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On One Page

Quickview |

Gene |

Product(s) |

Expression|

Evolution |

References |

Quickview

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Standard Name	rbn
Gene Synonym(s)	elaC, ECK2262, b2268, JW2263, ecoZ, rnz, zipD^[1]^[2], zipD
Product Desc.	ElaC^[3]; Rbn^[2]; Component of RNase BN^[2] RNase BN, tRNA processing enzyme; has zinc phosphodiesterase activity^[4]
Product Synonyms(s)	binuclear zinc phosphodiesterase^[1], ZipD^[3]^[1], Rnz^[3]^[1], B2268^[3]^[1], EcoZ^[3]^[1], ElaC^[3]^[1] , ECK2262, ecoZ, elaC, JW2263, rnz, zipD, b2268
Function from GO	<GO_nr />
Knock-Out Phenotype
Regulation/Expression	transcription unit(s): elaC^[3]
Regulation/Activity
Quick Links
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Notes

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elaC is renamed rbn. The elaABCD genes are named, without a phenotypic explanation, in Genbank U58768. yihY was previously thought to be rbn. rbn is an essential gene [not clear this is correct]. Schilling, et al. Biochem Biophys Res Commun. 2004 Aug 6;320(4):1365-73. has erratum in Biochem Biophys Res Commun. 2005 Feb 4;327(1):371.^[4]

Gene

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Nomenclature

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See Help:Gene_nomenclature for help with entering information in the Gene Nomenclature table.

Standard name	rbn
Mnemonic	RNase BN
Synonyms	elaC, ECK2262, b2268, JW2263, ecoZ, rnz, zipD^[1]^[2], zipD
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Notes

Location(s) and DNA Sequence

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<protect> See Help:Gene_location for help entering information in the Gene Location and DNA sequence table.

Strain	Map location	Genome coordinates	Genome browsers	Sequence links
MG1655	51.29 minutes, 51.29 minutes	MG1655: 2379630..2380547 <gbrowseImage> name=NC_000913:2379630..2380547 source=MG1655 preset=GeneLocation </gbrowseImage>	EcoCyc GBrowse(MG1655)	FASTA Dump EcoCyc Sequence Dump
BW2952		NC_012759: 2265435..2266352 <gbrowseImage> name=NC_012759:2265435..2266352 source=BW2952 preset=GeneLocation </gbrowseImage>	GBrowse (BW2952)	FASTA Dump
W3110		W3110: 2386278..2387195 <gbrowseImage> name=NC_007779:2386278..2387195 source=W3110 preset=GeneLocation </gbrowseImage>	GBrowse(W3110)	FASTA Dump
DH10B		DH10B: 4173866..4174738 <gbrowseImage> name=NC_010473:4173866..4174738 source=DH10B preset=GeneLocation </gbrowseImage>	GBrowse(DH10B)	FASTA Dump
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Notes

Sequence Features

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See Help:Gene_sequence_features for help in entering sequence features in EcoliWiki.

Feature Type	Strain	Genomic Location	Evidence	Reference	Notes
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Notes

Alleles and Phenotypes

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See Help:Gene_alleles for how to enter or edit alleles and phenotypes in EcoliWiki.

Allele	Nt change(s)	AA change(s)	Phenotype: Type	Phenotype: Description	Reference	Availability	Comments
Δrbn (Keio:JW3857)	deletion	deletion			PMID:16738554	Shigen CGSC10785^[5]
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Notes

Genetic Interactions

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Interactor	Interaction	Allele	Score(s)	Reference(s)	Accessions	Notes
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Notes

Genetic Resources

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See Help:Gene_resources for help entering information into the Genetic Resources table.

Resource	Resource Type	Source	Notes/Reference
JW3857	Plasmid clone	Shigen	PMID:16769691 Status:Clone OK Primer 1:GCCCTAAAAACCATTCAGGACAA Primer 2:CCTGGTTCGTCGTCTTCTTCTTG
5H12	Kohara Phage	Genobase	PMID:3038334
9F11	Kohara Phage	Genobase	PMID:3038334
4C8	Kohara Phage	Genobase	PMID:3038334
6H5	Kohara Phage	Genobase	PMID:3038334
6H9	Kohara Phage	Genobase	PMID:3038334
9H1	Kohara Phage	Genobase	PMID:3038334
zih-35::Tn10	Linked marker	CAG18495 = CGSC7467^[5]	est. P1 cotransduction: 72% ^[6]
pflD501::Tn10	Linked marker	CAG18477 = CGSC7470^[5]	est. P1 cotransduction: 2% ^[6] Synonyms:zij-501::Tn10 nnnCAG18477 also carries metF79(Am) (CGSC).
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Notes

Accessions in Other Databases

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See Help:Gene_accessions for help with entering information into the Gene Accessions table.

