Escherichia coli K-12 substr. MG1655 Enzyme: oligoribonuclease

Gene: orn Accession Numbers: G7842 (EcoCyc), b4162, ECK4158

Synonyms: yjeR

Regulation Summary Diagram: ?

Regulation summary diagram for orn

Subunit composition of oligoribonuclease = [Orn]2
         oligoribonuclease monomer = Orn

Oligoribonuclease (Orn) is a processive 3'-to-5' exoribonuclease specific for short oligoribonucleotides [Niyogi75, Datta75, Zhang98c]. Orn participates in the mRNA decay pathway; the enzyme is required for wild-type decay of small, partially degraded RNAs to mononucleotides and is essential for growth [Ghosh99].

Orn binds adenosine-3',5'-bisphosphate (pAp), but does not hydrolyze it under the conditions tested [Mechold06].

Crystal structures of Orn have been solved [Fiedler04].

Orn: "oligoribonuclease" [Zhang98c]

Review: [Condon07]

Locations: cytosol

Map Position: [4,389,627 -> 4,390,172] (94.61 centisomes, 341°)
Length: 546 bp / 181 aa

Molecular Weight of Polypeptide: 20.816 kD (from nucleotide sequence), 20 kD (experimental) [Zhang98c ]

Molecular Weight of Multimer: 40 kD (experimental) [Zhang98c]

Unification Links: ASAP:ABE-0013631 , DIP:DIP-10412N , EchoBASE:EB2373 , EcoGene:EG12480 , EcoliWiki:b4162 , OU-Microarray:b4162 , PortEco:orn , PR:PRO_000023466 , Pride:P0A784 , Protein Model Portal:P0A784 , RefSeq:NP_418586 , RegulonDB:G7842 , SMR:P0A784 , String:511145.b4162 , Swiss-Model:P0A784 , UniProt:P0A784

Relationship Links: InterPro:IN-FAMILY:IPR006055 , InterPro:IN-FAMILY:IPR012337 , InterPro:IN-FAMILY:IPR013520 , InterPro:IN-FAMILY:IPR022894 , PDB:Structure:1YTA , PDB:Structure:2IGI , Pfam:IN-FAMILY:PF00929 , Smart:IN-FAMILY:SM00479

Gene-Reaction Schematic: ?

Gene-Reaction Schematic

GO Terms:

Biological Process: GO:0006259 - DNA metabolic process Inferred from experiment [Mechold06]
GO:0006401 - RNA catabolic process Inferred from experiment [Ghosh99]
GO:0090501 - RNA phosphodiester bond hydrolysis Inferred from experiment [Datta75]
GO:0090503 - RNA phosphodiester bond hydrolysis, exonucleolytic Inferred from experiment Inferred by computational analysis [GOA06, Zhang98c]
GO:0090305 - nucleic acid phosphodiester bond hydrolysis Inferred by computational analysis [Gaudet10]
Molecular Function: GO:0000175 - 3'-5'-exoribonuclease activity Inferred from experiment [Zhang98c]
GO:0008310 - single-stranded DNA 3'-5' exodeoxyribonuclease activity Inferred from experiment [Mechold06]
GO:0034611 - oligoribonucleotidase activity Inferred from experiment [Datta75]
GO:0003676 - nucleic acid binding Inferred by computational analysis [GOA01a]
GO:0004518 - nuclease activity Inferred by computational analysis [UniProtGOA11a]
GO:0004527 - exonuclease activity Inferred by computational analysis [UniProtGOA11a, GOA01a]
GO:0016787 - hydrolase activity Inferred by computational analysis [UniProtGOA11a]
GO:0016788 - hydrolase activity, acting on ester bonds Inferred by computational analysis [GOA01a]
GO:0016896 - exoribonuclease activity, producing 5'-phosphomonoesters Inferred by computational analysis [GOA06]
GO:0046872 - metal ion binding Inferred by computational analysis [UniProtGOA11a]
Cellular Component: GO:0005829 - cytosol Inferred from experiment Inferred by computational analysis [DiazMejia09, Ishihama08, LopezCampistrou05]
GO:0005737 - cytoplasm Inferred by computational analysis [UniProtGOA11, UniProtGOA11a, GOA06]

MultiFun Terms: information transfer RNA related RNA degradation

Essentiality data for orn 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 No 37 Aerobic 7   No [Baba06, Comment 2]

Last-Curated ? 17-Jul-2008 by Keseler I , SRI International

Enzymatic reaction of: oligoribonuclease

Synonyms: oligonucleotidase

EC Number:

an oligonucleotide + 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.

