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Entry version 156 (11 Dec 2019)
Sequence version 3 (23 Jan 2007)
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Protein

23S rRNA (uracil(1939)-C(5))-methyltransferase RlmD

Gene

rlmD

Organism
Escherichia coli (strain K12)
Status
Reviewed-Annotation score:

Annotation score:5 out of 5

<p>The annotation score provides a heuristic measure of the annotation content of a UniProtKB entry or proteome. This score <strong>cannot</strong> be used as a measure of the accuracy of the annotation as we cannot define the ‘correct annotation’ for any given protein.<p><a href='/help/annotation_score' target='_top'>More...</a></p>
-Experimental evidence at protein leveli <p>This indicates the type of evidence that supports the existence of the protein. Note that the ‘protein existence’ evidence does not give information on the accuracy or correctness of the sequence(s) displayed.<p><a href='/help/protein_existence' target='_top'>More...</a></p>

<p>This section provides any useful information about the protein, mostly biological knowledge.<p><a href='/help/function_section' target='_top'>More...</a></p>Functioni

Catalyzes the formation of 5-methyl-uridine at position 1939 (m5U1939) in 23S rRNA.UniRule annotation2 Publications

Miscellaneous

The function of the iron-sulfur cluster remains unclear. It may be involved in the correct folding of the protein or may have a role in RNA binding.1 Publication

<p>This subsection of the <a href="http://www.uniprot.org/help/function_section">Function</a> section describes the catalytic activity of an enzyme, i.e. a chemical reaction that the enzyme catalyzes.<p><a href='/help/catalytic_activity' target='_top'>More...</a></p>Catalytic activityi

Sites

Feature keyPosition(s)DescriptionActionsGraphical viewLength
<p>This subsection of the <a href="http://www.uniprot.org/help/function_section">Function</a> section indicates at which position the protein binds a given metal ion. The nature of the metal is indicated in the ‘Description’ field.<p><a href='/help/metal' target='_top'>More...</a></p>Metal bindingi81Iron-sulfur (4Fe-4S)2 Publications1
Metal bindingi87Iron-sulfur (4Fe-4S)2 Publications1
Metal bindingi90Iron-sulfur (4Fe-4S)2 Publications1
Metal bindingi162Iron-sulfur (4Fe-4S)2 Publications1
<p>This subsection of the <a href="http://www.uniprot.org/help/function_section">Function</a> section describes the interaction between a single amino acid and another chemical entity. Priority is given to the annotation of physiological ligands.<p><a href='/help/binding' target='_top'>More...</a></p>Binding sitei265S-adenosyl-L-methionine1 Publication1
Binding sitei294S-adenosyl-L-methionine; via carbonyl oxygen1 Publication1
Binding sitei299S-adenosyl-L-methionine1 Publication1
Binding sitei315S-adenosyl-L-methionine1 Publication1
Binding sitei342S-adenosyl-L-methionine1 Publication1
Binding sitei363S-adenosyl-L-methionine1 Publication1
<p>This subsection of the <a href="http://www.uniprot.org/help/function_section">Function</a> section is used for enzymes and indicates the residues directly involved in catalysis.<p><a href='/help/act_site' target='_top'>More...</a></p>Active sitei389NucleophileUniRule annotation1 Publication1

<p>The <a href="http://www.geneontology.org/">Gene Ontology (GO)</a> project provides a set of hierarchical controlled vocabulary split into 3 categories:<p><a href='/help/gene_ontology' target='_top'>More...</a></p>GO - Molecular functioni

GO - Biological processi

<p>UniProtKB Keywords constitute a <a href="http://www.uniprot.org/keywords">controlled vocabulary</a> with a hierarchical structure. Keywords summarise the content of a UniProtKB entry and facilitate the search for proteins of interest.<p><a href='/help/keywords' target='_top'>More...</a></p>Keywordsi

Molecular functionMethyltransferase, Transferase
Biological processrRNA processing
Ligand4Fe-4S, Iron, Iron-sulfur, Metal-binding, S-adenosyl-L-methionine

