rlmD:Gene Product(s)

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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

RlmD

Synonyms

23S rRNA m(5)U747 methyltransferase[1], B0859[2][1], YbjF[2][1], RumB[2][1] , ECK0850, JW0843, ybjF, b0859

Product description

23S ribosomal RNA 5-methyluridine methyltransferase[2][3]

23S rRNA (uracil-5)-methyltransferase, responsible for modification at position U747, SAM-dependent[4]

EC number (for enzymes)
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Notes

Function

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<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

C

Seeded from Riley et al 2006 [1].

Missing: evidence, reference

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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

nadE

PMID:16606699[5]

Experiment(s):EBI-1138195

Protein

rplB

PMID:16606699[5]

Experiment(s):EBI-1138195

Protein

rplA

PMID:16606699[5]

Experiment(s):EBI-1138195

Protein

groL

PMID:16606699[5]

Experiment(s):EBI-1138195

Protein

yciH

PMID:16606699[5]

Experiment(s):EBI-1138195

Protein

rhaS

PMID:16606699[5]

Experiment(s):EBI-1138195

Protein

appY

PMID:16606699[5]

Experiment(s):EBI-1138195
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Notes

Localization

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

Compartment Description Evidence Reference/Source Notes
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Notes

Structure and Physical Properties

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<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 

MQCALYDAGR CRSCQWIMQP IPEQLSAKTA DLKNLLADFP VEEWCAPVSG PEQGFRNKAK
MVVSGSVEKP LLGMLHRDGT PEDLCDCPLY PASFAPVFAA LKPFIARAGL TPYNVARKRG
ELKYILLTES QSDGGMMLRF VLRSDTKLAQ LRKALPWLHE QLPQLKVITV NIQPVHMAIM
EGETEIYLTE QQALAERFND VPLWIRPQSF FQTNPAVASQ LYATARDWVR QLPVKHMWDL
FCGVGGFGLH CATPDMQLTG IEIASEAIAC AKQSAAELGL TRLQFQALDS TQFATAQGDV
PELVLVNPPR RGIGKPLCDY LSTMAPRFII YSSCNAQTMA KDIRELPGFR IERVQLFDMF
PHTAHYEVLT LLVKQ
Length

375

Mol. Wt

41.956 kDa

pI

7.1 (calculated)

Extinction coefficient

46,410 - 47,785 (calc based on 9 Y, 6 W, and 11 C residues)

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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

184..375

PF05958 tRNA (Uracil-5-)-methyltransferase

PMID:19920124[6]

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

Structures

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

Models

View models at:

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Structure figures

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Notes

Gene Product Resources

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

Resource type Source Notes/Reference
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Notes

Accessions in Other Databases

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

Database Accession Notes

NCBI (Protein) (EcoliWiki Page)

GI:16128827

Escherichia coli str. K-12 substr. MG1655

NCBI (Protein) (EcoliWiki Page)

GeneID:947260

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0009127

Escherichia coli str. K-12 substr. MG1655

UniProt (EcoliWiki Page)

UniProtKB/Swiss-Prot:P75817

Escherichia coli str. K-12 substr. MG1655

EcoCyc

EcoCyc:EG11247

Escherichia coli str. K-12 substr. MG1655

EcoGene

EcoGene:EG11247

Escherichia coli str. K-12 substr. MG1655

NCBI (Gene) (EcoliWiki Page)

GeneID:947260

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120001223

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB1228

Escherichia coli str. K-12 substr. MG1655

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Notes

Links

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References

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

  1. ↑ 1.0 1.1 1.2 1.3 1.4 1.5 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. ↑ EcoCyc (release 11.1; 2007) Keseler, IM et al. (2005) Nucleic Acids Res. 33(Database issue):D334-7
  4. ↑ EcoGene: Rudd, KE (2000) EcoGene: a genome sequence database for Escherichia coli K-12. Nucleic Acids Res 28:60-4.
  5. ↑ 5.0 5.1 5.2 5.3 5.4 5.5 5.6 Arifuzzaman, M et al. (2006) Large-scale identification of protein-protein interaction of Escherichia coli K-12. Genome Res. 16 686-91 PubMed
  6. ↑ Finn, RD et al. (2010) The Pfam protein families database. Nucleic Acids Res. 38 D211-22 PubMed

Categories

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