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Protein

tRNA dimethylallyltransferase, mitochondrial

Gene

MOD5

Organism
Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)
Status
Reviewed-Annotation score: Annotation score: 5 out of 5-Experimental evidence at protein leveli

Functioni

Catalyzes the transfer of a dimethylallyl group onto the adenine at position 37 in the anticodon loop on a specific subset of tRNAs both in the cytosol and the mitochondrion, leading to the formation of N6-(dimethylallyl)adenosine (i6A). This modification optimizes the codon:anticodon fit in the ribosome and promotes translational fidelity. Competes with the farnesyl pyrophosphate synthase ERG20 for the common substrate dimethylallyl diphosphate (DMAPP).3 Publications

Catalytic activityi

Dimethylallyl diphosphate + adenine(37) in tRNA = diphosphate + N(6)-dimethylallyladenine(37) in tRNA.

Regions

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Nucleotide bindingi21 – 288ATPSequence analysis
Zinc fingeri373 – 40937Matrin-typeAdd
BLAST

GO - Molecular functioni

  • ATP binding Source: UniProtKB-KW
  • metal ion binding Source: UniProtKB-KW
  • tRNA binding Source: SGD
  • tRNA dimethylallyltransferase activity Source: SGD

GO - Biological processi

  • transfer RNA gene-mediated silencing Source: SGD
  • tRNA modification Source: SGD
Complete GO annotation...

Keywords - Molecular functioni

Prion, Transferase

Keywords - Biological processi

tRNA processing

Keywords - Ligandi

ATP-binding, Metal-binding, Nucleotide-binding, Zinc

Enzyme and pathway databases

BioCyciYEAST:YOR274W-MONOMER.
BRENDAi2.5.1.75. 984.
ReactomeiR-SCE-6782315. tRNA modification in the nucleus and cytosol.

Names & Taxonomyi

Protein namesi
Recommended name:
tRNA dimethylallyltransferase, mitochondrial (EC:2.5.1.75)
Short name:
DMATase
Alternative name(s):
Isopentenyl-diphosphate: tRNA isopentenyltransferase
Short name:
IPP transferase
Short name:
IPPT
tRNA isopentenyltransferase
Short name:
IPTase
Gene namesi
Name:MOD5
Ordered Locus Names:YOR274W
OrganismiSaccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)
Taxonomic identifieri559292 [NCBI]
Taxonomic lineageiEukaryotaFungiDikaryaAscomycotaSaccharomycotinaSaccharomycetesSaccharomycetalesSaccharomycetaceaeSaccharomyces
Proteomesi
  • UP000002311 Componenti: Chromosome XV

Organism-specific databases

EuPathDBiFungiDB:YOR274W.
SGDiS000005800. MOD5.

Subcellular locationi

GO - Cellular componenti

  • cytosol Source: SGD
  • mitochondrion Source: SGD
  • nucleolus Source: SGD
  • nucleus Source: SGD
Complete GO annotation...

Keywords - Cellular componenti

Amyloid, Cytoplasm, Mitochondrion, Nucleus

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 428428tRNA dimethylallyltransferase, mitochondrialPRO_0000019025Add
BLAST

Proteomic databases

MaxQBiP07884.

Interactioni

Sites

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Sitei112 – 1121Interaction with substrate tRNA
Sitei193 – 1931Interaction with substrate tRNA

Protein-protein interaction databases

BioGridi34663. 48 interactions.
DIPiDIP-4094N.
IntActiP07884. 2 interactions.
MINTiMINT-536616.