Enzyme and pathway databases

BioCyc Collection of Pathway/Genome Databases

More...
BioCyci
EcoCyc:EG11247-MONOMER
ECOL316407:JW2756-MONOMER
MetaCyc:EG11247-MONOMER

BRENDA Comprehensive Enzyme Information System

More...
BRENDAi
2.1.1.190 2026

<p>This section provides information about the protein and gene name(s) and synonym(s) and about the organism that is the source of the protein sequence.<p><a href='/help/names_and_taxonomy_section' target='_top'>More...</a></p>Names & Taxonomyi

<p>This subsection of the <a href="http://www.uniprot.org/help/names_and_taxonomy_section">Names and taxonomy</a> section provides an exhaustive list of all names of the protein, from commonly used to obsolete, to allow unambiguous identification of a protein.<p><a href='/help/protein_names' target='_top'>More...</a></p>Protein namesi
Recommended name:
23S rRNA (uracil(1939)-C(5))-methyltransferase RlmDUniRule annotation (EC:2.1.1.190UniRule annotation)
Alternative name(s):
23S rRNA(m5U1939)-methyltransferaseUniRule annotation
<p>This subsection of the <a href="http://www.uniprot.org/help/names_and_taxonomy_section">Names and taxonomy</a> section indicates the name(s) of the gene(s) that code for the protein sequence(s) described in the entry. Four distinct tokens exist: ‘Name’, ‘Synonyms’, ‘Ordered locus names’ and ‘ORF names’.<p><a href='/help/gene_name' target='_top'>More...</a></p>Gene namesi
Name:rlmDUniRule annotation
Synonyms:rumA, ygcA
Ordered Locus Names:b2785, JW2756
<p>This subsection of the <a href="http://www.uniprot.org/help/names_and_taxonomy_section">Names and taxonomy</a> section provides information on the name(s) of the organism that is the source of the protein sequence.<p><a href='/help/organism-name' target='_top'>More...</a></p>OrganismiEscherichia coli (strain K12)
<p>This subsection of the <a href="http://www.uniprot.org/help/names_and_taxonomy_section">Names and taxonomy</a> section shows the unique identifier assigned by the NCBI to the source organism of the protein. This is known as the ‘taxonomic identifier’ or ‘taxid’.<p><a href='/help/taxonomic_identifier' target='_top'>More...</a></p>Taxonomic identifieri83333 [NCBI]
<p>This subsection of the <a href="http://www.uniprot.org/help/names_and_taxonomy_section">Names and taxonomy</a> section contains the taxonomic hierarchical classification lineage of the source organism. It lists the nodes as they appear top-down in the taxonomic tree, with the more general grouping listed first.<p><a href='/help/taxonomic_lineage' target='_top'>More...</a></p>Taxonomic lineageiBacteriaProteobacteriaGammaproteobacteriaEnterobacteralesEnterobacteriaceaeEscherichia
<p>This subsection of the <a href="http://www.uniprot.org/help/names_and_taxonomy_section">Names and taxonomy</a> section is present for entries that are part of a <a href="http://www.uniprot.org/proteomes">proteome</a>, i.e. of a set of proteins thought to be expressed by organisms whose genomes have been completely sequenced.<p><a href='/help/proteomes_manual' target='_top'>More...</a></p>Proteomesi
  • UP000000318 <p>A UniProt <a href="http://www.uniprot.org/manual/proteomes_manual">proteome</a> can consist of several components. <br></br>The component name refers to the genomic component encoding a set of proteins.<p><a href='/help/proteome_component' target='_top'>More...</a></p> Componenti: Chromosome
  • UP000000625 Componenti: Chromosome

<p>This section describes post-translational modifications (PTMs) and/or processing events.<p><a href='/help/ptm_processing_section' target='_top'>More...</a></p>PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
<p>This subsection of the <a href="http://www.uniprot.org/help/ptm_processing_section">PTM / Processing</a> section indicates that the initiator methionine is cleaved from the mature protein.<p><a href='/help/init_met' target='_top'>More...</a></p>Initiator methionineiRemoved1 Publication
<p>This subsection of the ‘PTM / Processing’ section describes the extent of a polypeptide chain in the mature protein following processing.<p><a href='/help/chain' target='_top'>More...</a></p>ChainiPRO_00001618932 – 43323S rRNA (uracil(1939)-C(5))-methyltransferase RlmDAdd BLAST432

