rlmH:Quickview: Difference between revisions

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{{Tab On|Quickview|ybeA}}{{Tab|Gene|ybeA}}{{Tab|Gene Product(s)|ybeA}}{{Tab|Expression|ybeA}}{{Tab|Evolution|ybeA}}{{Tab|On One Page|ybeA}}{{TabsBottom}}
{{Tab On|Quickview|rlmH}}{{Tab|Gene|rlmH}}{{Tab|Gene Product(s)|rlmH}}{{Tab|Expression|rlmH}}{{Tab|Evolution|rlmH}}{{Tab|On One Page|rlmH}}{{TabsBottom}}
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!{{table_heading_style}} |Gene Name
!align=left {{table_heading_style}} |Standard Name
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[[ybeA:Gene|''ybeA]]'' (synonyms: ''ECK0629, b0636, JW0631'')<ref name='LIB:Riley_2006'/>
''rlmH''
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!{{table_heading_style}} |Product(s)  
!align=left {{table_heading_style}} |Gene Synonym(s)
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[[ybeA:Gene_Product(s)|YbeA product]]<ref name='LIB:Riley_2006'/>: conserved protein product, B0636 product
''ECK0629, b0636, JW0631'', ybeA<ref name='LIB:Riley_2006'/>, JW0631, ybeA''
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!{{table_heading_style}} |Description
!align=left {{table_heading_style}} |Product Desc.
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conserved protein<ref name='LIB:EcoCyc10.6'/><ref name='LIB:EcoCyc11.1'/>  
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"/>.


Component of [[:Category:Complex:conserved protein|conserved protein]]<ref name='LIB:EcoCyc11.1'/>
Purta <em>et al.</em> 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 <ref name='LIB:Neidhardt et al. 1996'/><ref name='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.'/>, and Andersen and Douthwaite, 2006 <ref name='PMID:16678201'/>.


Putative methyltransferase, function unknown<ref name='LIB:EcoGene'/>
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!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'/> , ECK0629, JW0631, ybeA, b0636''
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!align=left {{table_heading_style}} |Function from GO
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<GO_nr />
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!{{table_heading_style}} |Knock-Out Phenotype
!align=left {{table_heading_style}} |Knock-Out Phenotype
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|-
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!{{table_heading_style}} |Regulation/Expression
!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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!{{table_heading_style}} |Regulation/Activity
!align=left {{table_heading_style}} |Regulation/Activity
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!align=left {{table_heading_style}} |Quick Links
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[[File:porteco.png|link=http://porteco.org/AjaxSearch.jsp?searchString=ybeA&s=search]] <br/><br/> [[File:dnadisplay.png|link=http://ecoliwiki.net/tools/display_dna.php?gene=ybeA&loc=MG1655%3A667938..667471,W3110%3A669137..668670,DH10B%3A607270..606803,DH10B%3A720530..720063,BW2952%3A570231..570698]] [[File:proteindisplay.png|link=http://ecoliwiki.net/tools/display_protein.php?f=NC_000913&start=570231&end=570698&gene=ybeA&aa=mklqlvavgtkmpdwvqtgfteylrrfpkdmpfelieipagkrgknadikrildkegeqmlaaagknrivtldipgkpwdtpqlaaelerwkldgrdvslliggpeglspackaaaeqswslsaltlphplvrvlvaeslyrawsittnhpyhre]]&nbsp;&nbsp;  [[File:pubmed.jpg|link=http://www.ncbi.nlm.nih.gov/sites/entrez?db=pubmed&cmd=Search&Term=ybeA+AND+escherichia+coli]]&nbsp;&nbsp;  [[File:textpresso.jpg|link=http://textpresso.tamu.edu/cgi-bin/textpresso/search?q=ybeA]]&nbsp;&nbsp;
 
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===Notes===
===Notes===
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AFMB Structural Genomics target No. 125 (http://afmb.cnrs-mrs.fr/article171.html). Structural similarity to known SAM-dependent SPOUT family methyltransferases.<ref name='LIB:EcoGene'/>




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==References==
==References==
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Latest revision as of 21:44, 27 May 2013

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

rlmH

Gene Synonym(s)

ECK0629, b0636, JW0631, ybeA[1], JW0631, ybeA

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] , ECK0629, JW0631, ybeA, b0636

Function from GO

<GO_nr />

Knock-Out Phenotype
Regulation/Expression

transcription unit(s): rlpA[2]

Regulation/Activity
Quick Links



        

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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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