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Escherichia coli K-12 substr. MG1655 Enzyme: isopentenyl-adenosine A37 tRNA methylthiolase



Gene: miaB Accession Numbers: G6364 (EcoCyc), b0661, ECK0653

Synonyms: yleA

Regulation Summary Diagram: ?

Summary:
MiaB is an isopentenyl-adenosine tRNA methylthiolase. Most E. coli tRNAs that read codons starting with U contain the modified base 2-methylthio-N6-isopentenyladenosine-37 (ms2i6A37) [Grosjean85]. MiaB is required for both sulfur insertion and methylation at carbon 2 of N6-isopentenyladenosine-37 in tRNA, yielding the final modified ms2i6A37 tRNA [Esberg95, Esberg99, Pierrel02].

MiaB is a member of the Radical SAM protein superfamily [Sofia01] and is a monomeric iron-sulfur cluster protein [Pierrel02] containing two 4Fe-4S clusters [Boutigny13]. A structural model of MiaB has been built [Kaminska08]. The reaction is thought to involve two molecules of SAM and one of the two Fe-S clusters as the sulfur source, thus requiring Fe-S cluster repair for multiple turnover catalysis [Boutigny13]. MiaB interacts with NfuA and GrxD. NfuA, but not GrxD, can transfer a 4Fe-4S cluster to apo-MiaB in vitro, and both proteins affect MiaB activity in vivo [Boutigny13].

A miaB mutant accumulates under-modified i6A tRNA [Esberg99]. However, unlike mutants in the associated gene miaA, miaB mutants do not have a mutator phenotype or a drop in tetracycline resistance [Zhao01a, Taylor98b].

Reviews: [Booker07, Atta12, Lanz12, El12]

Citations: [Waller10, Waller12, Hasnain12]

Locations: cytosol

Map Position: [692,754 <- 694,178] (14.93 centisomes)
Length: 1425 bp / 474 aa

Molecular Weight of Polypeptide: 53.663 kD (from nucleotide sequence)

Unification Links: ASAP:ABE-0002260 , DIP:DIP-48018N , EchoBASE:EB3421 , EcoGene:EG13657 , EcoliWiki:b0661 , Mint:MINT-1233637 , ModBase:P0AEI1 , OU-Microarray:b0661 , PortEco:miaB , PR:PRO_000023236 , Pride:P0AEI1 , Protein Model Portal:P0AEI1 , RefSeq:NP_415194 , RegulonDB:G6364 , SMR:P0AEI1 , String:511145.b0661 , UniProt:P0AEI1

Relationship Links: InterPro:IN-FAMILY:IPR002792 , InterPro:IN-FAMILY:IPR005839 , InterPro:IN-FAMILY:IPR006463 , InterPro:IN-FAMILY:IPR006638 , InterPro:IN-FAMILY:IPR007197 , InterPro:IN-FAMILY:IPR013848 , InterPro:IN-FAMILY:IPR020612 , InterPro:IN-FAMILY:IPR023404 , InterPro:IN-FAMILY:IPR023970 , Panther:IN-FAMILY:PTHR11918 , Pfam:IN-FAMILY:PF00919 , Pfam:IN-FAMILY:PF01938 , Pfam:IN-FAMILY:PF04055 , Prosite:IN-FAMILY:PS01278 , Prosite:IN-FAMILY:PS50926 , Prosite:IN-FAMILY:PS51449 , Smart:IN-FAMILY:SM00729

In Paralogous Gene Group: 174 (3 members)

Gene-Reaction Schematic: ?

GO Terms:

