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Q4K898

- RLMD_PSEF5

UniProt

Q4K898 - RLMD_PSEF5

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Protein
23S rRNA (uracil(1939)-C(5))-methyltransferase RlmD
Gene
rlmD, rumA, PFL_4447
Organism
Pseudomonas fluorescens (strain Pf-5 / ATCC BAA-477)
Status
Reviewed - Annotation score: 3 out of 5 - Protein inferred from homologyi

Functioni

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

Catalytic activityi

S-adenosyl-L-methionine + uracil(1939) in 23S rRNA = S-adenosyl-L-homocysteine + 5-methyluracil(1939) in 23S rRNA.UniRule annotation

Sites

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Metal bindingi91 – 911Iron-sulfur (4Fe-4S) By similarity
Metal bindingi97 – 971Iron-sulfur (4Fe-4S) By similarity
Metal bindingi100 – 1001Iron-sulfur (4Fe-4S) By similarity
Metal bindingi179 – 1791Iron-sulfur (4Fe-4S) By similarity
Binding sitei283 – 2831S-adenosyl-L-methionine By similarity
Binding sitei312 – 3121S-adenosyl-L-methionine; via carbonyl oxygen By similarity
Binding sitei317 – 3171S-adenosyl-L-methionine By similarity
Binding sitei333 – 3331S-adenosyl-L-methionine By similarity
Binding sitei360 – 3601S-adenosyl-L-methionine By similarity
Binding sitei381 – 3811S-adenosyl-L-methionine By similarity
Active sitei407 – 4071Nucleophile By similarity

GO - Molecular functioni

  1. 4 iron, 4 sulfur cluster binding Source: UniProtKB-KW
  2. RNA binding Source: InterPro
  3. iron ion binding Source: UniProtKB-HAMAP
  4. rRNA (uridine-C5-)-methyltransferase activity Source: UniProtKB-HAMAP
Complete GO annotation...

GO - Biological processi

    Complete GO annotation...

    Keywords - Molecular functioni

    Methyltransferase, Transferase

    Keywords - Biological processi

    rRNA processing

    Keywords - Ligandi

    4Fe-4S, Iron, Iron-sulfur, Metal-binding, S-adenosyl-L-methionine

    Enzyme and pathway databases

    BioCyciPFLU220664:GIX8-4482-MONOMER.

    Names & Taxonomyi

    Protein namesi
    Recommended name:
    23S rRNA (uracil(1939)-C(5))-methyltransferase RlmD (EC:2.1.1.190)
    Alternative name(s):
    23S rRNA(m5U1939)-methyltransferase
    Gene namesi
    Name:rlmD
    Synonyms:rumA
    Ordered Locus Names:PFL_4447
    OrganismiPseudomonas fluorescens (strain Pf-5 / ATCC BAA-477)
    Taxonomic identifieri220664 [NCBI]
    Taxonomic lineageiBacteriaProteobacteriaGammaproteobacteriaPseudomonadalesPseudomonadaceaePseudomonas
    ProteomesiUP000008540: Chromosome

    PTM / Processingi

    Molecule processing

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Chaini1 – 45045023S rRNA (uracil(1939)-C(5))-methyltransferase RlmDUniRule annotation
    PRO_0000229876Add
    BLAST

    Interactioni

    Protein-protein interaction databases

    STRINGi220664.PFL_4447.

    Structurei

    3D structure databases

    ProteinModelPortaliQ4K898.

    Family & Domainsi

    Domains and Repeats

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Domaini20 – 7859TRAM
    Add
    BLAST

    Sequence similaritiesi

    Contains 1 TRAM domain.

    Phylogenomic databases

    eggNOGiCOG2265.
    HOGENOMiHOG000029868.
    KOiK03215.
    OMAiDFIQVND.
    OrthoDBiEOG6V4GKM.

    Family and domain databases

    Gene3Di2.40.50.140. 1 hit.
    3.40.50.150. 1 hit.
    HAMAPiMF_01010. 23SrRNA_methyltr_RlmD.
    InterProiIPR001566. 23S_rRNA_MeTrfase_RlmD.
    IPR012340. NA-bd_OB-fold.
    IPR029063. SAM-dependent_MTases-like.
    IPR002792. TRAM_dom.
    IPR010280. U5_MeTrfase_fam.
    [Graphical view]
    PfamiPF01938. TRAM. 1 hit.
    PF05958. tRNA_U5-meth_tr. 1 hit.
    [Graphical view]
    SUPFAMiSSF50249. SSF50249. 1 hit.
    SSF53335. SSF53335. 1 hit.
    TIGRFAMsiTIGR00479. rumA. 1 hit.
    PROSITEiPS51687. SAM_MT_RNA_M5U. 1 hit.
    PS50926. TRAM. 1 hit.
    PS01230. TRMA_1. 1 hit.
    PS01231. TRMA_2. 1 hit.
    [Graphical view]

    Sequencei

    Sequence statusi: Complete.

