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Q87B36

- RLMN_XYLFT

UniProt

Q87B36 - RLMN_XYLFT

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Protein

Dual-specificity RNA methyltransferase RlmN

Gene

rlmN

Organism
Xylella fastidiosa (strain Temecula1 / ATCC 700964)
Status
Reviewed - Annotation score: 4 out of 5- Protein inferred from homologyi

Functioni

Specifically methylates position 2 of adenine 2503 in 23S rRNA and position 2 of adenine 37 in tRNAs. m2A2503 modification seems to play a crucial role in the proofreading step occurring at the peptidyl transferase center and thus would serve to optimize ribosomal fidelity.UniRule annotation

Catalytic activityi

2 S-adenosyl-L-methionine + adenine(2503) in 23S rRNA = S-adenosyl-L-homocysteine + L-methionine + 5'-deoxyadenosine + 2-methyladenine(2503) in 23S rRNA.UniRule annotation
2 S-adenosyl-L-methionine + adenine(37) in tRNA = S-adenosyl-L-homocysteine + L-methionine + 5'-deoxyadenosine + 2-methyladenine(37) in tRNA.UniRule annotation

Cofactori

[4Fe-4S] clusterUniRule annotationNote: Binds 1 [4Fe-4S] cluster. The cluster is coordinated with 3 cysteines and an exchangeable S-adenosyl-L-methionine.UniRule annotation

Sites

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Active sitei119 – 1191Proton acceptorUniRule annotation
Metal bindingi139 – 1391Iron-sulfur (4Fe-4S-S-AdoMet)UniRule annotation
Metal bindingi143 – 1431Iron-sulfur (4Fe-4S-S-AdoMet)UniRule annotation
Metal bindingi146 – 1461Iron-sulfur (4Fe-4S-S-AdoMet)UniRule annotation
Binding sitei224 – 2241S-adenosyl-L-methionineUniRule annotation
Binding sitei332 – 3321S-adenosyl-L-methionine; via amide nitrogen and carbonyl oxygenUniRule annotation
Active sitei375 – 3751S-methylcysteine intermediateUniRule annotation

GO - Molecular functioni

  1. 4 iron, 4 sulfur cluster binding Source: UniProtKB-HAMAP
  2. metal ion binding Source: UniProtKB-KW
  3. rRNA (adenine-C2-)-methyltransferase activity Source: UniProtKB-HAMAP
  4. rRNA binding Source: UniProtKB-HAMAP
  5. tRNA (adenine-C2-)-methyltransferase activity Source: UniProtKB-HAMAP
  6. tRNA binding Source: UniProtKB-HAMAP

GO - Biological processi

  1. rRNA base methylation Source: UniProtKB-HAMAP
Complete GO annotation...

Keywords - Molecular functioni

Methyltransferase, Transferase

Keywords - Biological processi

rRNA processing, tRNA processing

Keywords - Ligandi

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

Enzyme and pathway databases

BioCyciXFAS183190:GIX4-1624-MONOMER.

Names & Taxonomyi

Protein namesi
Recommended name:
Dual-specificity RNA methyltransferase RlmNUniRule annotation (EC:2.1.1.-UniRule annotation, EC:2.1.1.192UniRule annotation)
Alternative name(s):
23S rRNA (adenine(2503)-C(2))-methyltransferaseUniRule annotation
23S rRNA m2A2503 methyltransferaseUniRule annotation
Ribosomal RNA large subunit methyltransferase NUniRule annotation
tRNA (adenine(37)-C(2))-methyltransferaseUniRule annotation
tRNA m2A37 methyltransferaseUniRule annotation
Gene namesi
Name:rlmNUniRule annotation
Ordered Locus Names:PD_1624
OrganismiXylella fastidiosa (strain Temecula1 / ATCC 700964)
Taxonomic identifieri183190 [NCBI]
Taxonomic lineageiBacteriaProteobacteriaGammaproteobacteriaXanthomonadalesXanthomonadaceaeXylella
ProteomesiUP000002516: Chromosome

Subcellular locationi

Cytoplasm UniRule annotation

GO - Cellular componenti

  1. cytoplasm Source: UniProtKB-HAMAP
Complete GO annotation...

Keywords - Cellular componenti

Cytoplasm

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 406406Dual-specificity RNA methyltransferase RlmNPRO_0000350536Add
BLAST

Amino acid modifications

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Disulfide bondi132 ↔ 375(transient)UniRule annotation

Keywords - PTMi

Disulfide bond

Interactioni

Protein-protein interaction databases

STRINGi183190.PD1624.

Structurei

3D structure databases

ProteinModelPortaliQ87B36.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Region

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Regioni192 – 1932S-adenosyl-L-methionine bindingUniRule annotation
Regioni246 – 2483S-adenosyl-L-methionine bindingUniRule annotation

Sequence similaritiesi

Belongs to the radical SAM superfamily. RlmN family.UniRule annotation

Phylogenomic databases

eggNOGiCOG0820.
KOiK06941.
OMAiPEAPYAK.
OrthoDBiEOG6DJZ2N.

Family and domain databases

Gene3Di3.20.20.70. 1 hit.
HAMAPiMF_01849. RNA_methyltr_RlmN.
InterProiIPR013785. Aldolase_TIM.
IPR006638. Elp3/MiaB/NifB.
IPR027492. RNA_MTrfase_RlmN.
IPR004383. rRNA_lsu_MTrfase_RlmN/Cfr.
IPR007197. rSAM.
[Graphical view]
PANTHERiPTHR30544. PTHR30544. 1 hit.
PfamiPF04055. Radical_SAM. 1 hit.
[Graphical view]
PIRSFiPIRSF006004. CHP00048. 1 hit.
SMARTiSM00729. Elp3. 1 hit.
[Graphical view]
TIGRFAMsiTIGR00048. TIGR00048. 1 hit.