Structurei

Secondary structure

1
428
Legend: HelixTurnBeta strand
Show more details
Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Beta strandi15 – 217Combined sources
Beta strandi23 – 264Combined sources
Helixi27 – 3812Combined sources
Beta strandi40 – 445Combined sources
Turni47 – 504Combined sources
Beta strandi51 – 533Combined sources
Turni55 – 595Combined sources
Helixi63 – 653Combined sources
Turni66 – 683Combined sources
Beta strandi71 – 733Combined sources
Helixi85 – 10016Combined sources
Turni101 – 1033Combined sources
Beta strandi105 – 1095Combined sources
Helixi113 – 1208Combined sources
Beta strandi127 – 1293Combined sources
Helixi135 – 1417Combined sources
Beta strandi144 – 1485Combined sources
Helixi149 – 1557Combined sources
Helixi158 – 1614Combined sources
Helixi169 – 18214Combined sources
Helixi186 – 1916Combined sources
Beta strandi198 – 20710Combined sources
Helixi210 – 22617Combined sources
Helixi229 – 24012Combined sources
Turni241 – 2444Combined sources
Helixi247 – 2493Combined sources
Helixi253 – 2564Combined sources
Helixi261 – 2677Combined sources
Helixi278 – 30225Combined sources
Helixi304 – 3074Combined sources
Turni308 – 3103Combined sources
Beta strandi312 – 3165Combined sources
Turni320 – 3223Combined sources
Turni324 – 3274Combined sources
Helixi328 – 33912Combined sources
Helixi351 – 3577Combined sources
Helixi359 – 3613Combined sources
Helixi363 – 3653Combined sources
Beta strandi372 – 3798Combined sources
Beta strandi385 – 3906Combined sources
Helixi391 – 3988Combined sources
Helixi401 – 41818Combined sources

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
3EPHX-ray2.95A/B13-421[»]
3EPJX-ray3.10A/B13-421[»]
3EPKX-ray3.20A/B13-421[»]
3EPLX-ray3.60A/B13-421[»]
ProteinModelPortaliP07884.
SMRiP07884. Positions 13-421.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiP07884.

Family & Domainsi

Region

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Regioni23 – 286Substrate binding
Regioni46 – 494Interaction with substrate tRNA
Regioni170 – 1745Interaction with substrate tRNA
Regioni199 – 2079Core aggregation region
Regioni210 – 23223Interaction with isopentenylpyrophosphate transferaseAdd
BLAST
Regioni256 – 2583Interaction with substrate tRNA
Regioni284 – 30219Interaction with substrate tRNAAdd
BLAST
Regioni294 – 3018Interaction with substrate tRNABy similarity

Domaini

The core aggregation region, although lacking the prion-typical Gln/Asn (Q/N)-rich domain, is required for the formation of the amyloid-like fibrillar aggregates.

Sequence similaritiesi

Belongs to the IPP transferase family.Curated
Contains 1 matrin-type zinc finger.Curated

Zinc finger

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Zinc fingeri373 – 40937Matrin-typeAdd
BLAST

Keywords - Domaini

Zinc-finger

Phylogenomic databases

GeneTreeiENSGT00390000015214.
HOGENOMiHOG000039995.
InParanoidiP07884.
KOiK00791.
OMAiKWINNRF.
OrthoDBiEOG7SR4WC.

Family and domain databases

Gene3Di3.40.50.300. 1 hit.
HAMAPiMF_00185. IPP_trans.
InterProiIPR018022. IPP_trans.
IPR030666. IPP_transferase_euk.
IPR027417. P-loop_NTPase.
[Graphical view]
PfamiPF01715. IPPT. 1 hit.
[Graphical view]
PIRSFiPIRSF039110. IPP_transferase. 1 hit.
SUPFAMiSSF52540. SSF52540. 1 hit.
TIGRFAMsiTIGR00174. miaA. 1 hit.

Sequences (2)i

Sequence statusi: Complete.

This entry describes 2 isoformsi produced by alternative initiation. AlignAdd to basket

Isoform I (identifier: P07884-1) [UniParc]FASTAAdd to basket

This isoform has been chosen as the 'canonical' sequence. All positional information in this entry refers to it. This is also the sequence that appears in the downloadable versions of the entry.