Database	Accession	Notes
EcoCyc	EcoCyc:G7175	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG14260	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120003751	Escherichia coli str. K-12 substr. MG1655
NCBI (EcoliWiki Page)	GeneID:946760	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB4008	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0007496	Escherichia coli str. K-12 substr. MG1655
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Notes

Links

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Name	URL	Comments
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Product(s)

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Nomenclature

See Help:Product_nomenclature for help entering or editing information in this section of EcoliWiki.

Standard name	Rbn
Synonyms	binuclear zinc phosphodiesterase^[1], ZipD^[3]^[1], Rnz^[3]^[1], B2268^[3]^[1], EcoZ^[3]^[1], ElaC^[3]^[1] , ECK2262, ecoZ, elaC, JW2263, rnz, zipD, b2268
Product description	ElaC^[3]; Rbn^[2]; Component of RNase BN^[2] RNase BN, tRNA processing enzyme; has zinc phosphodiesterase activity^[4]
EC number (for enzymes)
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Notes

Function

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<protect> Gene Ontology
See Help:Gene_ontology for help entering or editing GO terms and GO annotations in EcoliWiki.

Qualifier	GO ID	GO term name	Reference	Evidence Code	with/from	Aspect	Notes	Status
	GO:0008033	tRNA processing	PMID:10625642	IDA: Inferred from Direct Assay		P	Table IV. Activity of RNase BN greatest when tRNA is substrate; RNase BN involved in tRNA processing.	complete
	GO:0004518	nuclease activity	PMID:19366704	IDA: Inferred from Direct Assay		F	Figure 1. Gel showing different sizes of RNA. RNase BN is cleaving the DNA at various places.	complete
	GO:0004518	nuclease activity	GOA:spkw SP_KW:GO_REF:0000004	IEA: Inferred from Electronic Annotation	SP_KW:KW-0540	F	Seeded from EcoCyc (v14.0)	complete
	GO:0004519	endonuclease activity	GOA:spkw SP_KW:GO_REF:0000004	IEA: Inferred from Electronic Annotation	SP_KW:KW-0255	F	Seeded from EcoCyc (v14.0)	complete
	GO:0008033	tRNA processing	GOA:hamap GO_REF:0000020	IEA: Inferred from Electronic Annotation	HAMAP:MF_01818	P	Seeded from EcoCyc (v14.0)	complete
	GO:0008033	tRNA processing	GOA:spkw SP_KW:GO_REF:0000004	IEA: Inferred from Electronic Annotation	SP_KW:KW-0819	P	Seeded from EcoCyc (v14.0)	complete
	GO:0008270	zinc ion binding	GOA:hamap GO_REF:0000020	IEA: Inferred from Electronic Annotation	HAMAP:MF_01818	F	Seeded from EcoCyc (v14.0)	complete
	GO:0008270	zinc ion binding	GOA:spkw SP_KW:GO_REF:0000004	IEA: Inferred from Electronic Annotation	SP_KW:KW-0862	F	Seeded from EcoCyc (v14.0)	complete
	GO:0016787	hydrolase activity	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR001279	F	Seeded from EcoCyc (v14.0)	complete
	GO:0016787	hydrolase activity	GOA:spkw SP_KW:GO_REF:0000004	IEA: Inferred from Electronic Annotation	SP_KW:KW-0378	F	Seeded from EcoCyc (v14.0)	complete
Under review	GO:0046872	metal ion binding	PMID:19366704	IDA: Inferred from Direct Assay		F	Table 1. Activity of apo enzyme increased in the presence of various metals. Binding of metals increased activity of enzyme.	complete
	GO:0016891	endoribonuclease activity, producing 5'-phosphomonoesters	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR013469	F	Seeded from EcoCyc (v14.0)	complete
	GO:0016891	endoribonuclease activity, producing 5'-phosphomonoesters	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR013471	F	Seeded from EcoCyc (v14.0)	complete
	GO:0042779	tRNA 3'-trailer cleavage	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR013469	P	Seeded from EcoCyc (v14.0)	complete
	GO:0004532	exoribonuclease activity	PMID:10625642	IDA: Inferred from Direct Assay		F	Table VI. if RNase BN were exonuclease, acid soluble product expected to be AMP, which would be converted to neutral molecule after treatment with alkaline phosphatase. If RNase BN endoribonuclease, acid-soluble oligonucleotides would remain charged and elute with nucleotide fraction. Seen in table, majority eluted with nucleoside fraction (uncharged)	complete
	GO:0042779	tRNA 3'-trailer cleavage	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR013471	P	Seeded from EcoCyc (v14.0)	complete
	GO:0042781	3'-tRNA processing endoribonuclease activity	GOA:hamap GO_REF:0000020	IEA: Inferred from Electronic Annotation	HAMAP:MF_01818	F	Seeded from EcoCyc (v14.0)	complete
	GO:0046872	metal ion binding	GOA:spkw SP_KW:GO_REF:0000004	IEA: Inferred from Electronic Annotation	SP_KW:KW-0479	F	Seeded from EcoCyc (v14.0)	complete
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Interactions See Help:Product_interactions for help entering or editing information about gene product interactions in this section of EcoliWiki.

