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Protein

tRNA-2-methylthio-N(6)-dimethylallyladenosine synthase

Gene

miaB

Organism
Dichelobacter nodosus (strain VCS1703A)
Status
Reviewed-Annotation score: Annotation score: 3 out of 5-Protein inferred from homologyi

Functioni

Catalyzes the methylthiolation of N6-(dimethylallyl)adenosine (i6A), leading to the formation of 2-methylthio-N6-(dimethylallyl)adenosine (ms2i6A) at position 37 in tRNAs that read codons beginning with uridine.UniRule annotation

Catalytic activityi

N(6)-dimethylallyladenine(37) in tRNA + sulfur-(sulfur carrier) + 2 S-adenosyl-L-methionine = 2-methylthio-N(6)-dimethylallyladenine(37) in tRNA + S-adenosyl-L-homocysteine + (sulfur carrier) + L-methionine + 5'-deoxyadenosine.UniRule annotation

Cofactori

[4Fe-4S] clusterUniRule annotationNote: Binds 2 [4Fe-4S] clusters. One cluster is coordinated with 3 cysteines and an exchangeable S-adenosyl-L-methionine.UniRule annotation

Sites

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Metal bindingi15 – 151Iron-sulfur (4Fe-4S)UniRule annotation
Metal bindingi52 – 521Iron-sulfur (4Fe-4S)UniRule annotation
Metal bindingi86 – 861Iron-sulfur (4Fe-4S)UniRule annotation
Metal bindingi160 – 1601Iron-sulfur (4Fe-4S-S-AdoMet)UniRule annotation
Metal bindingi164 – 1641Iron-sulfur (4Fe-4S-S-AdoMet)UniRule annotation
Metal bindingi167 – 1671Iron-sulfur (4Fe-4S-S-AdoMet)UniRule annotation

GO - Molecular functioni

  1. 4 iron, 4 sulfur cluster binding Source: UniProtKB-HAMAP
  2. iron ion binding Source: UniProtKB-HAMAP
  3. transferase activity Source: UniProtKB-HAMAP

GO - Biological processi

  1. tRNA modification Source: UniProtKB-HAMAP
Complete GO annotation...

Keywords - Molecular functioni

Transferase

Keywords - Biological processi

tRNA processing

Keywords - Ligandi

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

Enzyme and pathway databases

BioCyciDNOD246195:GHHS-1242-MONOMER.

Names & Taxonomyi

Protein namesi
Recommended name:
tRNA-2-methylthio-N(6)-dimethylallyladenosine synthaseUniRule annotation (EC:2.8.4.3UniRule annotation)
Alternative name(s):
(Dimethylallyl)adenosine tRNA methylthiotransferase MiaBUniRule annotation
tRNA-i(6)A37 methylthiotransferaseUniRule annotation
Gene namesi
Name:miaBUniRule annotation
Ordered Locus Names:DNO_1245
OrganismiDichelobacter nodosus (strain VCS1703A)
Taxonomic identifieri246195 [NCBI]
Taxonomic lineageiBacteriaProteobacteriaGammaproteobacteriaCardiobacterialesCardiobacteriaceaeDichelobacter
ProteomesiUP000000248: Chromosome

Subcellular locationi

Cytoplasm UniRule annotation

GO - Cellular componenti

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

Keywords - Cellular componenti

Cytoplasm

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 456456tRNA-2-methylthio-N(6)-dimethylallyladenosine synthasePRO_0000374269Add
BLAST

Interactioni

Subunit structurei

Monomer.UniRule annotation

Protein-protein interaction databases

STRINGi246195.DNO_1245.

Structurei

3D structure databases

ProteinModelPortaliA5EXA7.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Domaini6 – 123118MTTase N-terminalUniRule annotationAdd
BLAST
Domaini381 – 44464TRAMUniRule annotationAdd
BLAST

Sequence similaritiesi

Belongs to the methylthiotransferase family. MiaB subfamily.UniRule annotation
Contains 1 MTTase N-terminal domain.UniRule annotation
Contains 1 TRAM domain.UniRule annotation

Phylogenomic databases

eggNOGiCOG0621.
HOGENOMiHOG000224767.
KOiK06168.
OMAiGCQMNKA.
OrthoDBiEOG6P5ZD8.

Family and domain databases

Gene3Di3.80.30.20. 1 hit.
HAMAPiMF_01864. tRNA_metthiotr_MiaB.
InterProiIPR006638. Elp3/MiaB/NifB.
IPR023970. MeThioTfrase/rSAM.
IPR005839. Methylthiotransferase.
IPR020612. Methylthiotransferase_CS.
IPR013848. Methylthiotransferase_N.
IPR006463. MiaB_methiolase.
IPR007197. rSAM.
IPR023404. rSAM_horseshoe.
IPR002792. TRAM_dom.
[Graphical view]
PANTHERiPTHR11918. PTHR11918. 1 hit.
PfamiPF04055. Radical_SAM. 1 hit.
PF01938. TRAM. 1 hit.
PF00919. UPF0004. 1 hit.
[Graphical view]
SMARTiSM00729. Elp3. 1 hit.
[Graphical view]
TIGRFAMsiTIGR00089. TIGR00089. 1 hit.
PROSITEiPS51449. MTTASE_N. 1 hit.
PS01278. MTTASE_RADICAL. 1 hit.
PS50926. TRAM. 1 hit.
[Graphical view]

Sequencei

Sequence statusi: Complete.

