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Escherichia coli K-12 substr. MG1655 Enzyme: RNase BN



Gene: rbn Accession Numbers: G7175 (EcoCyc), b2268, ECK2262

Synonyms: zipD, ecoZ, rnz, elaC, binuclear zinc phosphodiesterase, tRNase Z

Regulation Summary Diagram: ?

Subunit composition of RNase BN = [Rbn]2

Summary:
RNase BN, also identified as binuclear zinc phosphodiesterase, cleaves the 3'-terminal portion of tRNAs as well as various short unstructured RNAs.

RNase BN carries out the exoribonucleolytic cleavage of the 3'-terminus of tRNA with terminal nucleotide substitutions or deletions. It has demonstrated particular affinity for tRNA-CU and tRNA-CA, but not intact tRNA-CCA [Callahan00, Ezraty05, Takaku04]. Substrate identification depends on a region of RNase BN known as the ZiPD exosite [Schilling05].

RNase BN has also been shown to cleave unstructured RNA [Shibata06].

RNase BN is a member of the metallo-beta-lactamase family and functions as a dimer [Vogel02, Callahan00]. A crystal structure of RNase BN has been determined to 2.9 Å resolution [Kostelecky06].

Deletion of elaC alone has no effect on growth, but loss of the RNases BN, II, T, PH and D results in inviability [Schilling04]. RNase BN alone can restore some viability [Kelly92].

Site-directed mutagenesis has elucidated a potential zinc binding site, though other studies point to divalent cobalt or magnesium as being required for tRNase activity [Vogel04, Callahan00].

Prior to its identification as RNase BN, the activity of ElaC was gauged in vitro using the nonphysiological substrate bis-(p-nitrophenyl)phosphate in the presence of divalent zinc cation. Kinetic parameters for this reaction have been determined [Vogel02].

The gene coding for RNase BN was originally incorrectly identified as yihY [Callahan96].

Citations: [Deutscher90]

Locations: cytosol

Map Position: [2,379,630 -> 2,380,547] (51.29 centisomes)
Length: 918 bp / 305 aa

Molecular Weight of Polypeptide: 32.93 kD (from nucleotide sequence)

Unification Links: ASAP:ABE-0007496 , EchoBASE:EB4008 , EcoGene:EG14260 , EcoliWiki:b2268 , Mint:MINT-1275952 , ModBase:P0A8V0 , OU-Microarray:b2268 , PortEco:rbn , PR:PRO_000023801 , Pride:P0A8V0 , Protein Model Portal:P0A8V0 , RefSeq:NP_416771 , RegulonDB:G7175 , SMR:P0A8V0 , String:511145.b2268 , Swiss-Model:P0A8V0 , UniProt:P0A8V0

Relationship Links: InterPro:IN-FAMILY:IPR001279 , InterPro:IN-FAMILY:IPR013469 , InterPro:IN-FAMILY:IPR013471 , PDB:Structure:2CBN , Pfam:IN-FAMILY:PF00753 , Smart:IN-FAMILY:SM00849

Gene-Reaction Schematic: ?

GO Terms:

Biological Process: GO:0008033 - tRNA processing Inferred from experiment Inferred by computational analysis [UniProtGOA11, GOA06, Callahan00]
GO:0090503 - RNA phosphodiester bond hydrolysis, exonucleolytic Inferred from experiment [Callahan00]
GO:0042779 - tRNA 3'-trailer cleavage Inferred by computational analysis [GOA01]
GO:0090502 - RNA phosphodiester bond hydrolysis, endonucleolytic Inferred by computational analysis [GOA01]
Molecular Function: GO:0004518 - nuclease activity Inferred from experiment Inferred by computational analysis [UniProtGOA11, Dutta09]
GO:0004532 - exoribonuclease activity Inferred from experiment [Callahan00]
GO:0004519 - endonuclease activity Inferred by computational analysis [UniProtGOA11, GOA06]
GO:0004527 - exonuclease activity Inferred by computational analysis [UniProtGOA11, GOA06]
GO:0008270 - zinc ion binding Inferred by computational analysis [GOA06]
GO:0016787 - hydrolase activity Inferred by computational analysis [UniProtGOA11]
GO:0016891 - endoribonuclease activity, producing 5'-phosphomonoesters Inferred by computational analysis [GOA01]
GO:0046872 - metal ion binding Inferred by computational analysis [UniProtGOA11]
Cellular Component: GO:0005829 - cytosol Inferred by computational analysis [DiazMejia09]

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

Essentiality data for rbn 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 BN exoribonuclease

mutated tRNA + 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 Enzyme Commission system.

The reaction is physiologically favored in the direction shown.


Enzymatic reaction of: RNase BN exoribonuclease

a tRNA precursor with a 5' extension and a long 3' trailer + H2O <=> 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 physiologically favored in the direction shown.

