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rbn:Gene Product(s)

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Nomenclature Function Interactions Localization Sequence Domains Structure Resources Accessions Links References Suggestions

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[2][1], Rnz[2][1], B2268[2][1], EcoZ[2][1], ElaC[2][1] , ECK2262, ecoZ, elaC, JW2263, rnz, zipD, b2268

Product description

ElaC[2]; Rbn[3];

Component of RNase BN[3]

RNase BN, tRNA processing enzyme; has zinc phosphodiesterase activity[4]

EC number (for enzymes)


Notes

Function

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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[5]

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[6]

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[6]

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[5]

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

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[5]

Protein

ycjU

PMID:16606699[7]

Experiment(s):EBI-1142406

Protein

tnaA

PMID:16606699[7]

Experiment(s):EBI-1142406

Protein

rplF

PMID:16606699[7]

Experiment(s):EBI-1142406

Protein

fkpA

PMID:16606699[7]

Experiment(s):EBI-1142406

Protein

ydeI

PMID:16606699[7]

Experiment(s):EBI-1142406

Notes

The Deutscher lab initially published that RNase BN was an exonuclease and not and endonuclease on tRNA substrates[8]. The later showed that RNase BN also has endonuclease activity on oligo rA and rA:rU substrates [6].

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]


Notes

Structure and Physical Properties

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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)


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[10]


rectanglemotifs

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

Structures

No results found for a best structure.

Models

View models at:

Structure figures

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

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

Notes

Links

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References

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

  1. 1.0 1.1 1.2 1.3 1.4 1.5 Riley, M. et al. (2006) Nucleic Acids Res 34:1-6 (corrected supplemental data from B. Wanner)
  2. 2.0 2.1 2.2 2.3 2.4 2.5 EcoCyc (release 10.6; 2007) Keseler, IM et al. (2005) Nucleic Acids Res. 33(Database issue):D334-7
  3. 3.0 3.1 EcoCyc (release 11.1; 2007) Keseler, IM et al. (2005) Nucleic Acids Res. 33(Database issue):D334-7
  4. EcoGene: Rudd, KE (2000) EcoGene: a genome sequence database for Escherichia coli K-12. Nucleic Acids Res 28:60-4.
  5. 5.0 5.1 5.2 Callahan, C et al. (2000) Purification and characterization of the tRNA-processing enzyme RNase BN. J. Biol. Chem. 275 1030-4 PubMed EcoliWiki page
  6. 6.0 6.1 6.2 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 EcoliWiki page
  7. 7.0 7.1 7.2 7.3 7.4 Arifuzzaman, M et al. (2006) Large-scale identification of protein-protein interaction of Escherichia coli K-12. Genome Res. 16 686-91 PubMed EcoliWiki page
  8. Callahan, C et al. (2000) Purification and characterization of the tRNA-processing enzyme RNase BN. J. Biol. Chem. 275 1030-4 PubMed EcoliWiki page
  9. Daley, DO et al. (2005) Global topology analysis of the Escherichia coli inner membrane proteome. Science 308 1321-3 PubMed EcoliWiki page
  10. Finn, RD et al. (2010) The Pfam protein families database. Nucleic Acids Res. 38 D211-22 PubMed EcoliWiki page

Categories

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