rlmH:Gene Product(s)

From EcoliWiki
Jump to: navigation, search

{{#css:Suppresslinks.css}}<css>h1 .editsection { display:none;} h2 .editsection { display:none;}</css>

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

rlmH, rRNA large subunit methyltransferase

Synonyms

conserved protein[1], B0636[2][1], YbeA[2][1] , ECK0629, JW0631, ybeA, b0636

Product description

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]

EC number (for enzymes)


edit table

<protect></protect>

Notes

Function

[back to top]


<protect> 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 Evidence Code with/from Aspect Notes Status
GO:0005737

cytoplasm

GOA:hamap
GO_REF:0000020

IEA: Inferred from Electronic Annotation

HAMAP:MF_00658

C

Seeded from EcoCyc (v14.0)

complete

GO:0005737

cytoplasm

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR003742

C

Seeded from EcoCyc (v14.0)

complete

GO:0005737

cytoplasm

GOA:spkw
SP_KW:GO_REF:0000004

IEA: Inferred from Electronic Annotation

SP_KW:KW-0963

C

Seeded from EcoCyc (v14.0)

complete

GO:0005737

cytoplasm

GO_REF:0000023

IEA: Inferred from Electronic Annotation

SP_SL:SL-0086

C

Seeded from EcoCyc (v14.0)

complete

GO:0005737

cytoplasm

PMID:18755835[4]

IC: Inferred by Curator

GO:0070038

C

Seeded from EcoCyc (v14.0)

complete

GO:0031167

rRNA methylation

PMID:18755836[10]

IDA: Inferred from Direct Assay

P

Seeded from EcoCyc (v14.0)

complete

GO:0042803

protein homodimerization activity

PMID:18755835[4]

NAS: Non-traceable Author Statement

F

Seeded from EcoCyc (v14.0)

complete

GO:0043022

ribosome binding

PMID:18755835[4]

NAS: Non-traceable Author Statement

F

Seeded from EcoCyc (v14.0)

complete

GO:0070038

rRNA (pseudouridine-N3-)-methyltransferase activity

GOA:hamap
GO_REF:0000020

IEA: Inferred from Electronic Annotation

HAMAP:MF_00658

F

Seeded from EcoCyc (v14.0)

complete

GO:0070475

rRNA base methylation

PMID:18755835[4]

IMP: Inferred from Mutant Phenotype

P

Seeded from EcoCyc (v14.0)

complete

GO:0070475

rRNA base methylation

PMID:18755836[10]

IMP: Inferred from Mutant Phenotype

P

Seeded from EcoCyc (v14.0)

complete

edit table

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 conserved protein

could be indirect

Protein

rpsB

PMID:15690043[11]

Experiment(s):EBI-887739

Protein

groL

PMID:16606699[12]

Experiment(s):EBI-1137503

Protein

gfcD

PMID:16606699[12]

Experiment(s):EBI-1137503

Protein

Homodimer

Docking simulation and sequence similarity [4]


edit table

</protect>

Notes

Localization

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

Compartment Description Evidence Reference/Source Notes
edit table

<protect></protect>

Notes

Structure and Physical Properties

[back to top]


<protect> Physical Properties See Help:Product_physical_properties for help entering or editing information about the physical properties of this gene product.

Name
Sequence

at EcoCyc 

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

155

Mol. Wt

17.341 kDa

pI

8.9 (calculated)

Extinction coefficient

31,970 - 32,095 (calc based on 3 Y, 5 W, and 1 C residues)

edit table


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

Domain

1..153

PF02590 Predicted SPOUT methyltransferase

PMID:19920124[13]

edit table

<motif_map/>

Structure
See Help:Product_structure for help entering or editing information in this section of EcoliWiki.

Structures

<beststructure> gene=ybeA taxon=562,83333 </beststructure>

Models

View models at:

edit table
</protect>

Structure figures

<protect>

</protect>

Notes

Gene Product Resources

[back to top]


See Help:Product_resources for help with entering or editing information in this section of EcoliWiki.

Resource type Source Notes/Reference
edit table

<protect></protect>

Notes

Accessions in Other Databases

[back to top]


See Help:Gene_accessions for help with entering information into the Gene Accessions table.

Database Accession Notes

NCBI (Protein) (EcoliWiki Page)

GI:16128619

Escherichia coli str. K-12 substr. MG1655

NCBI (Protein) (EcoliWiki Page)

GeneID:945239

Escherichia coli str. K-12 substr. MG1655

UniProt (EcoliWiki Page)

UniProtKB/Swiss-Prot:P0A8I8

Escherichia coli str. K-12 substr. MG1655

NCBI (Gene) (EcoliWiki Page)

GeneID:945239

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:

Escherichia coli str. K-12 substr. MG1655

edit table

<protect></protect>

Notes

Links

[back to top]




References

[back to top]


See Help:References for how to manage references in EcoliWiki.

  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 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 4.4 4.5 4.6 4.7 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. ↑
  7. ↑
  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. ↑ EcoGene: Rudd, KE (2000) EcoGene: a genome sequence database for Escherichia coli K-12. Nucleic Acids Res 28:60-4.
  10. ↑ 10.0 10.1 Ero, R et al. (2008) Identification of pseudouridine methyltransferase in Escherichia coli. RNA 14 2223-33 PubMed
  11. ↑ Butland, G et al. (2005) Interaction network containing conserved and essential protein complexes in Escherichia coli. Nature 433 531-7 PubMed
  12. ↑ 12.0 12.1 Arifuzzaman, M et al. (2006) Large-scale identification of protein-protein interaction of Escherichia coli K-12. Genome Res. 16 686-91 PubMed
  13. ↑ Finn, RD et al. (2010) The Pfam protein families database. Nucleic Acids Res. 38 D211-22 PubMed

Categories

[back to top]


Retrieved from "https://ecoliwiki.org/colipedia/index.php?title=rlmH:Gene_Product(s)&oldid=1489515"