:0090501 - RNA phosphodiester bond hydrolysis Inferred from experiment [Kelly92a]
GO:0006139 - nucleobase-containing compound metabolic process Inferred by computational analysis [GOA01a]
GO:0042780 - tRNA 3'-end processing Inferred by computational analysis [GOA06]
GO:0044237 - cellular metabolic process Inferred by computational analysis [GOA01a]
GO:0090305 - nucleic acid phosphodiester bond hydrolysis Inferred by computational analysis [UniProtGOA11a, GOA01a]
GO:0090503 - RNA phosphodiester bond hydrolysis, exonucleolytic Inferred by computational analysis [GOA06, GOA01, GOA01a]
Molecular Function: GO:0004540 - ribonuclease activity Inferred from experiment [Kelly92a]
GO:0000166 - nucleotide binding Inferred by computational analysis [GOA01a]
GO:0003676 - nucleic acid binding Inferred by computational analysis [GOA01a]
GO:0003824 - catalytic activity Inferred by computational analysis [GOA01a]
GO:0004518 - nuclease activity Inferred by computational analysis [UniProtGOA11a]
GO:0004527 - exonuclease activity Inferred by computational analysis [UniProtGOA11a]
GO:0008408 - 3'-5' exonuclease activity Inferred by computational analysis [GOA01a]
GO:0016787 - hydrolase activity Inferred by computational analysis [UniProtGOA11a]
GO:0033890 - ribonuclease D activity Inferred by computational analysis [GOA06, GOA01, GOA01a]
Cellular Component: GO:0005622 - intracellular Inferred by computational analysis [GOA01a]
GO:0005737 - cytoplasm Inferred by computational analysis [UniProtGOA11, UniProtGOA11a, GOA06]
GO:0005829 - cytosol Inferred by computational analysis [DiazMejia09]

MultiFun Terms: information transfer RNA related RNA modification
metabolism degradation of macromolecules RNA

Essentiality data for rnd 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:
Revised 25-May-2011 by Brito D


Enzymatic reaction of: RNase D exonuclease

EC Number: 3.1.13.5

a tRNA precursor with a short 3' extension <=> an uncharged tRNA + 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 Enzyme Commission system.

The reaction is favored in the direction shown.

In Pathways: tRNA processing


Enzymatic reaction of: RNase D exonuclease

EC Number: 3.1.13.5

a tRNA precursor with a 5' extension and a short 3' extension <=> a tRNA precursor with a 5' extension + a ribonucleoside 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 favored in the direction shown.

In Pathways: tRNA processing


Enzymatic reaction of: RNase D exonuclease

EC Number: 3.1.13.5

a tRNA precursor + H2O <=> a tRNA + 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.

Summary:
The pH optimum is from 9.1-9.5 [Cudny81].

Cofactors or Prosthetic Groups: Mg2+ [Ghosh78]

Activators (Unknown Mechanism): K+ [Ghosh78] , ammonium [Ghosh78]

pH(opt): 9.3 [Cudny81]


Sequence Features

Feature Class Location Citations Comment
Conserved-Region 3 -> 169
[UniProt11]
UniProt: 3'-5' exonuclease.
Conserved-Region 210 -> 289
[UniProt09]
UniProt: HRDC;


Gene Local Context (not to scale): ?

Transcription Unit:

Notes:

History:
10/20/97 Gene b1804 from Blattner lab Genbank (v. M52) entry merged into EcoCyc gene EG10858; 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

Cudny80: Cudny H, Deutscher MP (1980). "Apparent involvement of ribonuclease D in the 3' processing of tRNA precursors." Proc Natl Acad Sci U S A 77(2);837-41. PMID: 6153805

Cudny81: Cudny H, Zaniewski R, Deutscher MP (1981). "Escherichia coli RNase D. Catalytic properties and substrate specificity." J Biol Chem 256(11);5633-7. PMID: 6263886

Cudny81a: Cudny H, Zaniewski R, Deutscher MP (1981). "Escherichia coli RNase D. Purification and structural characterization of a putative processing nuclease." J Biol Chem 256(11);5627-32. PMID: 6263885

Deutscher90: Deutscher MP (1990). "Ribonucleases active at 3' terminus of transfer RNA." Methods Enzymol 181;421-33. PMID: 2166215

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

Ghosh78: Ghosh RK, Deutscher MP (1978). "Identification of an Escherichia coli nuclease acting on structurally altered transfer RNA molecules." J Biol Chem 253(4);997-1000. PMID: 342522

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."

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

Kelly92a: Kelly KO, Deutscher MP (1992). "The presence of only one of five exoribonucleases is sufficient to support the growth of Escherichia coli." J Bacteriol 174(20);6682-4. PMID: 1400219

Li94: Li Z, Deutscher MP (1994). "The role of individual exoribonucleases in processing at the 3' end of Escherichia coli tRNA precursors." J Biol Chem 269(8);6064-71. PMID: 7509797

Reuven93: Reuven NB, Deutscher MP (1993). "Multiple exoribonucleases are required for the 3' processing of Escherichia coli tRNA precursors in vivo." FASEB J 7(1);143-8. PMID: 8422961

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

UniProt11: UniProt Consortium (2011). "UniProt version 2011-11 released on 2011-11-22 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."

Zaniewski84: Zaniewski R, Petkaitis E, Deutscher MP (1984). "A multiple mutant of Escherichia coli lacking the exoribonucleases RNase II, RNase D, and RNase BN." J Biol Chem 259(19);11651-3. PMID: 6207170

Zhang88a: Zhang JR, Deutscher MP (1988). "Transfer RNA is a substrate for RNase D in vivo." J Biol Chem 263(34);17909-12. PMID: 3056931

Zhang88b: Zhang JR, Deutscher MP (1988). "Cloning, characterization, and effects of overexpression of the Escherichia coli rnd gene encoding RNase D." J Bacteriol 170(2);522-7. PMID: 2828310

Zhang89b: Zhang JR, Deutscher MP (1989). "Analysis of the upstream region of the Escherichia coli rnd gene encoding RNase D. Evidence for translational regulation of a putative tRNA processing enzyme." J Biol Chem 264(30);18228-33. PMID: 2681190

Zhang92c: Zhang J, Deutscher MP (1992). "A uridine-rich sequence required for translation of prokaryotic mRNA." Proc Natl Acad Sci U S A 89(7);2605-9. PMID: 1372983


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 Dec 22, 2014, BIOCYC13B.