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Protein

Diphthine methyl ester synthase

Gene

DPH5

Organism
Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)
Status
Reviewed-Annotation score: Annotation score: 4 out of 5-Experimental evidence at protein leveli

Functioni

S-adenosyl-L-methionine-dependent methyltransferase that catalyzes four methylations of the modified target histidine residue in translation elongation factor 2 (EF-2), to form an intermediate called diphthine methyl ester. The four successive methylation reactions represent the second step of diphthamide biosynthesis.2 Publications

Catalytic activityi

4 S-adenosyl-L-methionine + 2-((3S)-3-carboxy-3-aminopropyl)-L-histidine-[translation elongation factor 2] = 4 S-adenosyl-L-homocysteine + diphthine methyl ester-[translation elongation factor 2].1 Publication

Pathwayi: peptidyl-diphthamide biosynthesis

This protein is involved in the pathway peptidyl-diphthamide biosynthesis, which is part of Protein modification.
View all proteins of this organism that are known to be involved in the pathway peptidyl-diphthamide biosynthesis and in Protein modification.

Sites

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Binding sitei9 – 91S-adenosyl-L-methionine; via carbonyl oxygenBy similarity
Binding sitei85 – 851S-adenosyl-L-methionine; via amide nitrogen and carbonyl oxygenBy similarity
Binding sitei88 – 881S-adenosyl-L-methionine; via carbonyl oxygenBy similarity
Binding sitei164 – 1641S-adenosyl-L-methionine; via amide nitrogen and carbonyl oxygenBy similarity
Binding sitei222 – 2221S-adenosyl-L-methionine; via amide nitrogen and carbonyl oxygenBy similarity
Binding sitei247 – 2471S-adenosyl-L-methionine; via carbonyl oxygenBy similarity

GO - Molecular functioni

  • diphthine synthase activity Source: SGD

GO - Biological processi

  • peptidyl-diphthamide biosynthetic process from peptidyl-histidine Source: SGD
Complete GO annotation...

Keywords - Molecular functioni

Methyltransferase, Transferase

Keywords - Ligandi

S-adenosyl-L-methionine

Enzyme and pathway databases

BioCyciMetaCyc:MONOMER-15582.
YEAST:MONOMER-15582.
ReactomeiR-SCE-5358493. Synthesis of diphthamide-EEF2.
UniPathwayiUPA00559.

Names & Taxonomyi

Protein namesi
Recommended name:
Diphthine methyl ester synthase (EC:2.1.1.3141 Publication)
Alternative name(s):
Diphthamide biosynthesis methyltransferase
Gene namesi
Name:DPH5
Ordered Locus Names:YLR172C
ORF Names:L9470.17
OrganismiSaccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)
Taxonomic identifieri559292 [NCBI]
Taxonomic lineageiEukaryotaFungiDikaryaAscomycotaSaccharomycotinaSaccharomycetesSaccharomycetalesSaccharomycetaceaeSaccharomyces
Proteomesi
  • UP000002311 Componenti: Chromosome XII

Organism-specific databases

EuPathDBiFungiDB:YLR172C.
SGDiS000004162. DPH5.

Subcellular locationi

GO - Cellular componenti

Complete GO annotation...

Keywords - Cellular componenti

Cytoplasm

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 300300Diphthine methyl ester synthasePRO_0000156147Add
BLAST

Amino acid modifications

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Modified residuei172 – 1721PhosphoserineCombined sources
Modified residuei298 – 2981PhosphoserineCombined sources

Keywords - PTMi

Phosphoprotein

Proteomic databases

MaxQBiP32469.

PTM databases

iPTMnetiP32469.

Interactioni

Protein-protein interaction databases

BioGridi31443. 84 interactions.
DIPiDIP-4237N.
IntActiP32469. 7 interactions.
MINTiMINT-567664.

Structurei

3D structure databases

ProteinModelPortaliP32469.
SMRiP32469. Positions 1-267.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Region

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Regioni113 – 1142S-adenosyl-L-methionine bindingBy similarity

Sequence similaritiesi

Belongs to the diphthine synthase family.Curated

Phylogenomic databases

GeneTreeiENSGT00390000010568.
HOGENOMiHOG000205302.
InParanoidiP32469.
KOiK00586.
OMAiTLQQMCT.
OrthoDBiEOG7Z3FG9.