Proteomic databases

jPOST - Japan Proteome Standard Repository/Database

More...
jPOSTi
P55135

PaxDb, a database of protein abundance averages across all three domains of life

More...
PaxDbi
P55135

PRoteomics IDEntifications database

More...
PRIDEi
P55135

<p>This section provides information on the quaternary structure of a protein and on interaction(s) with other proteins or protein complexes.<p><a href='/help/interaction_section' target='_top'>More...</a></p>Interactioni

Sites

Feature keyPosition(s)DescriptionActionsGraphical viewLength
<p>This subsection describes interesting single amino acid sites on the sequence that are not defined in any other subsection. This subsection can be displayed in different sections (‘Function’, ‘PTM / Processing’, ‘Pathology and Biotech’) according to its content.<p><a href='/help/site' target='_top'>More...</a></p>Sitei132Interaction with RNA1
Sitei149Interaction with RNA1

Protein-protein interaction databases

The Biological General Repository for Interaction Datasets (BioGrid)

More...
BioGridi
4262285, 70 interactors

Database of interacting proteins

More...
DIPi
DIP-12119N

Protein interaction database and analysis system

More...
IntActi
P55135, 2 interactors

STRING: functional protein association networks

More...
STRINGi
511145.b2785

<p>This section provides information on the tertiary and secondary structure of a protein.<p><a href='/help/structure_section' target='_top'>More...</a></p>Structurei

Secondary structure

1433
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details

3D structure databases

SWISS-MODEL Repository - a database of annotated 3D protein structure models

More...
SMRi
P55135

Database of comparative protein structure models

More...
ModBasei
Search...

Protein Data Bank in Europe - Knowledge Base

More...
PDBe-KBi
Search...

Miscellaneous databases

Relative evolutionary importance of amino acids within a protein sequence

More...
EvolutionaryTracei
P55135

<p>This section provides information on sequence similarities with other proteins and the domain(s) present in a protein.<p><a href='/help/family_and_domains_section' target='_top'>More...</a></p>Family & Domainsi

Domains and Repeats

Feature keyPosition(s)DescriptionActionsGraphical viewLength
<p>This subsection of the <a href="http://www.uniprot.org/help/family_and_domains_section">Family and Domains</a> section describes the position and type of a domain, which is defined as a specific combination of secondary structures organized into a characteristic three-dimensional structure or fold.<p><a href='/help/domain' target='_top'>More...</a></p>Domaini10 – 68TRAMUniRule annotationAdd BLAST59

Region

Feature keyPosition(s)DescriptionActionsGraphical viewLength
<p>This subsection of the ‘Family and Domains’ section describes a region of interest that cannot be described in other subsections.<p><a href='/help/region' target='_top'>More...</a></p>Regioni23 – 40Interaction with RNAAdd BLAST18
Regioni58 – 63Interaction with RNA6

<p>This subsection of the ‘Family and domains’ section provides general information on the biological role of a domain. The term ‘domain’ is intended here in its wide acceptation, it may be a structural domain, a transmembrane region or a functional domain. Several domains are described in this subsection.<p><a href='/help/domain_cc' target='_top'>More...</a></p>Domaini

Contains three structural domains: an N-terminal TRAM domain, a central domain containing an iron-sulfur cluster, and a C-terminal domain that displays the typical SAM-dependent methyltransferase fold.1 Publication

<p>This subsection of the ‘Family and domains’ section provides information about the sequence similarity with other proteins.<p><a href='/help/sequence_similarities' target='_top'>More...</a></p>Sequence similaritiesi

Phylogenomic databases

evolutionary genealogy of genes: Non-supervised Orthologous Groups

More...
eggNOGi
ENOG4105BZT Bacteria
COG2265 LUCA

The HOGENOM Database of Homologous Genes from Fully Sequenced Organisms

More...
HOGENOMi
HOG000029868

InParanoid: Eukaryotic Ortholog Groups

More...
InParanoidi
P55135

KEGG Orthology (KO)

