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Protein

Diphthine synthase

Gene

dphB

Organism
Pyrococcus horikoshii (strain ATCC 700860 / DSM 12428 / JCM 9974 / NBRC 100139 / OT-3)
Status
Reviewed-Annotation score: -Experimental evidence at protein leveli

Functioni

S-adenosyl-L-methionine-dependent methyltransferase that catalyzes the trimethylation of the amino group of the modified target histidine residue in translation elongation factor 2 (EF-2), to form an intermediate called diphthine. The three successive methylation reactions represent the second step of diphthamide biosynthesis.UniRule annotation1 Publication

Miscellaneous

The diphthine intermediate is not stable in vitro and readily eliminates the trimethylamino group. It is not known whether the elimination reaction also occurs physiologically.

Catalytic activityi

3 S-adenosyl-L-methionine + 2-((3S)-3-carboxy-3-aminopropyl)-L-histidine-[translation elongation factor 2] = 3 S-adenosyl-L-homocysteine + diphthine-[translation elongation factor 2].UniRule annotation1 Publication

Pathwayi: peptidyl-diphthamide biosynthesis

This protein is involved in the pathway peptidyl-diphthamide biosynthesis, which is part of Protein modification.UniRule annotation1 Publication
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)DescriptionActionsGraphical viewLength
Binding sitei10S-adenosyl-L-methionine; via carbonyl oxygenUniRule annotation2 Publications1
Binding sitei87S-adenosyl-L-methionine; via amide nitrogen and carbonyl oxygenUniRule annotation2 Publications1
Binding sitei90S-adenosyl-L-methionine; via carbonyl oxygenUniRule annotation2 Publications1
Binding sitei166S-adenosyl-L-methionine; via amide nitrogen and carbonyl oxygenUniRule annotation2 Publications1
Binding sitei209S-adenosyl-L-methionine; via amide nitrogen and carbonyl oxygenUniRule annotation2 Publications1
Binding sitei234S-adenosyl-L-methionine; via carbonyl oxygenUniRule annotation2 Publications1

GO - Molecular functioni

  • diphthine synthase activity Source: UniProtKB

GO - Biological processi

  • peptidyl-diphthamide biosynthetic process from peptidyl-histidine Source: UniProtKB
  • S-adenosylmethionine catabolic process Source: UniProtKB

Keywordsi

Molecular functionMethyltransferase, Transferase
LigandS-adenosyl-L-methionine

Enzyme and pathway databases

BioCyciMetaCyc:MONOMER-18825
PHOR70601:G1G39-711-MONOMER
BRENDAi2.1.1.98 5244
UniPathwayiUPA00559

Names & Taxonomyi

Protein namesi
Recommended name:
Diphthine synthase1 PublicationUniRule annotation (EC:2.1.1.98UniRule annotation1 Publication)
Alternative name(s):
Diphthamide biosynthesis methyltransferaseUniRule annotation
Gene namesi
Name:dphBUniRule annotation
Synonyms:dph51 Publication
Ordered Locus Names:PH0725
OrganismiPyrococcus horikoshii (strain ATCC 700860 / DSM 12428 / JCM 9974 / NBRC 100139 / OT-3)
Taxonomic identifieri70601 [NCBI]
Taxonomic lineageiArchaeaEuryarchaeotaThermococciThermococcalesThermococcaceaePyrococcus
Proteomesi
  • UP000000752 Componenti: Chromosome

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_00001561261 – 265Diphthine synthaseAdd BLAST265