« Hide

        10         20         30         40         50
MLKGPLKGCL NMSKKVIVIA GTTGVGKSQL SIQLAQKFNG EVINSDSMQV
60 70 80 90 100
YKDIPIITNK HPLQEREGIP HHVMNHVDWS EEYYSHRFET ECMNAIEDIH
110 120 130 140 150
RRGKIPIVVG GTHYYLQTLF NKRVDTKSSE RKLTRKQLDI LESTDPDVIY
160 170 180 190 200
NTLVKCDPDI ATKYHPNDYR RVQRMLEIYY KTGKKPSETF NEQKITLKFD
210 220 230 240 250
TLFLWLYSKP EPLFQRLDDR VDDMLERGAL QEIKQLYEYY SQNKFTPEQC
260 270 280 290 300
ENGVWQVIGF KEFLPWLTGK TDDNTVKLED CIERMKTRTR QYAKRQVKWI
310 320 330 340 350
KKMLIPDIKG DIYLLDATDL SQWDTNASQR AIAISNDFIS NRPIKQERAP
360 370 380 390 400
KALEELLSKG ETTMKKLDDW THYTCNVCRN ADGKNVVAIG EKYWKIHLGS
410 420
RRHKSNLKRN TRQADFEKWK INKKETVE
Length:428
Mass (Da):50,237
Last modified:November 1, 1997 - v2
Checksum:iA956B17ABC05161F
GO
Isoform II (identifier: P07884-2) [UniParc]FASTAAdd to basket

The sequence of this isoform differs from the canonical sequence as follows:
     1-11: Missing.

Note: Produced by alternative initiation at Met-12 of isoform I.
Show »
Length:417
Mass (Da):49,081
Checksum:i2E3553D49DA2E0AC
GO

Experimental Info

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Sequence conflicti313 – 3131Missing in AAA34785 (PubMed:3031457).Curated
Sequence conflicti375 – 3751C → R in AAA34785 (PubMed:3031457).Curated

Alternative sequence

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Alternative sequencei1 – 1111Missing in isoform II. CuratedVSP_018811Add
BLAST

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
M15991 Genomic DNA. Translation: AAA34785.1.
X89633 Genomic DNA. Translation: CAA61780.1.
Z75182 Genomic DNA. Translation: CAA99499.1.
BK006948 Genomic DNA. Translation: DAA11040.1.
PIRiS67176.
RefSeqiNP_014917.3. NM_001183693.3. [P07884-1]

Genome annotation databases

EnsemblFungiiYOR274W; YOR274W; YOR274W. [P07884-1]
GeneIDi854448.
KEGGisce:YOR274W.

Keywords - Coding sequence diversityi

Alternative initiation

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
M15991 Genomic DNA. Translation: AAA34785.1.
X89633 Genomic DNA. Translation: CAA61780.1.
Z75182 Genomic DNA. Translation: CAA99499.1.
BK006948 Genomic DNA. Translation: DAA11040.1.
PIRiS67176.
RefSeqiNP_014917.3. NM_001183693.3. [P07884-1]

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
3EPHX-ray2.95A/B13-421[»]
3EPJX-ray3.10A/B13-421[»]
3EPKX-ray3.20A/B13-421[»]
3EPLX-ray3.60A/B13-421[»]
ProteinModelPortaliP07884.
SMRiP07884. Positions 13-421.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi34663. 48 interactions.
DIPiDIP-4094N.
IntActiP07884. 2 interactions.
MINTiMINT-536616.

Proteomic databases

MaxQBiP07884.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblFungiiYOR274W; YOR274W; YOR274W. [P07884-1]
GeneIDi854448.
KEGGisce:YOR274W.

Organism-specific databases

EuPathDBiFungiDB:YOR274W.
SGDiS000005800. MOD5.

Phylogenomic databases

GeneTreeiENSGT00390000015214.
HOGENOMiHOG000039995.
InParanoidiP07884.
KOiK00791.
OMAiKWINNRF.
OrthoDBiEOG7SR4WC.

Enzyme and pathway databases

BioCyciYEAST:YOR274W-MONOMER.
BRENDAi2.5.1.75. 984.
ReactomeiR-SCE-6782315. tRNA modification in the nucleus and cytosol.

Miscellaneous databases

EvolutionaryTraceiP07884.
PROiP07884.

Family and domain databases

Gene3Di3.40.50.300. 1 hit.
HAMAPiMF_00185. IPP_trans.
InterProiIPR018022. IPP_trans.
IPR030666. IPP_transferase_euk.
IPR027417. P-loop_NTPase.
[Graphical view]
PfamiPF01715. IPPT. 1 hit.
[Graphical view]
PIRSFiPIRSF039110. IPP_transferase. 1 hit.
SUPFAMiSSF52540. SSF52540. 1 hit.
TIGRFAMsiTIGR00174. miaA. 1 hit.
ProtoNetiSearch...