Family and domain databases

Gene3Di3.30.950.10. 1 hit.
3.40.1010.10. 1 hit.
HAMAPiMF_01084. Diphthine_synth.
InterProiIPR000878. 4pyrrol_Mease.
IPR014777. 4pyrrole_Mease_sub1.
IPR014776. 4pyrrole_Mease_sub2.
IPR004551. Dphthn_synthase.
[Graphical view]
PfamiPF00590. TP_methylase. 1 hit.
[Graphical view]
PIRSFiPIRSF036432. Diphthine_synth. 1 hit.
SUPFAMiSSF53790. SSF53790. 1 hit.
TIGRFAMsiTIGR00522. dph5. 1 hit.

Sequencei

Sequence statusi: Complete.

P32469-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MLYLIGLGLS YKSDITVRGL EAIKKCSRVY LEHYTSILMA ASQEELESYY
60 70 80 90 100
GKEIILADRE LVETGSKQIL NNADKEDVAF LVVGDPFGAT THTDLVLRAK
110 120 130 140 150
REAIPVEIIH NASVMNAVGA CGLQLYNFGQ TVSMVFFTDN WRPDSWYDKI
160 170 180 190 200
WENRKIGLHT LVLLDIKVKE QSIENMARGR LIYEPPRYMS IAQCCEQLLE
210 220 230 240 250
IEEKRGTKAY TPDTPAVAIS RLGSSSQSFK SGTISELANY DSGEPLHSLV
260 270 280 290 300
ILGRQCHELE LEYLLEFADD KEKFGKDVAN DQEYFKPAAW VPPTEDDSDE
Length:300
Mass (Da):33,847
Last modified:October 1, 1993 - v1
Checksum:i405411F6BF2E6DF9
GO

Experimental Info

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Sequence conflicti287 – 2871P → L in AAS56273 (PubMed:17322287).Curated

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
M83375 Genomic DNA. Translation: AAA34577.1.
U17246 Genomic DNA. Translation: AAB67469.1.
AY557947 Genomic DNA. Translation: AAS56273.1.
X70279 Genomic DNA. Translation: CAA49764.1.
BK006945 Genomic DNA. Translation: DAA09492.1.
PIRiS30890.
RefSeqiNP_013273.1. NM_001182059.1.

Genome annotation databases

EnsemblFungiiYLR172C; YLR172C; YLR172C.
GeneIDi850869.
KEGGisce:YLR172C.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
M83375 Genomic DNA. Translation: AAA34577.1.
U17246 Genomic DNA. Translation: AAB67469.1.
AY557947 Genomic DNA. Translation: AAS56273.1.
X70279 Genomic DNA. Translation: CAA49764.1.
BK006945 Genomic DNA. Translation: DAA09492.1.
PIRiS30890.
RefSeqiNP_013273.1. NM_001182059.1.

3D structure databases

ProteinModelPortaliP32469.
SMRiP32469. Positions 1-267.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi31443. 84 interactions.
DIPiDIP-4237N.
IntActiP32469. 7 interactions.
MINTiMINT-567664.

PTM databases

iPTMnetiP32469.

Proteomic databases

MaxQBiP32469.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblFungiiYLR172C; YLR172C; YLR172C.
GeneIDi850869.
KEGGisce:YLR172C.

Organism-specific databases

EuPathDBiFungiDB:YLR172C.
SGDiS000004162. DPH5.

Phylogenomic databases

GeneTreeiENSGT00390000010568.
HOGENOMiHOG000205302.
InParanoidiP32469.
KOiK00586.
OMAiTLQQMCT.
OrthoDBiEOG7Z3FG9.

Enzyme and pathway databases

UniPathwayiUPA00559.
BioCyciMetaCyc:MONOMER-15582.
YEAST:MONOMER-15582.
ReactomeiR-SCE-5358493. Synthesis of diphthamide-EEF2.

Miscellaneous databases

PROiP32469.

Family and domain databases

Gene3Di3.30.950.10. 1 hit.
3.40.1010.10. 1 hit.
HAMAPiMF_01084. Diphthine_synth.
InterProiIPR000878. 4pyrrol_Mease.
IPR014777. 4pyrrole_Mease_sub1.
IPR014776. 4pyrrole_Mease_sub2.
IPR004551. Dphthn_synthase.
[Graphical view]
PfamiPF00590. TP_methylase. 1 hit.
[Graphical view]
PIRSFiPIRSF036432. Diphthine_synth. 1 hit.
SUPFAMiSSF53790. SSF53790. 1 hit.
TIGRFAMsiTIGR00522. dph5. 1 hit.
ProtoNetiSearch...