Sequencei

Sequence statusi: Complete.

Q87B36-1 [UniParc]FASTAAdd to Basket

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        10         20         30         40         50
MNGFAVIPSV TTTTTSGEPI ASDVARKQNL LELDREGLER FFEDVLGEKR
60 70 80 90 100
YRAHQVMKWI HHRYVADFEQ MTDVGKALRT RLQACAEVRV PRVVFDKHSA
110 120 130 140 150
DGTHKWLLAM GTDRKNAIET VYIPDKGRGT LCVSSQIGCG LNCTFCSTAT
160 170 180 190 200
QGFNRNLTTA EIIGQVWVAA RHLGNVPHQQ RRLTNVVMMG MGEPLMNFDN
210 220 230 240 250
VVRAMSVMRD DLGYGLSNKR VTLSTSGLVP MIDRLSTESD VSLAVSLHAP
260 270 280 290 300
NDKLREQLVP LNKKYPIVEL MASCERYLSV NRKRDSVTFE YTLMKGVNDK
310 320 330 340 350
QEHAHELAKL MRQFDCAMQV KGAAKVNLIP FNPFPGTCYE RSTEVDIRAF
360 370 380 390 400
QKILLDAQIL AMVRRTRGDD IDAACGQLKG QVVDRTRRQA EFRRTIEDRV

GRDVAA
Length:406
Mass (Da):45,706
Last modified:June 1, 2003 - v1
Checksum:iAA90F341DC96A7C2
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AE009442 Genomic DNA. Translation: AAO29464.1.
RefSeqiNP_779815.1. NC_004556.1.

Genome annotation databases

EnsemblBacteriaiAAO29464; AAO29464; PD_1624.
GeneIDi1142966.
KEGGixft:PD1624.
PATRICi24151562. VBIXylFas71109_2084.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AE009442 Genomic DNA. Translation: AAO29464.1 .
RefSeqi NP_779815.1. NC_004556.1.

3D structure databases

ProteinModelPortali Q87B36.
ModBasei Search...
MobiDBi Search...

Protein-protein interaction databases

STRINGi 183190.PD1624.

Protocols and materials databases

Structural Biology Knowledgebase Search...

Genome annotation databases

EnsemblBacteriai AAO29464 ; AAO29464 ; PD_1624 .
GeneIDi 1142966.
KEGGi xft:PD1624.
PATRICi 24151562. VBIXylFas71109_2084.

Phylogenomic databases

eggNOGi COG0820.
KOi K06941.
OMAi PEAPYAK.
OrthoDBi EOG6DJZ2N.

Enzyme and pathway databases

BioCyci XFAS183190:GIX4-1624-MONOMER.

Family and domain databases

Gene3Di 3.20.20.70. 1 hit.
HAMAPi MF_01849. RNA_methyltr_RlmN.
InterProi IPR013785. Aldolase_TIM.
IPR006638. Elp3/MiaB/NifB.
IPR027492. RNA_MTrfase_RlmN.
IPR004383. rRNA_lsu_MTrfase_RlmN/Cfr.
IPR007197. rSAM.
[Graphical view ]
PANTHERi PTHR30544. PTHR30544. 1 hit.
Pfami PF04055. Radical_SAM. 1 hit.
[Graphical view ]
PIRSFi PIRSF006004. CHP00048. 1 hit.
SMARTi SM00729. Elp3. 1 hit.
[Graphical view ]
TIGRFAMsi TIGR00048. TIGR00048. 1 hit.
ProtoNeti Search...

Publicationsi

  1. "Comparative analyses of the complete genome sequences of Pierce's disease and citrus variegated chlorosis strains of Xylella fastidiosa."
    Van Sluys M.A., de Oliveira M.C., Monteiro-Vitorello C.B., Miyaki C.Y., Furlan L.R., Camargo L.E.A., da Silva A.C.R., Moon D.H., Takita M.A., Lemos E.G.M., Machado M.A., Ferro M.I.T., da Silva F.R., Goldman M.H.S., Goldman G.H., Lemos M.V.F., El-Dorry H., Tsai S.M.
    , Carrer H., Carraro D.M., de Oliveira R.C., Nunes L.R., Siqueira W.J., Coutinho L.L., Kimura E.T., Ferro E.S., Harakava R., Kuramae E.E., Marino C.L., Giglioti E., Abreu I.L., Alves L.M.C., do Amaral A.M., Baia G.S., Blanco S.R., Brito M.S., Cannavan F.S., Celestino A.V., da Cunha A.F., Fenille R.C., Ferro J.A., Formighieri E.F., Kishi L.T., Leoni S.G., Oliveira A.R., Rosa V.E. Jr., Sassaki F.T., Sena J.A.D., de Souza A.A., Truffi D., Tsukumo F., Yanai G.M., Zaros L.G., Civerolo E.L., Simpson A.J.G., Almeida N.F. Jr., Setubal J.C., Kitajima J.P.
    J. Bacteriol. 185:1018-1026(2003) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: Temecula1 / ATCC 700964.

Entry informationi

Entry nameiRLMN_XYLFT
AccessioniPrimary (citable) accession number: Q87B36
Entry historyi
Integrated into UniProtKB/Swiss-Prot: September 2, 2008
Last sequence update: June 1, 2003
Last modified: November 26, 2014
This is version 82 of the entry and version 1 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programProkaryotic Protein Annotation Program

Miscellaneousi

Miscellaneous

Reaction proceeds by a ping-pong mechanism involving intermediate methylation of a conserved cysteine residue.UniRule annotation

Keywords - Technical termi

Complete proteome

Documents

  1. SIMILARITY comments
    Index of protein domains and families

External Data

Dasty 3