rlmH:Quickview: Difference between revisions

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!align=left |Standard Name
!align=left {{table_heading_style}} |Standard Name
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''rlmH''  
''rlmH''  
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!align=left |Gene Synonym(s)
!align=left {{table_heading_style}} |Gene Synonym(s)
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''ECK0629, b0636, JW0631''<ref name='LIB:Riley_2006'/>, ybeA product
''ECK0629, b0636, JW0631'', ybeA<ref name='LIB:Riley_2006'/>
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!align=left |Product Desc.
!align=left {{table_heading_style}} |Product Desc.
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conserved protein<ref name='LIB:EcoCyc10.6'/><ref name='LIB:EcoCyc11.1'/>; Component of [[:Category:Complex:conserved protein|conserved protein]]<ref name='LIB:EcoCyc11.1'/>.  Sequence similarity indicates rlmH is an S-adenosylmethionine-dependent (SPOUT) methyltransferase <ref name="PMID:18755835"/>.  Inactivation of the rlmH gene (Keio collection knockout <ref name='PMID:16738554'/>) leads to loss of methylation at nucleotide Psi1915 in 23S rRNA <ref name="PMID:18755835"/>.  Computational docking suggests that a YbeA methyltransferase homodimer fits comfortably into the ribosomal A site without encroaching into the P site <ref name="PMID:18755835"/>.
conserved protein<ref name='LIB:EcoCyc10.6'/><ref name='LIB:EcoCyc11.1'/>; Component of [[:Category:Complex:conserved protein|conserved protein]]<ref name='LIB:EcoCyc11.1'/>.  Sequence similarity indicates rlmH is an S-adenosylmethionine-dependent (SPOUT) methyltransferase <ref name="PMID:18755835"/>.  Inactivation of the rlmH gene (Keio collection knockout <ref name='PMID:16738554'/>) leads to loss of methylation at nucleotide Psi1915 in 23S rRNA <ref name="PMID:18755835"/>.  Computational docking suggests that a YbeA methyltransferase homodimer fits comfortably into the ribosomal A site without encroaching into the P site <ref name="PMID:18755835"/>.
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Putative methyltransferase, function unknown<ref name='LIB:EcoGene'/>
Putative methyltransferase, function unknown<ref name='LIB:EcoGene'/>
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!align=left |Product Synonyms(s)
!align=left {{table_heading_style}} |Product Synonyms(s)
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conserved protein<ref name='LIB:Riley_2006'/>, B0636<ref name='LIB:EcoCyc10.6'/><ref name='LIB:Riley_2006'/>, YbeA<ref name='LIB:EcoCyc10.6'/><ref name='LIB:Riley_2006'/>  
conserved protein<ref name='LIB:Riley_2006'/>, B0636<ref name='LIB:EcoCyc10.6'/><ref name='LIB:Riley_2006'/>, YbeA<ref name='LIB:EcoCyc10.6'/><ref name='LIB:Riley_2006'/>  
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!align=left |Knock-Out Phenotype
!align=left {{table_heading_style}} |Function from GO
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!align=left |Regulation/Expression
!align=left {{table_heading_style}} |Knock-Out Phenotype
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!align=left {{table_heading_style}} |Regulation/Expression
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transcription unit(s): [[:Category:Txn_unit:rlpA|rlpA]]<ref name='LIB:EcoCyc10.6'/>  
transcription unit(s): [[:Category:Txn_unit:rlpA|rlpA]]<ref name='LIB:EcoCyc10.6'/>  
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!align=left |Regulation/Activity
!align=left {{table_heading_style}} |Regulation/Activity
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!align=left {{table_heading_style}} |Quick Links
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[http://ecoliwiki.net/tools/display_dna.php?gene=ybeA&loc=MG1655:667938..667471,W3110:669137..668670,DH10B:607270..606803,DH10B:720530..720063 DNA display]&nbsp;&nbsp;&nbsp; [http://ecoliwiki.net/tools/display_protein.php?f=NC_000913&start=720530&end=720063&gene=ybeA&aa=mklqlvavgtkmpdwvqtgfteylrrfpkdmpfelieipagkrgknadikrildkegeqmlaaagknrivtldipgkpwdtpqlaaelerwkldgrdvslliggpeglspackaaaeqswslsaltlphplvrvlvaeslyrawsittnhpyhre Protein display]&nbsp;&nbsp;&nbsp; [http://www.ncbi.nlm.nih.gov/sites/entrez?db=pubmed&cmd=Search&Term=ybeA+AND+escherichia+coli Pubmed(ybeA)]&nbsp;&nbsp;&nbsp; [http://trimer.tamu.edu/cgi-bin/textpresso/2.1/ecoli/search?searchstring=ybeA Textpresso(ybeA)]