A5EXA7-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MQTVLKHVYI ETYGCQMNEY DSSKMLAVLK NSHGITPVAT PEEADVLLLN
60 70 80 90 100
TCSVREKAQE KVFSQLGRWK SLKERKPHLI IGVGGCVASQ EGEMIRRRAP
110 120 130 140 150
EVDVVFGPQT LHRLPNLIEE AQRSRGGVVD VSFPEIEKFD HLPEPRAEGP
160 170 180 190 200
TAYVSVMEGC SKYCTYCVVP YTRGAEISRP FDDVLAECAT LAAQGVREIN
210 220 230 240 250
LLGQNVNAYR GAMHDGTIAD LALLIEYVAA IPNIGRIRFT TSHPSEFSDA
260 270 280 290 300
LIETYRRVPK LVSHLHLPVQ SGSNRILALM KRDYKVAEYQ EKLAKIRAIR
310 320 330 340 350
PDISFSSDFI VGFPGEEEED FQATMDLIEA VFFDTSYSFI YSQRPGTPAS
360 370 380 390 400
TMPDRVPLTV KKERLARLQA RILEMAASIS EAMVGTEQWV LVDRLSRKSE
410 420 430 440 450
REVSGRTENN RVVNFSAPAS LIGRFAKVQI TAAYKNSLRG RLIEAELLPD

PVVYTR
Length:456
Mass (Da):51,013
Last modified:June 12, 2007 - v1
Checksum:iB20D924B8494970D
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
CP000513 Genomic DNA. Translation: ABQ14300.1.
RefSeqiWP_012031540.1. NC_009446.1.
YP_001210121.1. NC_009446.1.

Genome annotation databases

EnsemblBacteriaiABQ14300; ABQ14300; DNO_1245.
GeneIDi5122130.
KEGGidno:DNO_1245.
PATRICi21786844. VBIDicNod48475_1238.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
CP000513 Genomic DNA. Translation: ABQ14300.1.
RefSeqiWP_012031540.1. NC_009446.1.
YP_001210121.1. NC_009446.1.

3D structure databases

ProteinModelPortaliA5EXA7.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

STRINGi246195.DNO_1245.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiABQ14300; ABQ14300; DNO_1245.
GeneIDi5122130.
KEGGidno:DNO_1245.
PATRICi21786844. VBIDicNod48475_1238.

Phylogenomic databases

eggNOGiCOG0621.
HOGENOMiHOG000224767.
KOiK06168.
OMAiGCQMNKA.
OrthoDBiEOG6P5ZD8.

Enzyme and pathway databases

BioCyciDNOD246195:GHHS-1242-MONOMER.

Family and domain databases

Gene3Di3.80.30.20. 1 hit.
HAMAPiMF_01864. tRNA_metthiotr_MiaB.
InterProiIPR006638. Elp3/MiaB/NifB.
IPR023970. MeThioTfrase/rSAM.
IPR005839. Methylthiotransferase.
IPR020612. Methylthiotransferase_CS.
IPR013848. Methylthiotransferase_N.
IPR006463. MiaB_methiolase.
IPR007197. rSAM.
IPR023404. rSAM_horseshoe.
IPR002792. TRAM_dom.
[Graphical view]
PANTHERiPTHR11918. PTHR11918. 1 hit.
PfamiPF04055. Radical_SAM. 1 hit.
PF01938. TRAM. 1 hit.
PF00919. UPF0004. 1 hit.
[Graphical view]
SMARTiSM00729. Elp3. 1 hit.
[Graphical view]
TIGRFAMsiTIGR00089. TIGR00089. 1 hit.
PROSITEiPS51449. MTTASE_N. 1 hit.
PS01278. MTTASE_RADICAL. 1 hit.
PS50926. TRAM. 1 hit.
[Graphical view]
ProtoNetiSearch...

Publicationsi

  1. Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: VCS1703A.

Entry informationi

Entry nameiMIAB_DICNV
AccessioniPrimary (citable) accession number: A5EXA7
Entry historyi
Integrated into UniProtKB/Swiss-Prot: May 5, 2009
Last sequence update: June 12, 2007
Last modified: March 4, 2015
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, Reference proteome

Documents

  1. SIMILARITY comments
    Index of protein domains and families

External Data

Dasty 3

Similar proteinsi

Links to similar proteins from the UniProt Reference Clusters (UniRef) at 100%, 90% and 50% sequence identity:
100%UniRef100 combines identical sequences and sub-fragments with 11 or more residues from any organism into Uniref entry.
90%UniRef90 is built by clustering UniRef100 sequences that have at least 90% sequence identity to, and 80% overlap with, the longest sequence (a.k.a seed sequence).
50%UniRef50 is built by clustering UniRef90 seed sequences that have at least 50% sequence identity to, and 80% overlap with, the longest sequence in the cluster.