Biological Process: GO:0030488 - tRNA methylation Inferred from experiment [Esberg99]
GO:0035600 - tRNA methylthiolation Inferred from experiment [Pierrel02, Esberg99]
GO:0006400 - tRNA modification Inferred by computational analysis [GOA06, GOA01a]
GO:0008033 - tRNA processing Inferred by computational analysis [UniProtGOA11a]
GO:0009451 - RNA modification Inferred by computational analysis [GOA01a]
GO:0043412 - macromolecule modification Inferred by computational analysis [GOA01a]
Molecular Function: GO:0005515 - protein binding Inferred from experiment [Boutigny13]
GO:0035597 - N6-isopentenyladenosine methylthiotransferase activity Inferred from experiment [Pierrel02, Esberg99]
GO:0051539 - 4 iron, 4 sulfur cluster binding Inferred from experiment Inferred by computational analysis [UniProtGOA11a, GOA06, GOA01a, Pierrel02]
GO:0003824 - catalytic activity Inferred by computational analysis [GOA01a]
GO:0005506 - iron ion binding Inferred by computational analysis [GOA06]
GO:0016740 - transferase activity Inferred by computational analysis [UniProtGOA11a, GOA06, GOA01a]
GO:0046872 - metal ion binding Inferred by computational analysis [UniProtGOA11a]
GO:0051536 - iron-sulfur cluster binding Inferred by computational analysis [UniProtGOA11a, GOA01a]
Cellular Component: GO:0005829 - cytosol Inferred from experiment Inferred by computational analysis [DiazMejia09, Ishihama08]
GO:0005737 - cytoplasm Inferred by computational analysis [UniProtGOA11, UniProtGOA11a, GOA06, GOA01a]

MultiFun Terms: information transfer RNA related RNA modification

Essentiality data for miaB knockouts: ?

Growth Medium Growth? T (°C) O2 pH Osm/L Growth Observations
LB enriched Yes 37 Aerobic 6.95   Yes [Gerdes03, Comment 1]
LB Lennox Yes 37 Aerobic 7   Yes [Baba06, Comment 2]
M9 medium with 1% glycerol Yes 37 Aerobic 7.2 0.35 Yes [Joyce06, Comment 3]
MOPS medium with 0.4% glucose Yes 37 Aerobic 7.2 0.22 Yes [Baba06, Comment 2]

Credits:
Curated 08-Feb-2006 by Shearer A , SRI International
Last-Curated ? 19-Apr-2013 by Keseler I , SRI International


Enzymatic reaction of: isopentenyl-adenosine tRNA methylthiolase (isopentenyl-adenosine A37 tRNA methylthiolase)

Synonyms: tRNA-i(6)A37 methylthiotransferase

EC Number: 2.8.4.3

N6-dimethylallyladenosine37 in tRNA + 2 S-adenosyl-L-methionine + a sulfurated [sulfur carrier] <=> 2-methylthio-N6-dimethylallyladenosine37 in tRNA + S-adenosyl-L-homocysteine + L-methionine + 5'-deoxyadenosine + an unsulfurated [sulfur carrier] + H+

The reaction direction shown, that is, A + B ↔ C + D versus C + D ↔ A + B, is in accordance with the Enzyme Commission system.

The reaction is physiologically favored in the direction shown.


Sequence Features

Feature Class Location Citations Comment
Conserved-Region 3 -> 120
[UniProt09]
UniProt: MTTase N-terminal;
Metal-Binding-Site 12
[UniProt10]
UniProt: Iron-sulfur (4Fe-4S); Non-Experimental Qualifier: by similarity;
Metal-Binding-Site 49
[UniProt10]
UniProt: Iron-sulfur (4Fe-4S); Non-Experimental Qualifier: by similarity;
Metal-Binding-Site 83
[UniProt10]
UniProt: Iron-sulfur (4Fe-4S); Non-Experimental Qualifier: by similarity;
Mutagenesis-Variant 157
[Pierrel02, UniProt11]
Alternate sequence: C → A; UniProt: Loss of activity.
Metal-Binding-Site 157
[UniProt10]
UniProt: Iron-sulfur (4Fe-4S-S-AdoMet); Non-Experimental Qualifier: probable;
Metal-Binding-Site 157, 161, 164
[Pierrel02]
Each of the cysteines in this conserved iron-binding motif is individually required for MiaB enzymatic activity.
Mutagenesis-Variant 161
[Pierrel02, UniProt11]
Alternate sequence: C → A; UniProt: Loss of activity.
Metal-Binding-Site 161
[UniProt10]
UniProt: Iron-sulfur (4Fe-4S-S-AdoMet); Non-Experimental Qualifier: probable;
Mutagenesis-Variant 164
[Pierrel02, UniProt11]
Alternate sequence: C → A; UniProt: Loss of activity.
Metal-Binding-Site 164
[UniProt10]
UniProt: Iron-sulfur (4Fe-4S-S-AdoMet); Non-Experimental Qualifier: probable;
Conserved-Region 378 -> 441
[UniProt09]
UniProt: TRAM;


Gene Local Context (not to scale): ?