Publicationsi

« Hide 'large scale' publications
  1. "DNA sequence and transcript mapping of MOD5: features of the 5' region which suggest two translational starts."
    Najarian D., Dihanich M.E., Martin N.C., Hopper A.K.
    Mol. Cell. Biol. 7:185-191(1987) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
  2. "DNA sequence analysis of the VPH1-SNF2 region on chromosome XV of Saccharomyces cerevisiae."
    Cheret G., Bernardi A., Sor F.J.
    Yeast 12:1059-1064(1996) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
    Strain: ATCC 204508 / S288c.
  3. "The nucleotide sequence of Saccharomyces cerevisiae chromosome XV."
    Dujon B., Albermann K., Aldea M., Alexandraki D., Ansorge W., Arino J., Benes V., Bohn C., Bolotin-Fukuhara M., Bordonne R., Boyer J., Camasses A., Casamayor A., Casas C., Cheret G., Cziepluch C., Daignan-Fornier B., Dang V.-D.
    , de Haan M., Delius H., Durand P., Fairhead C., Feldmann H., Gaillon L., Galisson F., Gamo F.-J., Gancedo C., Goffeau A., Goulding S.E., Grivell L.A., Habbig B., Hand N.J., Hani J., Hattenhorst U., Hebling U., Hernando Y., Herrero E., Heumann K., Hiesel R., Hilger F., Hofmann B., Hollenberg C.P., Hughes B., Jauniaux J.-C., Kalogeropoulos A., Katsoulou C., Kordes E., Lafuente M.J., Landt O., Louis E.J., Maarse A.C., Madania A., Mannhaupt G., Marck C., Martin R.P., Mewes H.-W., Michaux G., Paces V., Parle-McDermott A.G., Pearson B.M., Perrin A., Pettersson B., Poch O., Pohl T.M., Poirey R., Portetelle D., Pujol A., Purnelle B., Ramezani Rad M., Rechmann S., Schwager C., Schweizer M., Sor F., Sterky F., Tarassov I.A., Teodoru C., Tettelin H., Thierry A., Tobiasch E., Tzermia M., Uhlen M., Unseld M., Valens M., Vandenbol M., Vetter I., Vlcek C., Voet M., Volckaert G., Voss H., Wambutt R., Wedler H., Wiemann S., Winsor B., Wolfe K.H., Zollner A., Zumstein E., Kleine K.
    Nature 387:98-102(1997) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: ATCC 204508 / S288c.
  4. Cited for: GENOME REANNOTATION.
    Strain: ATCC 204508 / S288c.
  5. "Isolation and characterization of MOD5, a gene required for isopentenylation of cytoplasmic and mitochondrial tRNAs of Saccharomyces cerevisiae."
    Dihanich M.E., Najarian D., Clark R., Gillman E.C., Martin N.C., Hopper A.K.
    Mol. Cell. Biol. 7:177-184(1987) [PubMed] [Europe PMC] [Abstract]
    Cited for: FUNCTION.
  6. "mRNA leader length and initiation codon context determine alternative AUG selection for the yeast gene MOD5."
    Slusher L.B., Gillman E.C., Martin N.C., Hopper A.K.
    Proc. Natl. Acad. Sci. U.S.A. 88:9789-9793(1991) [PubMed] [Europe PMC] [Abstract]
    Cited for: ALTERNATIVE INITIATION, SUBCELLULAR LOCATION.
  7. "MOD5 translation initiation sites determine N6-isopentenyladenosine modification of mitochondrial and cytoplasmic tRNA."
    Gillman E.C., Slusher L.B., Martin N.C., Hopper A.K.
    Mol. Cell. Biol. 11:2382-2390(1991) [PubMed] [Europe PMC] [Abstract]
    Cited for: ALTERNATIVE INITIATION, SUBCELLULAR LOCATION.
  8. "Subcellular locations of MOD5 proteins: mapping of sequences sufficient for targeting to mitochondria and demonstration that mitochondrial and nuclear isoforms commingle in the cytosol."
    Boguta M., Hunter L.A., Shen W.C., Gillman E.C., Martin N.C., Hopper A.K.
    Mol. Cell. Biol. 14:2298-2306(1994) [PubMed] [Europe PMC] [Abstract]
    Cited for: ALTERNATIVE INITIATION, SUBCELLULAR LOCATION.
  9. "Competition between a sterol biosynthetic enzyme and tRNA modification in addition to changes in the protein synthesis machinery causes altered nonsense suppression."
    Benko A.L., Vaduva G., Martin N.C., Hopper A.K.
    Proc. Natl. Acad. Sci. U.S.A. 97:61-66(2000) [PubMed] [Europe PMC] [Abstract]
    Cited for: FUNCTION.
  10. Cited for: LEVEL OF PROTEIN EXPRESSION [LARGE SCALE ANALYSIS].
  11. "Plasticity and diversity of tRNA anticodon determinants of substrate recognition by eukaryotic A37 isopentenyltransferases."
    Lamichhane T.N., Blewett N.H., Maraia R.J.
    RNA 17:1846-1857(2011) [PubMed] [Europe PMC] [Abstract]
    Cited for: FUNCTION.
  12. "A yeast prion, Mod5, promotes acquired drug resistance and cell survival under environmental stress."
    Suzuki G., Shimazu N., Tanaka M.
    Science 336:355-359(2012) [PubMed] [Europe PMC] [Abstract]
    Cited for: PRION FORMATION, SUBCELLULAR LOCATION.
  13. "Crystallographic snapshots of eukaryotic dimethylallyltransferase acting on tRNA: insight into tRNA recognition and reaction mechanism."
    Zhou C., Huang R.H.
    Proc. Natl. Acad. Sci. U.S.A. 105:16142-16147(2008) [PubMed] [Europe PMC] [Abstract]
    Cited for: X-RAY CRYSTALLOGRAPHY (2.95 ANGSTROMS) OF 13-421 IN COMPLEXES WITH SUBSTRATE TRNA; ISOPENTENYL DIPHOSPHATE AND ZINC IONS.