Proteomic databases

PRIDEiO58456

Interactioni

Subunit structurei

Homodimer.UniRule annotation2 Publications

Protein-protein interaction databases

STRINGi70601.PH0725

Structurei

Secondary structure

1265
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details
Feature keyPosition(s)DescriptionActionsGraphical viewLength
Beta strandi3 – 7Combined sources5
Beta strandi9 – 12Combined sources4
Helixi13 – 15Combined sources3
Helixi18 – 26Combined sources9
Beta strandi28 – 33Combined sources6
Beta strandi35 – 37Combined sources3
Helixi44 – 51Combined sources8
Beta strandi56 – 58Combined sources3
Helixi60 – 70Combined sources11
Helixi72 – 75Combined sources4
Beta strandi80 – 86Combined sources7
Beta strandi90 – 93Combined sources4
Helixi95 – 103Combined sources9
Beta strandi108 – 111Combined sources4
Helixi116 – 119Combined sources4
Helixi120 – 123Combined sources4
Helixi127 – 129Combined sources3
Beta strandi134 – 136Combined sources3
Beta strandi141 – 143Combined sources3
Helixi147 – 157Combined sources11
Beta strandi161 – 166Combined sources6
Helixi170 – 172Combined sources3
Helixi178 – 192Combined sources15
Beta strandi195 – 197Combined sources3
Beta strandi202 – 208Combined sources7
Beta strandi211 – 213Combined sources3
Beta strandi215 – 220Combined sources6
Helixi221 – 224Combined sources4
Beta strandi234 – 238Combined sources5
Helixi244 – 254Combined sources11
Helixi258 – 261Combined sources4

3D structure databases

ProteinModelPortaliO58456
SMRiO58456
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiO58456

Family & Domainsi

Region

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Regioni115 – 116S-adenosyl-L-methionine bindingUniRule annotation2 Publications2

Sequence similaritiesi

Belongs to the diphthine synthase family.UniRule annotationCurated

Phylogenomic databases

eggNOGiarCOG04161 Archaea
COG1798 LUCA
HOGENOMiHOG000205302
KOiK20215
OMAiGLQNYRF
OrthoDBiPOG093Z0BZB

Family and domain databases

CDDicd11647 Diphthine_synthase, 1 hit
Gene3Di3.30.950.10, 1 hit
3.40.1010.10, 1 hit
HAMAPiMF_01084 Diphthine_synth, 1 hit
InterProiView protein in InterPro
IPR000878 4pyrrol_Mease
IPR035996 4pyrrol_Methylase_sf
IPR014777 4pyrrole_Mease_sub1
IPR014776 4pyrrole_Mease_sub2
IPR004551 Dphthn_synthase
PANTHERiPTHR10882:SF0 PTHR10882:SF0, 1 hit
PfamiView protein in Pfam
PF00590 TP_methylase, 1 hit
PIRSFiPIRSF036432 Diphthine_synth, 1 hit
SUPFAMiSSF53790 SSF53790, 1 hit
TIGRFAMsiTIGR00522 dph5, 1 hit

Sequencei

Sequence statusi: Complete.

O58456-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MVLYFIGLGL YDERDITVKG LEIAKKCDYV FAEFYTSLMA GTTLGRIQKL
60 70 80 90 100
IGKEIRVLSR EDVELNFENI VLPLAKENDV AFLTPGDPLV ATTHAELRIR
110 120 130 140 150
AKRAGVESYV IHAPSIYSAV GITGLHIYKF GKSATVAYPE GNWFPTSYYD
160 170 180 190 200
VIKENAERGL HTLLFLDIKA EKRMYMTANE AMELLLKVED MKKGGVFTDD
210 220 230 240 250
TLVVVLARAG SLNPTIRAGY VKDLIREDFG DPPHILIVPG KLHIVEAEYL
260
VEIAGAPREI LRVNV
Length:265
Mass (Da):29,576
Last modified:August 1, 1998 - v1
Checksum:iE0F313144BEECC91
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
BA000001 Genomic DNA Translation: BAA29816.1
PIRiF71119
RefSeqiWP_010884823.1, NC_000961.1

Genome annotation databases

EnsemblBacteriaiBAA29816; BAA29816; BAA29816
GeneIDi1443058
KEGGipho:PH0725

Similar proteinsi

Entry informationi

Entry nameiDPHB_PYRHO
AccessioniPrimary (citable) accession number: O58456
Entry historyiIntegrated into UniProtKB/Swiss-Prot: October 10, 2003
Last sequence update: August 1, 1998
Last modified: June 20, 2018
This is version 105 of the entry and version 1 of the sequence. See complete history.
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programProkaryotic Protein Annotation Program

Miscellaneousi

Keywords - Technical termi

3D-structure, Complete proteome

Documents

  1. PATHWAY comments
    Index of metabolic and biosynthesis pathways
  2. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
  3. SIMILARITY comments
    Index of protein domains and families

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