    Q4K898-1 [UniParc]FASTAAdd to Basket

    « Hide

    MAKHDRGLRF QPAGGSRAPQ IPVGKKQRLT IQRLANDGRG IAFVEGRTWF    50
    VSGALAGEEV EARVLGSHGK VVEARAERIF NASDLRRPAA CAHAGRCGGC 100
    SVQHLPHDEQ LALKQRMLAE QLSKVAGVEP EAWAAPLSGP EFGYRRRARV 150
    AVRWDAKGKQ LEVGFRAAGS QDIVAIDDCP VLVQALQPVM NRLPAMLRRL 200
    SKPQALGHVE LFSGSALAVL LRHMAPLSDS DLTILKDFCD FHQAQLWLHG 250
    EGEPQPFDPS QALGYRLETW DLHLAYRPGD FVQVNAGVNE AMVAQALEWL 300
    APQADERVLD LFCGLGNFAL PLARQVREVV AVEGVATMVA RAAENAASNN 350
    LHNTRFFQAD LSQPLSAAEW ADEGFSAVLL DPPRDGAFEV VRQLATLGAK 400
    RLVYVSCNPA TLARDTVELI KQGYRLKRAG ILDMFPQTAH VEAMALFEAS 450
    Length:450
    Mass (Da):49,118
    Last modified:August 2, 2005 - v1
    Checksum:iFE3C683D8B209F3E
    GO

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    CP000076 Genomic DNA. Translation: AAY93698.1.
    RefSeqiYP_261535.1. NC_004129.6.

    Genome annotation databases

    EnsemblBacteriaiAAY93698; AAY93698; PFL_4447.
    GeneIDi3478566.
    KEGGipfl:PFL_4447.
    PATRICi19878326. VBIPseFlu72549_4552.

    Cross-referencesi

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    CP000076 Genomic DNA. Translation: AAY93698.1 .
    RefSeqi YP_261535.1. NC_004129.6.

    3D structure databases

    ProteinModelPortali Q4K898.
    ModBasei Search...

    Protein-protein interaction databases

    STRINGi 220664.PFL_4447.

    Protocols and materials databases

    Structural Biology Knowledgebase Search...

    Genome annotation databases

    EnsemblBacteriai AAY93698 ; AAY93698 ; PFL_4447 .
    GeneIDi 3478566.
    KEGGi pfl:PFL_4447.
    PATRICi 19878326. VBIPseFlu72549_4552.

    Phylogenomic databases

    eggNOGi COG2265.
    HOGENOMi HOG000029868.
    KOi K03215.
    OMAi DFIQVND.
    OrthoDBi EOG6V4GKM.

    Enzyme and pathway databases

    BioCyci PFLU220664:GIX8-4482-MONOMER.

    Family and domain databases

    Gene3Di 2.40.50.140. 1 hit.
    3.40.50.150. 1 hit.
    HAMAPi MF_01010. 23SrRNA_methyltr_RlmD.
    InterProi IPR001566. 23S_rRNA_MeTrfase_RlmD.
    IPR012340. NA-bd_OB-fold.
    IPR029063. SAM-dependent_MTases-like.
    IPR002792. TRAM_dom.
    IPR010280. U5_MeTrfase_fam.
    [Graphical view ]
    Pfami PF01938. TRAM. 1 hit.
    PF05958. tRNA_U5-meth_tr. 1 hit.
    [Graphical view ]
    SUPFAMi SSF50249. SSF50249. 1 hit.
    SSF53335. SSF53335. 1 hit.
    TIGRFAMsi TIGR00479. rumA. 1 hit.
    PROSITEi PS51687. SAM_MT_RNA_M5U. 1 hit.
    PS50926. TRAM. 1 hit.
    PS01230. TRMA_1. 1 hit.
    PS01231. TRMA_2. 1 hit.
    [Graphical view ]
    ProtoNeti Search...

    Publicationsi

    1. Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
      Strain: Pf-5 / ATCC BAA-477.

    Entry informationi

    Entry nameiRLMD_PSEF5
    AccessioniPrimary (citable) accession number: Q4K898
    Entry historyi
    Integrated into UniProtKB/Swiss-Prot: April 4, 2006
    Last sequence update: August 2, 2005
    Last modified: June 11, 2014
    This is version 58 of the entry and version 1 of the sequence. [Complete history]
    Entry statusiReviewed (UniProtKB/Swiss-Prot)
    Annotation programProkaryotic Protein Annotation Program

    Miscellaneousi

    Keywords - Technical termi

    Complete proteome

    Documents

    1. SIMILARITY comments
      Index of protein domains and families

    External Data

    Dasty 3

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