More...
KOi
K03215

Database for complete collections of gene phylogenies

More...
PhylomeDBi
P55135

Family and domain databases

HAMAP database of protein families

More...
HAMAPi
MF_01010 23SrRNA_methyltr_RlmD, 1 hit

Integrated resource of protein families, domains and functional sites

More...
InterProi
View protein in InterPro
IPR001566 23S_rRNA_MeTrfase_RlmD
IPR030390 MeTrfase_TrmA_AS
IPR030391 MeTrfase_TrmA_CS
IPR012340 NA-bd_OB-fold
IPR029063 SAM-dependent_MTases
IPR002792 TRAM_dom
IPR010280 U5_MeTrfase_fam

The PANTHER Classification System

More...
PANTHERi
PTHR11061 PTHR11061, 1 hit

Pfam protein domain database

More...
Pfami
View protein in Pfam
PF01938 TRAM, 1 hit
PF05958 tRNA_U5-meth_tr, 1 hit

Superfamily database of structural and functional annotation

More...
SUPFAMi
SSF50249 SSF50249, 1 hit
SSF53335 SSF53335, 1 hit

PROSITE; a protein domain and family database

More...
PROSITEi
View protein in PROSITE
PS51687 SAM_MT_RNA_M5U, 1 hit
PS50926 TRAM, 1 hit
PS01230 TRMA_1, 1 hit
PS01231 TRMA_2, 1 hit

<p>This section displays by default the canonical protein sequence and upon request all isoforms described in the entry. It also includes information pertinent to the sequence(s), including <a href="http://www.uniprot.org/help/sequence_length">length</a> and <a href="http://www.uniprot.org/help/sequences">molecular weight</a>. The information is filed in different subsections. The current subsections and their content are listed below:<p><a href='/help/sequences_section' target='_top'>More...</a></p>Sequencei

<p>This subsection of the <a href="http://www.uniprot.org/help/sequences_section">Sequence</a> section indicates if the <a href="http://www.uniprot.org/help/canonical_and_isoforms">canonical sequence</a> displayed by default in the entry is complete or not.<p><a href='/help/sequence_status' target='_top'>More...</a></p>Sequence statusi: Complete.

<p>This subsection of the <a href="http://www.uniprot.org/help/sequences_section">Sequence</a> section indicates if the <a href="http://www.uniprot.org/help/canonical_and_isoforms">canonical sequence</a> displayed by default in the entry is in its mature form or if it represents the precursor.<p><a href='/help/sequence_processing' target='_top'>More...</a></p>Sequence processingi: The displayed sequence is further processed into a mature form.

P55135-1 [UniParc]FASTAAdd to basket
« Hide
        10         20         30         40         50
MAQFYSAKRR TTTRQIITVS VNDLDSFGQG VARHNGKTLF IPGLLPQENA
60 70 80 90 100
EVTVTEDKKQ YARAKVVRRL SDSPERETPR CPHFGVCGGC QQQHASVDLQ
110 120 130 140 150
QRSKSAALAR LMKHDVSEVI ADVPWGYRRR ARLSLNYLPK TQQLQMGFRK
160 170 180 190 200
AGSSDIVDVK QCPILAPQLE ALLPKVRACL GSLQAMRHLG HVELVQATSG
210 220 230 240 250
TLMILRHTAP LSSADREKLE RFSHSEGLDL YLAPDSEILE TVSGEMPWYD
260 270 280 290 300
SNGLRLTFSP RDFIQVNAGV NQKMVARALE WLDVQPEDRV LDLFCGMGNF
310 320 330 340 350
TLPLATQAAS VVGVEGVPAL VEKGQQNARL NGLQNVTFYH ENLEEDVTKQ
360 370 380 390 400
PWAKNGFDKV LLDPARAGAA GVMQQIIKLE PIRIVYVSCN PATLARDSEA
410 420 430
LLKAGYTIAR LAMLDMFPHT GHLESMVLFS RVK
Length:433
Mass (Da):48,052
Last modified:January 23, 2007 - v3
<p>The checksum is a form of redundancy check that is calculated from the sequence. It is useful for tracking sequence updates.</p> <p>It should be noted that while, in theory, two different sequences could have the same checksum value, the likelihood that this would happen is extremely low.</p> <p>However UniProtKB may contain entries with identical sequences in case of multiple genes (paralogs).</p> <p>The checksum is computed as the sequence 64-bit Cyclic Redundancy Check value (CRC64) using the generator polynomial: x<sup>64</sup> + x<sup>4</sup> + x<sup>3</sup> + x + 1. The algorithm is described in the ISO 3309 standard. </p> <p class="publication">Press W.H., Flannery B.P., Teukolsky S.A. and Vetterling W.T.<br /> <strong>Cyclic redundancy and other checksums</strong><br /> <a href="http://www.nrbook.com/b/bookcpdf.php">Numerical recipes in C 2nd ed., pp896-902, Cambridge University Press (1993)</a>)</p> Checksum:iA46C07B0BD18EAAC
GO