Transcription Unit:

Notes:

History:
Markus Krummenacker on Tue Oct 14, 1997:
Gene object created from Blattner lab Genbank (v. M52) entry.


References

Atta12: Atta M, Arragain S, Fontecave M, Mulliez E, Hunt JF, Luff JD, Forouhar F (2012). "The methylthiolation reaction mediated by the Radical-SAM enzymes." Biochim Biophys Acta 1824(11);1223-30. PMID: 22178611

Baba06: Baba T, Ara T, Hasegawa M, Takai Y, Okumura Y, Baba M, Datsenko KA, Tomita M, Wanner BL, Mori H (2006). "Construction of Escherichia coli K-12 in-frame, single-gene knockout mutants: the Keio collection." Mol Syst Biol 2;2006.0008. PMID: 16738554

Booker07: Booker SJ, Cicchillo RM, Grove TL (2007). "Self-sacrifice in radical S-adenosylmethionine proteins." Curr Opin Chem Biol 11(5);543-52. PMID: 17936058

Boutigny13: Boutigny S, Saini A, Baidoo EE, Yeung N, Keasling JD, Butland G (2013). "Physical and Functional Interactions of a Monothiol Glutaredoxin and an Iron Sulfur Cluster Carrier Protein with the Sulfur-donating Radical S-Adenosyl-L-methionine Enzyme MiaB." J Biol Chem 288(20);14200-11. PMID: 23543739

DiazMejia09: Diaz-Mejia JJ, Babu M, Emili A (2009). "Computational and experimental approaches to chart the Escherichia coli cell-envelope-associated proteome and interactome." FEMS Microbiol Rev 33(1);66-97. PMID: 19054114

El12: El Yacoubi B, Bailly M, de Crecy-Lagard V (2012). "Biosynthesis and function of posttranscriptional modifications of transfer RNAs." Annu Rev Genet 46;69-95. PMID: 22905870

Esberg95: Esberg B, Bjork GR (1995). "The methylthio group (ms2) of N6-(4-hydroxyisopentenyl)-2-methylthioadenosine (ms2io6A) present next to the anticodon contributes to the decoding efficiency of the tRNA." J Bacteriol 177(8);1967-75. PMID: 7536729

Esberg99: Esberg B, Leung HC, Tsui HC, Bjork GR, Winkler ME (1999). "Identification of the miaB gene, involved in methylthiolation of isopentenylated A37 derivatives in the tRNA of Salmonella typhimurium and Escherichia coli." J Bacteriol 181(23);7256-65. PMID: 10572129

Gerdes03: Gerdes SY, Scholle MD, Campbell JW, Balazsi G, Ravasz E, Daugherty MD, Somera AL, Kyrpides NC, Anderson I, Gelfand MS, Bhattacharya A, Kapatral V, D'Souza M, Baev MV, Grechkin Y, Mseeh F, Fonstein MY, Overbeek R, Barabasi AL, Oltvai ZN, Osterman AL (2003). "Experimental determination and system level analysis of essential genes in Escherichia coli MG1655." J Bacteriol 185(19);5673-84. PMID: 13129938

GOA01a: GOA, DDB, FB, MGI, ZFIN (2001). "Gene Ontology annotation through association of InterPro records with GO terms."

GOA06: GOA, SIB (2006). "Electronic Gene Ontology annotations created by transferring manual GO annotations between orthologous microbial proteins."

