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Protein

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

Gene

miaB

Organism
Burkholderia sp. (strain CCGE1002)
Status
Unreviewed-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 annotationSAAS 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 annotationSAAS annotation

Cofactori

Protein has several cofactor binding sites:
  • [4Fe-4S] clusterUniRule annotationSAAS annotationNote: Binds 2 [4Fe-4S] clusters. One cluster is coordinated with 3 cysteines and an exchangeable S-adenosyl-L-methionine.UniRule annotationSAAS annotation
  • [4Fe-4S] clusterNote: Binds 2 [4Fe-4S] clusters. One cluster is coordinated with 3 cysteines and an exchangeable S-adenosyl-L-methionine.

Sites

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Metal bindingi12 – 121Iron-sulfur (4Fe-4S)UniRule annotation
Metal bindingi49 – 491Iron-sulfur (4Fe-4S)UniRule annotation
Metal bindingi83 – 831Iron-sulfur (4Fe-4S)UniRule annotation
Metal bindingi157 – 1571Iron-sulfur (4Fe-4S-S-AdoMet)UniRule annotation
Metal bindingi161 – 1611Iron-sulfur (4Fe-4S-S-AdoMet)UniRule annotation
Metal bindingi164 – 1641Iron-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

TransferaseUniRule annotationSAAS annotation

Keywords - Biological processi

tRNA processingUniRule annotationSAAS annotation

Keywords - Ligandi

4Fe-4SUniRule annotationSAAS annotation, Iron, Iron-sulfur, Metal-binding, S-adenosyl-L-methionineUniRule annotationSAAS annotation

Enzyme and pathway databases

BioCyciBSP640511:GJ7J-2649-MONOMER.

Names & Taxonomyi

Protein namesi
Recommended name:
tRNA-2-methylthio-N(6)-dimethylallyladenosine synthaseUniRule annotationSAAS annotation (EC:2.8.4.3UniRule annotationSAAS annotation)
Alternative name(s):
(Dimethylallyl)adenosine tRNA methylthiotransferase MiaBUniRule annotation
tRNA-i(6)A37 methylthiotransferaseUniRule annotation
Gene namesi
Name:miaBUniRule annotation
Ordered Locus Names:BC1002_2597Imported
OrganismiBurkholderia sp. (strain CCGE1002)Imported
Taxonomic identifieri640511 [NCBI]
Taxonomic lineageiBacteriaProteobacteriaBetaproteobacteriaBurkholderialesBurkholderiaceaeBurkholderia
ProteomesiUP000002190 Componenti: Chromosome 1

Subcellular locationi

  1. Cytoplasm UniRule annotationSAAS annotation

GO - Cellular componenti

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

Keywords - Cellular componenti

CytoplasmUniRule annotationSAAS annotation

Interactioni

Subunit structurei

Monomer.UniRule annotationSAAS annotation

Structurei

3D structure databases

ProteinModelPortaliD5WD20.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Domaini3 – 120118MTTase N-terminalUniRule annotationAdd
BLAST
Domaini384 – 45168TRAMUniRule 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

HOGENOMiHOG000224767.
KOiK06168.

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.

D5WD20-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MTKKVYVKTF GCQMNEYDSD KMVDVLGAAE GLVKTDTPED ADVILFNTCS
60 70 80 90 100
VREKAQEKVF SDLGRVRELK DANPNLIIGV GGCVASQEGA SIVARAPYVD
110 120 130 140 150
IVFGPQTLHR LPQMIDERRA SGRAQVDISF PEIEKFDHLP PARVEGPSAF
160 170 180 190 200
VSIMEGCSKY CSYCVVPYTR GEEVSRPLDD VLTEIAGLAD QGVREVTLLG
210 220 230 240 250
QNVNAYRGKF GGALTLGSTE IADFATLIEY VADIPGIERI RYTTSHPKEF
260 270 280 290 300
TQRLIDTYAK VPKLVSHLHL PVQHGSDRIL MAMKRGYTVL EYKSVIRKLR
310 320 330 340 350
AIRPDLSLST DMIVGFPGET EEDFAKMMAL VEEMKYDTSF SFIYSPRPGT
360 370 380 390 400
PAANLHDDTP REVKLKRLQH LQATIEENVQ RISDAMVGNV ERILVERPAR
410 420 430 440 450
KDPNELAGRT ENNRVVNFPA PVASHARLIG QMVDVKIVHA YPHSLRGELV
460
MVRDDSTAAT H
Length:461
Mass (Da):51,233
Last modified:July 13, 2010 - v1
Checksum:iDEC344B16A61E009
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
CP002013 Genomic DNA. Translation: ADG16646.1.
RefSeqiWP_013090486.1. NC_014117.1.
YP_003606157.1. NC_014117.1.

Genome annotation databases

EnsemblBacteriaiADG16646; ADG16646; BC1002_2597.
KEGGibge:BC1002_2597.
PATRICi37214178. VBIBurSp41388_2663.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
CP002013 Genomic DNA. Translation: ADG16646.1.
RefSeqiWP_013090486.1. NC_014117.1.
YP_003606157.1. NC_014117.1.

3D structure databases

ProteinModelPortaliD5WD20.
ModBaseiSearch...
MobiDBiSearch...

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiADG16646; ADG16646; BC1002_2597.
KEGGibge:BC1002_2597.
PATRICi37214178. VBIBurSp41388_2663.

Phylogenomic databases

HOGENOMiHOG000224767.
KOiK06168.

Enzyme and pathway databases

BioCyciBSP640511:GJ7J-2649-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. "Complete sequence of chromosome 1 of Burkholderia sp. CCGE1002."
    US DOE Joint Genome Institute
    Lucas S., Copeland A., Lapidus A., Cheng J.-F., Bruce D., Goodwin L., Pitluck S., Chertkov O., Detter J.C., Han C., Tapia R., Land M., Hauser L., Kyrpides N., Ovchinnikova G., Martinez-Romero E., Hernandez M.A.R., Tiedje J.M., Woyke T.
    Submitted (APR-2010) to the EMBL/GenBank/DDBJ databases
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: CCGE1002Imported.

Entry informationi

Entry nameiD5WD20_BURSC
AccessioniPrimary (citable) accession number: D5WD20
Entry historyi
Integrated into UniProtKB/TrEMBL: July 13, 2010
Last sequence update: July 13, 2010
Last modified: April 29, 2015
This is version 35 of the entry and version 1 of the sequence. [Complete history]
Entry statusiUnreviewed (UniProtKB/TrEMBL)

Miscellaneousi

Keywords - Technical termi

Complete proteome, Reference proteomeImported

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.