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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)DescriptionActionsGraphical viewLength
Nucleotide bindingi21 – 28ATPSequence analysis8
Zinc fingeri373 – 409Matrin-typeAdd BLAST37

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)DescriptionActionsGraphical viewLength
ChainiPRO_00000190251 – 428tRNA dimethylallyltransferase, mitochondrialAdd BLAST428

Proteomic databases

PRIDEiP07884.

Interactioni

Sites

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Sitei112Interaction with substrate tRNA1
Sitei193Interaction with substrate tRNA1

Protein-protein interaction databases

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

Structurei

Secondary structure

1428
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details
Feature keyPosition(s)DescriptionActionsGraphical viewLength
Beta strandi15 – 21Combined sources7
Beta strandi23 – 26Combined sources4
Helixi27 – 38Combined sources12
Beta strandi40 – 44Combined sources5
Turni47 – 50Combined sources4
Beta strandi51 – 53Combined sources3
Turni55 – 59Combined sources5
Helixi63 – 65Combined sources3
Turni66 – 68Combined sources3
Beta strandi71 – 73Combined sources3
Helixi85 – 100Combined sources16
Turni101 – 103Combined sources3
Beta strandi105 – 109Combined sources5
Helixi113 – 120Combined sources8
Beta strandi127 – 129Combined sources3
Helixi135 – 141Combined sources7
Beta strandi144 – 148Combined sources5
Helixi149 – 155Combined sources7
Helixi158 – 161Combined sources4
Helixi169 – 182Combined sources14
Helixi186 – 191Combined sources6
Beta strandi198 – 207Combined sources10
Helixi210 – 226Combined sources17
Helixi229 – 240Combined sources12
Turni241 – 244Combined sources4
Helixi247 – 249Combined sources3
Helixi253 – 256Combined sources4
Helixi261 – 267Combined sources7
Helixi278 – 302Combined sources25
Helixi304 – 307Combined sources4
Turni308 – 310Combined sources3
Beta strandi312 – 316Combined sources5
Turni320 – 322Combined sources3
Turni324 – 327Combined sources4
Helixi328 – 339Combined sources12
Helixi351 – 357Combined sources7
Helixi359 – 361Combined sources3
Helixi363 – 365Combined sources3
Beta strandi372 – 379Combined sources8
Beta strandi385 – 390Combined sources6
Helixi391 – 398Combined sources8
Helixi401 – 418Combined sources18

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB 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.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiP07884.

Family & Domainsi

Region

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Regioni23 – 28Substrate binding6
Regioni46 – 49Interaction with substrate tRNA4
Regioni170 – 174Interaction with substrate tRNA5
Regioni199 – 207Core aggregation region9
Regioni210 – 232Interaction with isopentenylpyrophosphate transferaseAdd BLAST23
Regioni256 – 258Interaction with substrate tRNA3
Regioni284 – 302Interaction with substrate tRNAAdd BLAST19
Regioni294 – 301Interaction with substrate tRNABy similarity8

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)DescriptionActionsGraphical viewLength
Zinc fingeri373 – 409Matrin-typeAdd BLAST37

Keywords - Domaini

Zinc-finger

Phylogenomic databases

GeneTreeiENSGT00390000015214.
HOGENOMiHOG000039995.
InParanoidiP07884.
KOiK00791.
OMAiMYRGLPI.
OrthoDBiEOG092C2226.

Family and domain databases

Gene3Di3.40.50.300. 1 hit.
HAMAPiMF_00185. IPP_trans. 1 hit.
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)DescriptionActionsGraphical viewLength
Sequence conflicti313Missing in AAA34785 (PubMed:3031457).Curated1
Sequence conflicti375C → R in AAA34785 (PubMed:3031457).Curated1

Alternative sequence

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Alternative sequenceiVSP_0188111 – 11Missing in isoform II. CuratedAdd BLAST11

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
PDB 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.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

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

Proteomic databases

PRIDEiP07884.

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.
OMAiMYRGLPI.
OrthoDBiEOG092C2226.

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. 1 hit.
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...

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: November 2, 2016
This is version 160 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.