In Pathways: tRNA processing

Cofactors or Prosthetic Groups: Mg2+ [Callahan00], Co2+ [Callahan00]

Activators (Unknown Mechanism): K+ [Callahan00]

pH(opt): 6.5 [Callahan00]


Sequence Features

Feature Class Location Citations Comment
Metal-Binding-Site 64
[UniProt11]
UniProt: Zinc 1; catalytic.
Metal-Binding-Site 66
[UniProt11]
UniProt: Zinc 1; catalytic.
Metal-Binding-Site 68
[UniProt11]
UniProt: Zinc 2; catalytic.
Active-Site 68
[UniProt11]
UniProt: Proton acceptor; Non-Experimental Qualifier: potential.
Metal-Binding-Site 69
[UniProt11]
UniProt: Zinc 2; catalytic.
Metal-Binding-Site 141
[UniProt11]
UniProt: Zinc 1; catalytic.
Sequence-Conflict 154
[Huisman96, UniProt10]
Alternate sequence: D → Y; UniProt: (in Ref. 1; AAB02732);
Metal-Binding-Site 212
[UniProt11]
UniProt: Zinc 1; catalytic.
Sequence-Conflict 217
[Huisman96, UniProt10]
Alternate sequence: D → N; UniProt: (in Ref. 1; AAB02732);
Metal-Binding-Site 270
[UniProt11]
UniProt: Zinc 2; catalytic.


Gene Local Context (not to scale): ?

Transcription Unit:

Notes:

History:
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.


References

Asha83: Asha PK, Blouin RT, Zaniewski R, Deutscher MP (1983). "Ribonuclease BN: identification and partial characterization of a new tRNA processing enzyme." Proc Natl Acad Sci U S A 80(11);3301-4. PMID: 6344080

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

Callahan00: Callahan C, Neri-Cortes D, Deutscher MP (2000). "Purification and characterization of the tRNA-processing enzyme RNase BN." J Biol Chem 275(2);1030-4. PMID: 10625642

Callahan96: Callahan C, Deutscher MP (1996). "Identification and characterization of the Escherichia coli rbn gene encoding the tRNA processing enzyme RNase BN." J Bacteriol 178(24);7329-32. PMID: 8955422

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

Dutta09: Dutta T, Deutscher MP (2009). "Catalytic properties of RNase BN/RNase Z from Escherichia coli: RNase BN is both an exo- and endoribonuclease." J Biol Chem 284(23);15425-31. PMID: 19366704

Ezraty05: Ezraty B, Dahlgren B, Deutscher MP (2005). "The RNase Z homologue encoded by Escherichia coli elaC gene is RNase BN." J Biol Chem 280(17);16542-5. PMID: 15764599

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."

Huisman96: Huisman G.W. (1996). "Characterization of the ela locus from Escherichia coli." Data submission to EMBL/GenBank/DDBJ databases on 1996-06.

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

Kelly92: 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

Kostelecky06: Kostelecky B, Pohl E, Vogel A, Schilling O, Meyer-Klaucke W (2006). "The crystal structure of the zinc phosphodiesterase from Escherichia coli provides insight into function and cooperativity of tRNase Z-family proteins." J Bacteriol 188(4);1607-14. PMID: 16452444

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

Schilling04: Schilling O, Ruggeberg S, Vogel A, Rittner N, Weichert S, Schmidt S, Doig S, Franz T, Benes V, Andrews SC, Baum M, Meyer-Klaucke W (2004). "Characterization of an Escherichia coli elaC deletion mutant." Biochem Biophys Res Commun 320(4);1365-73. PMID: 15303284

Schilling05: Schilling O, Spath B, Kostelecky B, Marchfelder A, Meyer-Klaucke W, Vogel A (2005). "Exosite modules guide substrate recognition in the ZiPD/ElaC protein family." J Biol Chem 280(18);17857-62. PMID: 15699034

Shibata06: Shibata HS, Minagawa A, Takaku H, Takagi M, Nashimoto M (2006). "Unstructured RNA is a substrate for tRNase Z." Biochemistry 45(17);5486-92. PMID: 16634630

Takaku04: Takaku H, Minagawa A, Takagi M, Nashimoto M (2004). "The N-terminal half-domain of the long form of tRNase Z is required for the RNase 65 activity." Nucleic Acids Res 32(15);4429-38. PMID: 15317868

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 manual assignment of UniProtKB keywords in UniProtKB/Swiss-Prot entries."

Vogel02: Vogel A, Schilling O, Niecke M, Bettmer J, Meyer-Klaucke W (2002). "ElaC encodes a novel binuclear zinc phosphodiesterase." J Biol Chem 277(32);29078-85. PMID: 12029081

Vogel04: Vogel A, Schilling O, Meyer-Klaucke W (2004). "Identification of metal binding residues for the binuclear zinc phosphodiesterase reveals identical coordination as glyoxalase II." Biochemistry 43(32);10379-86. PMID: 15301536


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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 18.5 on Fri Dec 19, 2014, BIOCYC14B.