The substrate preferences of the enzyme have been characterized [Datta75, Niyogi75]. Orn was also shown to be active with DNA oligonucleotides [Mechold06].

Cofactors or Prosthetic Groups: Mn2+ [Young08, Niyogi75]

Inhibitors (Unknown Mechanism): adenosine 3',5'-bisphosphate [Mechold06]

T(opt): 50 °C [Niyogi75]

pH(opt): 8-9 [Niyogi75]

Sequence Features

Protein sequence of oligoribonuclease monomer with features indicated

Feature Class Location Citations Comment
Cleavage-of-Initial-Methionine 1
Chain 2 -> 181
UniProt: Oligoribonuclease;
Conserved-Region 8 -> 171
UniProt: Exonuclease;
Metal-Binding-Site 12
UniProt: Zinc.
Metal-Binding-Site 14
UniProt: Zinc.
Active-Site 129
UniProt: Non-Experimental Qualifier: potential;
Metal-Binding-Site 163
UniProt: Zinc.

Gene Local Context (not to scale): ?

Gene local context diagram

Transcription Unit:

Transcription-unit diagram


Peter D. Karp on Wed Jan 18, 2006:
Gene left-end position adjusted based on analysis performed in the 2005 E. coli annotation update [Riley06 ].
Markus Krummenacker on Tue Oct 14, 1997:
Gene object created from Blattner lab Genbank (v. M52) entry.


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

Condon07: Condon C (2007). "Maturation and degradation of RNA in bacteria." Curr Opin Microbiol 10(3);271-8. PMID: 17560162

Datta75: Datta AK, Niyogi K (1975). "A novel oligoribonuclease of Escherichia coli. II. Mechanism of action." J Biol Chem 250(18);7313-9. PMID: 170260

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

Fiedler04: Fiedler TJ, Vincent HA, Zuo Y, Gavrialov O, Malhotra A (2004). "Purification and crystallization of Escherichia coli oligoribonuclease." Acta Crystallogr D Biol Crystallogr 60(Pt 4);736-9. PMID: 15039570

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

Ghosh99: Ghosh S, Deutscher MP (1999). "Oligoribonuclease is an essential component of the mRNA decay pathway." Proc Natl Acad Sci U S A 96(8);4372-7. PMID: 10200269

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."

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

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

Mechold06: Mechold U, Ogryzko V, Ngo S, Danchin A (2006). "Oligoribonuclease is a common downstream target of lithium-induced pAp accumulation in Escherichia coli and human cells." Nucleic Acids Res 34(8);2364-73. PMID: 16682444

Niyogi75: Niyogi SK, Datta AK (1975). "A novel oligoribonuclease of Escherichia coli. I. Isolation and properties." J Biol Chem 250(18);7307-12. PMID: 240824

Riley06: Riley M, Abe T, Arnaud MB, Berlyn MK, Blattner FR, Chaudhuri RR, Glasner JD, Horiuchi T, Keseler IM, Kosuge T, Mori H, Perna NT, Plunkett G, Rudd KE, Serres MH, Thomas GH, Thomson NR, Wishart D, Wanner BL (2006). "Escherichia coli K-12: a cooperatively developed annotation snapshot--2005." Nucleic Acids Res 34(1);1-9. PMID: 16397293

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

UniProt10: UniProt Consortium (2010). "UniProt version 2010-07 released on 2010-06-15 00:00:00." Database.

UniProt15: UniProt Consortium (2015). "UniProt version 2015-01 released on 2015-01-16 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."

Young08: Young Park A, Elvin CM, Hamdan SM, Wood RJ, Liyou NE, Hamwood TE, Jennings PA, Dixon NE (2008). "Hydrolysis of the 5'-p-nitrophenyl ester of TMP by oligoribonucleases (ORN) from Escherichia coli, Mycobacterium smegmatis, and human." Protein Expr Purif 57(2);180-7. PMID: 18023590

Yu95: Yu D, Deutscher MP (1995). "Oligoribonuclease is distinct from the other known exoribonucleases of Escherichia coli." J Bacteriol 177(14);4137-9. PMID: 7608090

Zhang98c: Zhang X, Zhu L, Deutscher MP (1998). "Oligoribonuclease is encoded by a highly conserved gene in the 3'-5' exonuclease superfamily." J Bacteriol 180(10);2779-81. PMID: 9573169

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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 19.0 on Sun Oct 4, 2015, biocyc13.