Publicationsi

« Hide 'large scale' publications
  1. "DPH5, a methyltransferase gene required for diphthamide biosynthesis in Saccharomyces cerevisiae."
    Mattheakis L.C., Shen W.H., Collier R.J.
    Mol. Cell. Biol. 12:4026-4037(1992) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA], FUNCTION.
  2. "The nucleotide sequence of Saccharomyces cerevisiae chromosome XII."
    Johnston M., Hillier L.W., Riles L., Albermann K., Andre B., Ansorge W., Benes V., Brueckner M., Delius H., Dubois E., Duesterhoeft A., Entian K.-D., Floeth M., Goffeau A., Hebling U., Heumann K., Heuss-Neitzel D., Hilbert H.
    , Hilger F., Kleine K., Koetter P., Louis E.J., Messenguy F., Mewes H.-W., Miosga T., Moestl D., Mueller-Auer S., Nentwich U., Obermaier B., Piravandi E., Pohl T.M., Portetelle D., Purnelle B., Rechmann S., Rieger M., Rinke M., Rose M., Scharfe M., Scherens B., Scholler P., Schwager C., Schwarz S., Underwood A.P., Urrestarazu L.A., Vandenbol M., Verhasselt P., Vierendeels F., Voet M., Volckaert G., Voss H., Wambutt R., Wedler E., Wedler H., Zimmermann F.K., Zollner A., Hani J., Hoheisel J.D.
    Nature 387:87-90(1997) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: ATCC 204508 / S288c.
  3. Cited for: GENOME REANNOTATION.
    Strain: ATCC 204508 / S288c.
  4. Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
    Strain: ATCC 204508 / S288c.
  5. "Cloning of the YAP19 gene encoding a putative yeast homolog of AP19, the mammalian small chain of the clathrin-assembly proteins."
    Nakai M., Takada T., Endo T.
    Biochim. Biophys. Acta 1174:282-284(1993) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA] OF 228-300.
    Strain: SP1.
  6. Cited for: SUBCELLULAR LOCATION [LARGE SCALE ANALYSIS].
  7. Cited for: LEVEL OF PROTEIN EXPRESSION [LARGE SCALE ANALYSIS].
  8. "Large-scale phosphorylation analysis of alpha-factor-arrested Saccharomyces cerevisiae."
    Li X., Gerber S.A., Rudner A.D., Beausoleil S.A., Haas W., Villen J., Elias J.E., Gygi S.P.
    J. Proteome Res. 6:1190-1197(2007) [PubMed] [Europe PMC] [Abstract]
    Cited for: PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-298, IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
    Strain: ADR376.
  9. "A multidimensional chromatography technology for in-depth phosphoproteome analysis."
    Albuquerque C.P., Smolka M.B., Payne S.H., Bafna V., Eng J., Zhou H.
    Mol. Cell. Proteomics 7:1389-1396(2008) [PubMed] [Europe PMC] [Abstract]
    Cited for: PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-172, IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
  10. "Global analysis of Cdk1 substrate phosphorylation sites provides insights into evolution."
    Holt L.J., Tuch B.B., Villen J., Johnson A.D., Gygi S.P., Morgan D.O.
    Science 325:1682-1686(2009) [PubMed] [Europe PMC] [Abstract]
    Cited for: PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-298, IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
  11. "Dph7 catalyzes a previously unknown demethylation step in diphthamide biosynthesis."
    Lin Z., Su X., Chen W., Ci B., Zhang S., Lin H.
    J. Am. Chem. Soc. 136:6179-6182(2014) [PubMed] [Europe PMC] [Abstract]
    Cited for: FUNCTION, CATALYTIC ACTIVITY.

Entry informationi

Entry nameiDPH5_YEAST
AccessioniPrimary (citable) accession number: P32469
Secondary accession number(s): D6VYH6, Q6Q5L4
Entry historyi
Integrated into UniProtKB/Swiss-Prot: October 1, 1993
Last sequence update: October 1, 1993
Last modified: July 6, 2016
This is version 141 of the entry and version 1 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programFungal Protein Annotation Program

Miscellaneousi

Miscellaneous

2-[3-carboxy-3-(methylammonio)propyl]-L-histidine and the corresponding dimethyl compound can also act as acceptors.
Present with 13480 molecules/cell in log phase SD medium.1 Publication

Keywords - Technical termi

Complete proteome, Reference proteome

Documents

  1. PATHWAY comments
    Index of metabolic and biosynthesis pathways
  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 XII
    Yeast (Saccharomyces cerevisiae) chromosome XII: 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.