Sequence databases

Select the link destinations:

EMBL nucleotide sequence database

More...
EMBLi

GenBank nucleotide sequence database

More...
GenBanki

DNA Data Bank of Japan; a nucleotide sequence database

More...
DDBJi
Links Updated
U29580 Genomic DNA Translation: AAA69295.1
U00096 Genomic DNA Translation: AAC75827.1
AP009048 Genomic DNA Translation: BAE76859.1

Protein sequence database of the Protein Information Resource

More...
PIRi
E65060

NCBI Reference Sequences

More...
RefSeqi
NP_417265.1, NC_000913.3
WP_000046812.1, NZ_STEB01000030.1

Genome annotation databases

Ensembl bacterial and archaeal genome annotation project

More...
EnsemblBacteriai
AAC75827; AAC75827; b2785
BAE76859; BAE76859; BAE76859

Database of genes from NCBI RefSeq genomes

More...
GeneIDi
947243

KEGG: Kyoto Encyclopedia of Genes and Genomes

More...
KEGGi
ecj:JW2756
eco:b2785

Pathosystems Resource Integration Center (PATRIC)

More...
PATRICi
fig|1411691.4.peg.3950

<p>This section provides links to proteins that are similar to the protein sequence(s) described in this entry at different levels of sequence identity thresholds (100%, 90% and 50%) based on their membership in UniProt Reference Clusters (<a href="http://www.uniprot.org/help/uniref">UniRef</a>).<p><a href='/help/similar_proteins_section' target='_top'>More...</a></p>Similar proteinsi

<p>This section is used to point to information related to entries and found in data collections other than UniProtKB.<p><a href='/help/cross_references_section' target='_top'>More...</a></p>Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
U29580 Genomic DNA Translation: AAA69295.1
U00096 Genomic DNA Translation: AAC75827.1
AP009048 Genomic DNA Translation: BAE76859.1
PIRiE65060
RefSeqiNP_417265.1, NC_000913.3
WP_000046812.1, NZ_STEB01000030.1

3D structure databases

Select the link destinations:

Protein Data Bank Europe

More...
PDBei

Protein Data Bank RCSB

More...
RCSB PDBi

Protein Data Bank Japan

More...
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
1UWVX-ray1.95A1-433[»]
2BH2X-ray2.15A/B2-433[»]
SMRiP55135
ModBaseiSearch...
PDBe-KBiSearch...