Partner Type	Partner	Notes	References	Evidence
Protein	Subunits of RNase BN	Purified RNase BN is a homodimer	PMID:10625642
Protein	ycjU		PMID:16606699	Experiment(s):EBI-1142406
Protein	tnaA		PMID:16606699	Experiment(s):EBI-1142406
Protein	rplF		PMID:16606699	Experiment(s):EBI-1142406
Protein	fkpA		PMID:16606699	Experiment(s):EBI-1142406
Protein	ydeI		PMID:16606699	Experiment(s):EBI-1142406
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Notes

The Deutscher lab initially published that RNase BN was an exonuclease and not and endonuclease on tRNA substrates^[7]. The later showed that RNase BN also has endonuclease activity on oligo rA and rA:rU substrates ^[8].

Localization

See Help:Product_localization for how to add or edit information in this section of EcoliWiki.

Compartment	Description	Evidence	Reference/Source	Notes
plasma membrane	C-terminus localized in the cytoplasm with 6 predicted transmembrane domains	Daley et al. (2005) ^[9]
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Notes

Structure and Physical Properties

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<protect> Physical Properties See Help:Product_physical_properties for help entering or editing information about the physical properties of this gene product.

Name
Sequence	at EcoCyc MKRDELMELI FLGTSAGVPT RTRNVTAILL NLQHPTQSGL WLFDCGEGTQ HQLLHTAFNP GKLDKIFISH LHGDHLFGLP GLLCSRSMSG IIQPLTIYGP QGIREFVETA LRISGSWTDY PLEIVEIGAG EILDDGLRKV TAYPLEHPLE CYGYRIEEHD KPGALNAQAL KAAGVPPGPL FQELKAGKTI TLEDGRQING ADYLAAPVPG KALAIFGDTG PCDAALDLAK GVDVMVHEAT LDITMEAKAN SRGHSSTRQA ATLAREAGVG KLIITHVSSR YDDKGCQHLL RECRSIFPAT ELANDFTVFN V
Length	311
Mol. Wt	33.703 kDa
pI	6.1 (calculated)
Extinction coefficient	21,430 - 22,180 (calc based on 7 Y, 2 W, and 6 C residues)
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Domains/Motifs/Modification Sites

See Help:Product_domains_motifs for help entering or editing information in this section of EcoliWiki.

Type	Residues	Description	Notes	References
Domain	14..151	PF00753 Metallo-beta-lactamase superfamily		PMID:19920124
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<motif_map/>

Structure
See Help:Product_structure for help entering or editing information in this section of EcoliWiki.

Structures

<beststructure> gene=rbn taxon=562,83333 </beststructure>

Models

View models at:

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Structure figures

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Notes

Gene Product Resources

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See Help:Product_resources for help with entering or editing information in this section of EcoliWiki.

Resource type	Source	Notes/Reference
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Notes

Accessions in Other Databases

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See Help:Gene_accessions for help with entering information into the Gene Accessions table.

Database	Accession	Notes
NCBI (Protein) (EcoliWiki Page)	GI:90111412	Escherichia coli str. K-12 substr. MG1655
NCBI (Protein) (EcoliWiki Page)	GeneID:946760	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0007496	Escherichia coli str. K-12 substr. MG1655
UniProt (EcoliWiki Page)	UniProtKB/Swiss-Prot:P0A8V0	Escherichia coli str. K-12 substr. MG1655
EcoCyc	EcoCyc:G7175	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG14260	Escherichia coli str. K-12 substr. MG1655
NCBI (Gene) (EcoliWiki Page)	GeneID:946760	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120003751	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB4008	Escherichia coli str. K-12 substr. MG1655
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Notes

Links

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Name	URL	Comments
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Expression

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Overview

This is a placeholder for a summary statement on how expression of this gene product is regulated. You can help EcoliWiki by becoming a user and writing/editing this statement.

