rlmH:Gene Product(s): Difference between revisions
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[[Category:Proteins]] | [[Category:Proteins]] | ||
[[Category:Complex:conserved protein]][[Category:Products with structures in PDB]][[Category:Complex:23S rRNA methyltransferase]][[Category:Keio collection]] | [[Category:Complex:conserved protein]][[Category:Products with structures in PDB]][[Category:Complex:23S rRNA methyltransferase]][[Category:Genes in the Keio knockout collection]] | ||
Revision as of 12:10, 21 October 2008
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| Quickview | Gene | Gene Product(s) | Expression | Evolution | On One Page |
| 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
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 |
IPI: Inferred from Physical Interaction |
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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See Help:Product_interactions for help entering or editing information about gene product interactions in this section of EcoliWiki.
Notes
Localization
| Compartment | Description | Evidence | Notes |
|---|---|---|---|
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See Help:Product_localization for how to add or edit information in this section of EcoliWiki.
Notes
Structure and Physical Properties
Physical Properties
| Sequence |
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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See Help:Product_physical_properties for help entering or editing information about the physical properties of this gene product.
Domains/Motifs/Modification Sites
| Type | Residues | Description | Notes |
|---|---|---|---|
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See Help:Product_domains_motifs for help entering or editing information in this section of EcoliWiki.
Structure
| Structures |
<beststructure>ybeA 562</beststructure> |
|---|---|
| Models |
View models at: |
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See Help:Product_structure for help entering or editing information in this section of EcoliWiki.
Notes
Gene Product Resources
| Resource type | Source | Notes/Reference |
|---|---|---|
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Notes
Accessions in Other Databases
| Database | Accession | Notes |
|---|---|---|
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See Help:Product_accessions for help entering or editing information in this section of EcoliWiki.
Notes
Links
| Name | URL | Comments |
|---|---|---|
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References
See Help:References for how to manage references in EcoliWiki.
- ↑ 1.0 1.1 1.2 Riley, M. et al. (2006) Nucleic Acids Res 34:1-6 (corrected supplemental data from B. Wanner)
- ↑ 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
- ↑ 3.0 3.1 EcoCyc (release 11.1; 2007) Keseler, IM et al. (2005) Nucleic Acids Res. 33(Database issue):D334-7
- ↑ 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
- ↑ 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
- ↑ Cite error: Invalid
<ref>tag; no text was provided for refs namedLIB:Neidhardt et al. 1996 - ↑ Cite error: Invalid
<ref>tag; no text was provided for refs namedOfengand, 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. - ↑ Andersen, NM & Douthwaite, S (2006) YebU is a m5C methyltransferase specific for 16 S rRNA nucleotide 1407. J. Mol. Biol. 359 777-86 PubMed
- ↑ Butland, G et al. (2005) Interaction network containing conserved and essential protein complexes in Escherichia coli. Nature 433 531-7 PubMed
- ↑ EcoCyc (release 12.5; 2007) Keseler, IM et al. (2005) Nucleic Acids Res. 33(Database issue):D334-7
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