Grosjean85: Grosjean H, Nicoghosian K, Haumont E, Soll D, Cedergren R (1985). "Nucleotide sequences of two serine tRNAs with a GGA anticodon: the structure-function relationships in the serine family of E. coli tRNAs." Nucleic Acids Res 13(15);5697-706. PMID: 3898020

Hasnain12: Hasnain G, Waller JC, Alvarez S, Ravilious GE, Jez JM, Hanson AD (2012). "Mutational analysis of YgfZ, a folate-dependent protein implicated in iron/sulphur cluster metabolism." FEMS Microbiol Lett 326(2);168-72. PMID: 22092591

Ishihama08: Ishihama Y, Schmidt T, Rappsilber J, Mann M, Hartl FU, Kerner MJ, Frishman D (2008). "Protein abundance profiling of the Escherichia coli cytosol." BMC Genomics 9;102. PMID: 18304323

Joyce06: Joyce AR, Reed JL, White A, Edwards R, Osterman A, Baba T, Mori H, Lesely SA, Palsson BO, Agarwalla S (2006). "Experimental and computational assessment of conditionally essential genes in Escherichia coli." J Bacteriol 188(23);8259-71. PMID: 17012394

Kaminska08: Kaminska KH, Baraniak U, Boniecki M, Nowaczyk K, Czerwoniec A, Bujnicki JM (2008). "Structural bioinformatics analysis of enzymes involved in the biosynthesis pathway of the hypermodified nucleoside ms(2)io(6)A37 in tRNA." Proteins 70(1);1-18. PMID: 17910062

Lanz12: Lanz ND, Booker SJ (2012). "Identification and function of auxiliary iron-sulfur clusters in radical SAM enzymes." Biochim Biophys Acta 1824(11);1196-212. PMID: 22846545

Pierrel02: Pierrel F, Bjork GR, Fontecave M, Atta M (2002). "Enzymatic modification of tRNAs: MiaB is an iron-sulfur protein." J Biol Chem 277(16);13367-70. PMID: 11882645

Sofia01: Sofia HJ, Chen G, Hetzler BG, Reyes-Spindola JF, Miller NE (2001). "Radical SAM, a novel protein superfamily linking unresolved steps in familiar biosynthetic pathways with radical mechanisms: functional characterization using new analysis and information visualization methods." Nucleic Acids Res 29(5);1097-106. PMID: 11222759

Taylor98b: Taylor DE, Trieber CA, Trescher G, Bekkering M (1998). "Host mutations (miaA and rpsL) reduce tetracycline resistance mediated by Tet(O) and Tet(M)." Antimicrob Agents Chemother 42(1);59-64. PMID: 9449261

UniProt09: UniProt Consortium (2009). "UniProt version 15.8 released on 2009-10-01 00:00:00." Database.

UniProt10: UniProt Consortium (2010). "UniProt version 2010-07 released on 2010-06-15 00:00:00." Database.

UniProt11: UniProt Consortium (2011). "UniProt version 2011-06 released on 2011-06-30 00:00:00." Database.

UniProtGOA11: UniProt-GOA (2011). "Gene Ontology annotation based on the manual assignment of UniProtKB Subcellular Location terms in UniProtKB/Swiss-Prot entries."

UniProtGOA11a: UniProt-GOA (2011). "Gene Ontology annotation based on manual assignment of UniProtKB keywords in UniProtKB/Swiss-Prot entries."

Waller10: Waller JC, Alvarez S, Naponelli V, Lara-Nunez A, Blaby IK, Da Silva V, Ziemak MJ, Vickers TJ, Beverley SM, Edison AS, Rocca JR, Gregory JF, de Crecy-Lagard V, Hanson AD (2010). "A role for tetrahydrofolates in the metabolism of iron-sulfur clusters in all domains of life." Proc Natl Acad Sci U S A 107(23);10412-7. PMID: 20489182

Waller12: Waller JC, Ellens KW, Hasnain G, Alvarez S, Rocca JR, Hanson AD (2012). "Evidence that the Folate-Dependent Proteins YgfZ and MnmEG Have Opposing Effects on Growth and on Activity of the Iron-Sulfur Enzyme MiaB." J Bacteriol 194(2);362-7. PMID: 22081392

Zhao01a: Zhao J, Leung HE, Winkler ME (2001). "The miaA mutator phenotype of Escherichia coli K-12 requires recombination functions." J Bacteriol 183(5);1796-800. PMID: 11160115


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Please cite the following article in publications resulting from the use of EcoCyc: Nucleic Acids Research 41:D605-12 2013
Page generated by SRI International Pathway Tools version 18.5 on Sat Dec 20, 2014, biocyc12.