Cellular Levels

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See Help:Cellular levels

Molecule	Organism or Strain	Value	Units	Experimental Conditions	Assay used	Reference(s)
Protein	E. coli K-12 MG1655	468	molecules/cell/generation	Medium: MOPS Complete Temperature (°C): 37 Doubling time (min): *Growth phase: OD: other:	Ribosome Profiling	PMID: 24766808
Protein	E. coli K-12 MG1655	153	molecules/cell/generation	Medium: MOPS Minimal Temperature (°C): 37 Doubling time (min): *Growth phase: OD: other:	Ribosome Profiling	PMID: 24766808
Protein	E. coli K-12 MG1655	303	molecules/cell/generation	Medium: MOPS Complete without Methionine Temperature (°C): 37 Doubling time (min): *Growth phase: OD: other:	Ribosome Profiling	PMID: 24766808
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Notes

Transcription and Transcriptional Regulation

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See Help:Expression_transcription for help entering or editing information in this section of EcoliWiki.

Transcription unit(s)
elaC
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File:.jpg

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Notes

This is a placeholder for a summary statement about how transcription of this gene is regulated. You can help EcoliWiki by becoming a user and writing/editing this statement.

Translation and Regulation of Translation

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<protect><gbrowseImage> name=NC_000913:2379610..2379650 source=MG1655 type=Gene+DNA_+Protein preset=Nterminus </gbrowseImage> This picture shows the sequence around the N-terminus.

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Notes

This is a placeholder for a summary statement about how translation of this gene product is regulated. You can help EcoliWiki by becoming a user and writing/editing this statement.

Turnover and Regulation of Turnover

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Notes

This is a placeholder for a summary statement about turnover of this gene product. You can help EcoliWiki by becoming a user and writing/editing this statement.

Experimental

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<protect> Mutations Affecting Expression See Help:Expression_mutations for help entering or editing information in this section of EcoliWiki.

Allele Name	Mutation	Phenotype	Reference
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Expression Studies See Help:Expression_studies for help entering or editing information in this section of EcoliWiki.

Type	Reference	Notes
microarray	GEO Profiles:b2268 (EcoliWiki Page)	NCBI GEO profiles for rbn
microarray	GenExpDB:b2268 (EcoliWiki Page)	Summary of data for rbn from multiple microarray studies
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Expression Resources See Help:Expression_resources for help entering or editing information in this section of EcoliWiki.

Resource Name	Resource Type	Description	Source	Notes
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Notes

Accessions Related to rbn Expression

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See Help:Gene_accessions for help with entering information into the Gene Accessions table.

Database	Accession	Notes
EcoCyc	EcoCyc:G7175	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB4008	Escherichia coli str. K-12 substr. MG1655
EcoliGenExpDB (EcoliWiki Page)	EcoliGenExpDB:b2268
EcoGene	EcoGene:EG14260	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120003751	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0007496	Escherichia coli str. K-12 substr. MG1655
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Notes

Links

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Name	URL	Comments
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Evolution

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Homologs in Other Organisms

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See Help:Evolution_homologs for help entering or editing information in this section of EcoliWiki.

Organism	Homologs (Statistics)	Comments
Anopheles gambiae	ENSANGP00000010160 (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Apis mellifera	ENSAPMP00000006453 (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Arabidopsis thaliana	AT3G16260 (score: 1.000; bootstrap: 100%) AT1G52160 (score: 0.646)	From Inparanoid:20070104
Bos taurus	ENSBTAP00000007468 (score: 1.000; bootstrap: 99%)	From Inparanoid:20070104
Caenorhabditis briggsae	WBGene00024929 (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Caenorhabditis elegans	WBGene00001983 (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Canis familiaris	ENSCAFP00000000243 (score: 1.000; bootstrap: 99%)	From Inparanoid:20070104
Danio rerio	ZDB-GENE-040801-246 (score: 1.000; bootstrap: 99%) ZDB-CDNA-040801-261 (score: 1.000; bootstrap: 99%)	From Inparanoid:20070104
Dictyostelium discoideum	DDB0189002 (score: 1.000; bootstrap: 100%) DDB0202976 (score: 0.650) DDB0217796 (score: 0.062)	From Inparanoid:20070104
Drosophila melanogaster	FBgn0028426 (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Drosophila pseudoobscura	GA17222-PA (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Gallus gallus	ENSGALP00000001532 (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Homo sapiens	ENSP00000269466 (score: 1.000; bootstrap: 99%)	From Inparanoid:20070104
Macaca mulatta	ENSMMUP00000004181 (score: 1.000; bootstrap: 94%)	From Inparanoid:20070104
Monodelphis domestica	ENSMODP00000013731 (score: 1.000; bootstrap: 99%)	From Inparanoid:20070104
Mus musculus	MGI:1890495 (score: 1.000; bootstrap: 99%)	From Inparanoid:20070104
Pan troglodytes	ENSPTRP00000017046 (score: 1.000; bootstrap: 99%)	From Inparanoid:20070104
Rattus norvegicus	ENSRNOP00000000125 (score: 1.000; bootstrap: 99%)	From Inparanoid:20070104
Saccharomyces cerevisiae	YKR079C (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Schizosaccharomyces pombe	SPAC1D40 (score: 1.000; bootstrap: 100%) SPBC3D63c (score: 0.093)	From Inparanoid:20070104
Takifugu rubripes	NEWSINFRUP00000169451 (score: 1.000; bootstrap: 98%)	From Inparanoid:20070104
Tetraodon nigroviridis	GSTENP00032638001 (score: 1.000; bootstrap: 100%) GSTENP00002860001 (score: 0.467)	From Inparanoid:20070104
Xenopus tropicalis	ENSXETP00000027565 (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Shigella flexneri	ELAC	From SHIGELLACYC
E. coli O157	ELAC	From ECOO157CYC
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Do-It-Yourself Web Tools

