rlmH:Gene Product(s)

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Nomenclature Function Interactions Localization Sequence Structure Resources Accessions Links References Suggestions

Nomenclature

Standard name

YbeA product, rRNA large subunit methyltransferase

Synonyms

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

Product description

conserved protein[2][3]; Component of ; conserved protein[3]. Sequence similarity indicates ybeA is an S-adenosylmethionine-dependent (SPOUT) methyltransferase [4]. Inactivation of the ybeA 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].

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:0005515

protein_binding

PMID:15690043[9]

IPI: Inferred from Physical Interaction

UniProtKB:P0A7V0

F

Seeded from EcoCyc 12.5 [10]


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Interactions

Partner Type Partner Notes

Protein

Subunits of conserved protein

could be indirect

Protein

Homodimer

Docking simulation and sequence similarity [4]

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Notes

Localization

Compartment Description Evidence Notes
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Notes

Structure and Physical Properties

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Physical Properties

Sequence

at EcoCyc 

MKLQLVAVGT KMPDWVQTGF TEYLRRFPKD MPFELIEIPA GKRGKNADIK RILDKEGEQM
LAAAGKNRIV TLDIPGKPWD TPQLAAELER WKLDGRDVSL LIGGPEGLSP ACKAAAEQSW
SLSALTLPHP LVRVLVAESL YRAWSITTNH PYHRE
Mol. Wt

17.34 kDa (calc) [2]

pI
Extinction coefficient

31970 - 32095 (calc based on 3 Y, 5 W, and 1 C residues)

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Domains/Motifs/Modification Sites

Type Residues Description Notes
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Structure

Structures

<beststructure>ybeA 562</beststructure>

Models

View models at:

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Notes

Gene Product Resources

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Resource type Source Notes/Reference
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Notes

Accessions in Other Databases

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Database Accession Notes

EcoCyc (EcoliWiki Page)

EcoCyc:EG11254-MONOMER

UniProt (EcoliWiki Page)

UniProt:P0A8I8

PFAM (EcoliWiki Page)

PFAM:PF02590

RefSeq (EcoliWiki Page)

RefSeq:NP_415169

ModBase (EcoliWiki Page)

ModBase:P0A8I8

PDB (EcoliWiki Page)

PDB:1NS5

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Notes

Links

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Name URL Comments
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References

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  1. ↑ 1.0 1.1 1.2 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 4.3 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. ↑ Butland, G et al. (2005) Interaction network containing conserved and essential protein complexes in Escherichia coli. Nature 433 531-7 PubMed
  10. ↑ EcoCyc (release 12.5; 2007) Keseler, IM et al. (2005) Nucleic Acids Res. 33(Database issue):D334-7


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