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Revision as of 23:20, 21 January 2010

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Quickview   Gene   Gene Product(s)   Expression   Evolution   On One Page    
References Suggestions

See Help:Quickview for help with entering information in the Quickview table.

Standard Name

rlmH

Gene Synonym(s)

ECK0629, b0636, JW0631, ybeA[1]

Product Desc.

conserved protein[2][3]; Component of conserved protein[3]. Sequence similarity indicates rlmH is an S-adenosylmethionine-dependent (SPOUT) methyltransferase [4]. Inactivation of the rlmH gene (Keio collection knockout [5]) leads to loss of methylation at nucleotide Psi1915 in 23S rRNA [4]. Computational docking suggests that a YbeA methyltransferase homodimer fits comfortably into the ribosomal A site without encroaching into the P site [4].

Purta et al. suggest that a more suitable designation

for the SPOUT-superfamily member YbeA would be the rRNA large subunit methyltransferase RlmH, consistent with the terminology used for the other rRNA methyltransferase characterized in E. coli (see also Ofengand and Del Campo, 2004 [6][7], and Andersen and Douthwaite, 2006 [8].

Putative methyltransferase, function unknown[9]

Product Synonyms(s)

conserved protein[1], B0636[2][1], YbeA[2][1]

Function from GO
Knock-Out Phenotype
Regulation/Expression

transcription unit(s): rlpA[2]

Regulation/Activity
Quick Links

DNA display    Protein display    Pubmed(ybeA)    Textpresso(ybeA)

edit table

See Help:Quickview for help with entering information in the Quickview table.

Notes

[back to top]


AFMB Structural Genomics target No. 125 (http://afmb.cnrs-mrs.fr/article171.html). Structural similarity to known SAM-dependent SPOUT family methyltransferases.[9]



References

[back to top]


  1. ↑ 1.0 1.1 1.2 1.3 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 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. ↑ 4.0 4.1 4.2 Purta, E et al. (2008) YbeA is the m3Psi methyltransferase RlmH that targets nucleotide 1915 in 23S rRNA. RNA 14 2234-44 PubMed
  5. ↑ Baba, T et al. (2006) Construction of Escherichia coli K-12 in-frame, single-gene knockout mutants: the Keio collection. Mol. Syst. Biol. 2 2006.0008 PubMed
  6. ↑ Cite error: Invalid <ref> tag; no text was provided for refs named LIB:Neidhardt et al. 1996
  7. ↑ Cite error: Invalid <ref> tag; no text was provided for refs named Ofengand, J. and Del Campo, M 2004. Modified nucleotides of Escherichia coli ribosomal RNA. In EcoSal—Escherichia coli and Salmonella: Cellular and molecular biology (ed. R. Curtiss). ASM Press, Washington, DC.
  8. ↑ Andersen, NM & Douthwaite, S (2006) YebU is a m5C methyltransferase specific for 16 S rRNA nucleotide 1407. J. Mol. Biol. 359 777-86 PubMed
  9. ↑ 9.0 9.1 EcoGene: Rudd, KE (2000) EcoGene: a genome sequence database for Escherichia coli K-12. Nucleic Acids Res 28:60-4.
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