rbn:Gene Product(s): Difference between revisions

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Subunits of [[:Category:Complex:RNase BN|RNase BN]]  
Subunits of [[:Category:Complex:RNase BN|RNase BN]]  
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could be indirect
Purified RNase BN is a homodimer
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PMID:10625642
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Revision as of 14:17, 17 May 2010

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Quickview   Gene   Gene Product(s)   Expression   Evolution   On One Page    
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]

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)


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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(s) Evidence Code with/from Aspect Notes Status
GO:0046872

metal ion binding

GO_REF:0000004

IEA: Inferred from Electronic Annotation

SP_KW:KW-0479

F

Seeded from EcoCyc [5]

complete

GO:0042781

3'-tRNA processing endoribonuclease activity

GO_REF:0000020

IEA: Inferred from Electronic Annotation

HAMAP:MF_01818

F

Seeded from EcoCyc [5]

complete

GO:0042779

tRNA 3'-trailer cleavage

GO_REF:0000002
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR013469
InterPro:IPR013471

P

Seeded from EcoCyc [5]

complete

GO:0016891

endoribonuclease activity, producing 5'-phosphomonoesters

GO_REF:0000002
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR013469
InterPro:IPR013471

F

Seeded from EcoCyc [5]

complete

GO:0016787

hydrolase activity

GO_REF:0000002
GO_REF:0000004

IEA: Inferred from Electronic Annotation

InterPro:IPR001279
SP_KW:KW-0378

F

Seeded from EcoCyc [5]

complete

GO:0008270

zinc ion binding

GO_REF:0000004
GO_REF:0000020

IEA: Inferred from Electronic Annotation

SP_KW:KW-0862
HAMAP:MF_01818

F

Seeded from EcoCyc 12.5 [6]

complete

GO:0008033

tRNA processing

PMID:10625642[7]

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[8]

IDA: Inferred from Direct Assay

F

Figure 1. Gel showing different sizes of DNA. RNase BN is cleaving the DNA at various places.

complete

GO:0006401

RNA catabolic process

PMID:8955422[9]

IMP: Inferred from Mutant Phenotype

P

Seeded from EcoCyc 11.1[3].

complete

GO:0009451

RNA modification

P

Seeded from EcoCyc 11.1[3].

required fields missing

GO:0046872

metal ion binding

PMID:19366704[8]

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:0004519

endonuclease activity

GO_REF:0000004

IEA: Inferred from Electronic Annotation

SP_KW:KW-0255

F

Seeded from EcoCyc [5]

complete

GO:0008033

tRNA processing

GO_REF:0000004
GO_REF:0000020

IEA: Inferred from Electronic Annotation

SP_KW:KW-0819
HAMAP:MF_01818

P

Seeded from EcoCyc 12.5 [6]

complete

GO:0004518

nuclease activity

GO_REF:0000004

IEA: Inferred from Electronic Annotation

SP_KW:KW-0540

F

Seeded from EcoCyc [5]

complete

GO:0004532

exoribonuclease activity

PMID:10625642[7]

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

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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[7]

Protein

ycjU

PMID:16606699[10]

Experiment(s):EBI-1142406

Protein

tnaA

PMID:16606699[10]

Experiment(s):EBI-1142406

Protein

rplF

PMID:16606699[10]

Experiment(s):EBI-1142406

Protein

fkpA

PMID:16606699[10]

Experiment(s):EBI-1142406

Protein

ydeI

PMID:16606699[10]

Experiment(s):EBI-1142406
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Notes

Localization

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

Compartment Description Evidence Source Notes

plasma membrane

C-terminus localized in the cytoplasm with 6 predicted transmembrane domains

Daley et al. (2005) [11]


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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.

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
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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

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

EcoCyc (EcoliWiki Page)

EcoCyc:G7175-MONOMER

SwissModel (EcoliWiki Page)

SwissModel:P0A8V0

UniProt (EcoliWiki Page)

UniProt:P0A8V0

PFAM (EcoliWiki Page)

PFAM:PF00753

RefSeq (EcoliWiki Page)

RefSeq:NP_416771


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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 3.2 3.3 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 5.3 5.4 5.5 5.6 EcoCyc (release 13.0; 2009) Keseler, IM et al. (2009) Nucleic Acids Res. 37(Database issue):D464-70
  6. ↑ 6.0 6.1 EcoCyc (release 12.5; 2007) Keseler, IM et al. (2005) Nucleic Acids Res. 33(Database issue):D334-7
  7. ↑ 7.0 7.1 7.2 Callahan, C et al. (2000) Purification and characterization of the tRNA-processing enzyme RNase BN. J. Biol. Chem. 275 1030-4 PubMed
  8. ↑ 8.0 8.1 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
  9. ↑ Callahan, C & Deutscher, MP (1996) Identification and characterization of the Escherichia coli rbn gene encoding the tRNA processing enzyme RNase BN. J. Bacteriol. 178 7329-32 PubMed
  10. ↑ 10.0 10.1 10.2 10.3 10.4 Arifuzzaman, M et al. (2006) Large-scale identification of protein-protein interaction of Escherichia coli K-12. Genome Res. 16 686-91 PubMed
  11. ↑ Daley, DO et al. (2005) Global topology analysis of the Escherichia coli inner membrane proteome. Science 308 1321-3 PubMed

Categories

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