Notes

Families

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See Help:Gene_accessions for help with entering information into the Gene Accessions table.

Database	Accession	Notes
Pfam (EcoliWiki Page)	PF00753 Metallo-beta-lactamase superfamily
Panther (EcoliWiki Page)	PTHR12553:SF6
Superfamily (EcoliWiki Page)	SUPERFAMILY:56281
EcoCyc	EcoCyc:G7175	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG14260	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120003751	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB4008	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0007496	Escherichia coli str. K-12 substr. MG1655
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Notes

Links

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Name	URL	Comments
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References

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See Help:References for how to manage references in EcoliWiki.

↑ ^1.00 ^1.01 ^1.02 ^1.03 ^1.04 ^1.05 ^1.06 ^1.07 ^1.08 ^1.09 ^1.10 ^1.11 ^1.12 ^1.13 Riley, M. et al. (2006) Nucleic Acids Res 34:1-6 (corrected supplemental data from B. Wanner)
↑ ^2.0 ^2.1 ^2.2 ^2.3 ^2.4 ^2.5 EcoCyc (release 11.1; 2007) Keseler, IM et al. (2005) Nucleic Acids Res. 33(Database issue):D334-7
↑ ^3.00 ^3.01 ^3.02 ^3.03 ^3.04 ^3.05 ^3.06 ^3.07 ^3.08 ^3.09 ^3.10 ^3.11 ^3.12 EcoCyc (release 10.6; 2007) Keseler, IM et al. (2005) Nucleic Acids Res. 33(Database issue):D334-7
↑ ^4.0 ^4.1 ^4.2 EcoGene: Rudd, KE (2000) EcoGene: a genome sequence database for Escherichia coli K-12. Nucleic Acids Res 28:60-4.
↑ ^5.0 ^5.1 ^5.2 CGSC: The Coli Genetics Stock Center
↑ ^6.0 ^6.1 The Tn10 insertion sites determined by Nichols et al. 1998 (PMID:9829956) were reannotated by alignment with E. coli K-12 genome sequence (GenBank accession NC_000913). P1 contransduction frequencies were calculated using the formula of Wu (PMID:5338813).
↑ Callahan, C et al. (2000) Purification and characterization of the tRNA-processing enzyme RNase BN. J. Biol. Chem. 275 1030-4 [7 PubMed]
↑ 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 15425-31 PubMed
↑ Daley, DO et al. (2005) Global topology analysis of the Escherichia coli inner membrane proteome. Science 308 1321-3 PubMed

rbn:On One Page

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Notes

Gene

Nomenclature

Notes

Location(s) and DNA Sequence

Notes

Sequence Features

Notes

Alleles and Phenotypes

Notes

Genetic Interactions

Notes

Genetic Resources

Notes

Accessions in Other Databases

Notes

Links

Product(s)

Nomenclature

Notes

Function

Notes

Localization

Notes

Structure and Physical Properties

Structure figures

Notes

Gene Product Resources

Notes

Accessions in Other Databases

Notes

Links

Expression

Overview

Cellular Levels

Notes

Transcription and Transcriptional Regulation

Notes

Translation and Regulation of Translation

Notes

Turnover and Regulation of Turnover

Notes

Experimental

Notes

Accessions Related to rbn Expression

Notes

Links

Evolution

Homologs in Other Organisms

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Notes

Families

Notes

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