Entry informationi

Entry nameiMOD5_YEAST
AccessioniPrimary (citable) accession number: P07884
Secondary accession number(s): D6W2X4, Q12203
Entry historyi
Integrated into UniProtKB/Swiss-Prot: August 1, 1988
Last sequence update: November 1, 1997
Last modified: July 6, 2016
This is version 157 of the entry and version 2 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programFungal Protein Annotation Program

Miscellaneousi

Miscellaneous

[MOD+] is the prion form of MOD5. [MOD+] is the result of a conformational change of the cellular MOD5 protein that becomes self-propagating and infectious. This conformational change generates a form of MOD5 that assembles into amyloid-like fibrillar aggregates. [MOD+]-aggregates sequester soluble MOD5, resulting in decreased levels of (i6A)-modified tRNAs and higher ergosterol levels, due to less competition for ERG20, which uses the same substrate DMAPP than MOD5. [MOD+] can be cured by GdnHCl and by deletion of the molecular chaperone HSP104, which is required for [MOD+] propagation. The [MOD+] state acquires resistance against antifungal agents such as flucanozole, ketoconazole and clotrimazole that inhibit ergosterol biosynthesis. De novo appearance of [MOD+] is favored in the presence of antifungal agents, and the growth advantage of [MOD+] is lost when the cells are released from the selective pressure. Thus, the conformational switch of MOD5 from a soluble state to a prion state allows the cell to adapt to the harmful environment of anti-fungal drugs by up-regulating ergosterol biosynthesis at the expense of tRNA modification.1 Publication
Present with 2020 molecules/cell in log phase SD medium.1 Publication

Keywords - Technical termi

3D-structure, Complete proteome, Reference proteome

Documents

  1. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
  2. SIMILARITY comments
    Index of protein domains and families
  3. Yeast
    Yeast (Saccharomyces cerevisiae): entries, gene names and cross-references to SGD
  4. Yeast chromosome XV
    Yeast (Saccharomyces cerevisiae) chromosome XV: entries and gene names

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 one 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.