Protein-protein interaction databases

BioGridi4262285, 70 interactors
DIPiDIP-12119N
IntActiP55135, 2 interactors
STRINGi511145.b2785

Proteomic databases

jPOSTiP55135
PaxDbiP55135
PRIDEiP55135

Genome annotation databases

EnsemblBacteriaiAAC75827; AAC75827; b2785
BAE76859; BAE76859; BAE76859
GeneIDi947243
KEGGiecj:JW2756
eco:b2785
PATRICifig|1411691.4.peg.3950

Organism-specific databases

EchoBASE - an integrated post-genomic database for E. coli

More...
EchoBASEi
EB1228

Phylogenomic databases

eggNOGiENOG4105BZT Bacteria
COG2265 LUCA
HOGENOMiHOG000029868
InParanoidiP55135
KOiK03215
PhylomeDBiP55135

Enzyme and pathway databases

BioCyciEcoCyc:EG11247-MONOMER
ECOL316407:JW2756-MONOMER
MetaCyc:EG11247-MONOMER
BRENDAi2.1.1.190 2026

Miscellaneous databases

EvolutionaryTraceiP55135

Protein Ontology

More...
PROi
PR:P55135

Family and domain databases

HAMAPiMF_01010 23SrRNA_methyltr_RlmD, 1 hit
InterProiView protein in InterPro
IPR001566 23S_rRNA_MeTrfase_RlmD
IPR030390 MeTrfase_TrmA_AS
IPR030391 MeTrfase_TrmA_CS
IPR012340 NA-bd_OB-fold
IPR029063 SAM-dependent_MTases
IPR002792 TRAM_dom
IPR010280 U5_MeTrfase_fam
PANTHERiPTHR11061 PTHR11061, 1 hit
PfamiView protein in Pfam
PF01938 TRAM, 1 hit
PF05958 tRNA_U5-meth_tr, 1 hit
SUPFAMiSSF50249 SSF50249, 1 hit
SSF53335 SSF53335, 1 hit
PROSITEiView protein in PROSITE
PS51687 SAM_MT_RNA_M5U, 1 hit
PS50926 TRAM, 1 hit
PS01230 TRMA_1, 1 hit
PS01231 TRMA_2, 1 hit

ProtoNet; Automatic hierarchical classification of proteins

More...
ProtoNeti
Search...

MobiDB: a database of protein disorder and mobility annotations

More...
MobiDBi
Search...

<p>This section provides general information on the entry.<p><a href='/help/entry_information_section' target='_top'>More...</a></p>Entry informationi

<p>This subsection of the ‘Entry information’ section provides a mnemonic identifier for a UniProtKB entry, but it is not a stable identifier. Each reviewed entry is assigned a unique entry name upon integration into UniProtKB/Swiss-Prot.<p><a href='/help/entry_name' target='_top'>More...</a></p>Entry nameiRLMD_ECOLI
<p>This subsection of the ‘Entry information’ section provides one or more accession number(s). These are stable identifiers and should be used to cite UniProtKB entries. Upon integration into UniProtKB, each entry is assigned a unique accession number, which is called ‘Primary (citable) accession number’.<p><a href='/help/accession_numbers' target='_top'>More...</a></p>AccessioniPrimary (citable) accession number: P55135
Secondary accession number(s): Q2MA47
<p>This subsection of the ‘Entry information’ section shows the date of integration of the entry into UniProtKB, the date of the last sequence update and the date of the last annotation modification (‘Last modified’). The version number for both the entry and the <a href="http://www.uniprot.org/help/canonical_and_isoforms">canonical sequence</a> are also displayed.<p><a href='/help/entry_history' target='_top'>More...</a></p>Entry historyiIntegrated into UniProtKB/Swiss-Prot: October 1, 1996
Last sequence update: January 23, 2007
Last modified: December 11, 2019
This is version 156 of the entry and version 3 of the sequence. See complete history.
<p>This subsection of the ‘Entry information’ section indicates whether the entry has been manually annotated and reviewed by UniProtKB curators or not, in other words, if the entry belongs to the Swiss-Prot section of UniProtKB (<strong>reviewed</strong>) or to the computer-annotated TrEMBL section (<strong>unreviewed</strong>).<p><a href='/help/entry_status' target='_top'>More...</a></p>Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programProkaryotic Protein Annotation Program

<p>This section contains any relevant information that doesn’t fit in any other defined sections<p><a href='/help/miscellaneous_section' target='_top'>More...</a></p>Miscellaneousi

Keywords - Technical termi

3D-structure, Direct protein sequencing, Reference proteome

Documents

  1. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
  2. SIMILARITY comments
    Index of protein domains and families
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