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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: Annotation score: 4 out of 5-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

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
Complete GO annotation...

Keywords - Molecular functioni

Methyltransferase, Transferase

Keywords - Ligandi

S-adenosyl-L-methionine

Enzyme and pathway databases

BioCyciMetaCyc:MONOMER-18825.
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

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
1VCEX-ray2.10A/B1-265[»]
1WNGX-ray2.10A/B1-265[»]
2DEKX-ray1.65A/B1-265[»]
2DSGX-ray2.00A/B1-265[»]
2DSHX-ray2.00A/B1-265[»]
2DSIX-ray2.20A/B1-265[»]
2DV3X-ray1.90A/B1-265[»]
2DV4X-ray2.20A/B1-265[»]
2DV5X-ray2.20A/B1-265[»]
2DV7X-ray2.30A/B1-265[»]
2DXVX-ray1.90A/B1-265[»]
2DXWX-ray1.80A/B1-265[»]
2DXXX-ray1.75A/B1-265[»]
2E07X-ray1.90A/B1-265[»]
2E08X-ray2.00A/B1-265[»]
2E15X-ray1.80A/B1-265[»]
2E16X-ray2.00A/B1-265[»]
2E17X-ray1.90A/B1-265[»]
2E4NX-ray1.80A/B1-265[»]
2E4RX-ray2.20A/B1-265[»]
2E7RX-ray1.80A/B1-265[»]
2E8HX-ray2.10A/B1-265[»]
2E8QX-ray2.50A/B1-265[»]
2E8RX-ray2.00A/B1-265[»]
2E8SX-ray2.50A/B1-265[»]
2ED3X-ray2.50A/B1-265[»]
2ED5X-ray2.10A/B1-265[»]
2EEQX-ray2.50A/B1-265[»]
2EGBX-ray1.90A/B1-265[»]
2EGLX-ray1.80A/B1-265[»]
2EGSX-ray1.90A/B1-265[»]
2EH2X-ray2.00A/B1-265[»]
2EH4X-ray2.10A/B1-265[»]
2EH5X-ray2.30A/B1-265[»]
2EHCX-ray1.80A/B1-265[»]
2EHLX-ray1.60A/B1-265[»]
2EJJX-ray2.10A/B1-265[»]
2EJKX-ray2.40A/B1-265[»]
2EJZX-ray1.85A/B1-265[»]
2EK2X-ray2.20A/B1-265[»]
2EK3X-ray2.80A/B1-265[»]
2EK4X-ray2.20A/B1-265[»]
2EK7X-ray2.00A/B1-265[»]
2EKAX-ray2.30A/B1-265[»]
2EL0X-ray2.40A/B1-265[»]
2EL1X-ray2.20A/B1-265[»]
2EL2X-ray2.30A/B1-265[»]
2EL3X-ray2.40A/B1-265[»]
2ELDX-ray2.30A/B1-265[»]
2ELEX-ray2.40A/B1-265[»]
2EMRX-ray2.40A/B1-265[»]
2EMUX-ray2.20A/B1-265[»]
2EN5X-ray1.90A/B1-265[»]
2ENIX-ray2.50A/B1-265[»]
2HR8X-ray2.80A/B1-265[»]
2HUQX-ray2.20A/B1-265[»]
2HUTX-ray2.40A/B1-265[»]
2HUVX-ray2.10A/B1-265[»]
2HUXX-ray2.40A/B1-265[»]
2OWFX-ray2.20A1-265[»]
2OWGX-ray2.10A/B1-265[»]
2OWKX-ray2.00A/B1-265[»]
2OWUX-ray2.20A/B1-265[»]
2OWVX-ray2.80A/B1-265[»]
2P2XX-ray2.90A/B1-265[»]
2P5CX-ray2.40A/B1-265[»]
2P5FX-ray2.50A/B1-265[»]
2P6DX-ray2.40A/B1-265[»]
2P6IX-ray2.20A/B1-265[»]
2P6KX-ray2.10A/B1-265[»]
2P6LX-ray2.00A/B1-265[»]
2P9DX-ray2.10A/B1-265[»]
2PB4X-ray2.10A/B1-265[»]
2PB5X-ray2.10A/B1-265[»]
2PB6X-ray2.20A/B1-265[»]
2PCAX-ray2.00A/B1-265[»]
2PCGX-ray2.20A/B1-265[»]
2PCHX-ray2.00A/B1-265[»]
2PCIX-ray2.00A/B1-265[»]
2PCKX-ray2.60A/B1-265[»]
2PCMX-ray2.40A/B1-265[»]
2Z6RX-ray1.50A/B1-265[»]
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.
OMAiMTANEGL.

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.
InterProiIPR000878. 4pyrrol_Mease.
IPR014777. 4pyrrole_Mease_sub1.
IPR014776. 4pyrrole_Mease_sub2.
IPR004551. Dphthn_synthase.
[Graphical view]
PANTHERiPTHR10882:SF0. PTHR10882:SF0. 1 hit.
PfamiPF00590. TP_methylase. 1 hit.
[Graphical view]
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.

Cross-referencesi

Sequence databases

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

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
1VCEX-ray2.10A/B1-265[»]
1WNGX-ray2.10A/B1-265[»]
2DEKX-ray1.65A/B1-265[»]
2DSGX-ray2.00A/B1-265[»]
2DSHX-ray2.00A/B1-265[»]
2DSIX-ray2.20A/B1-265[»]
2DV3X-ray1.90A/B1-265[»]
2DV4X-ray2.20A/B1-265[»]
2DV5X-ray2.20A/B1-265[»]
2DV7X-ray2.30A/B1-265[»]
2DXVX-ray1.90A/B1-265[»]
2DXWX-ray1.80A/B1-265[»]
2DXXX-ray1.75A/B1-265[»]
2E07X-ray1.90A/B1-265[»]
2E08X-ray2.00A/B1-265[»]
2E15X-ray1.80A/B1-265[»]
2E16X-ray2.00A/B1-265[»]
2E17X-ray1.90A/B1-265[»]
2E4NX-ray1.80A/B1-265[»]
2E4RX-ray2.20A/B1-265[»]
2E7RX-ray1.80A/B1-265[»]
2E8HX-ray2.10A/B1-265[»]
2E8QX-ray2.50A/B1-265[»]
2E8RX-ray2.00A/B1-265[»]
2E8SX-ray2.50A/B1-265[»]
2ED3X-ray2.50A/B1-265[»]
2ED5X-ray2.10A/B1-265[»]
2EEQX-ray2.50A/B1-265[»]
2EGBX-ray1.90A/B1-265[»]
2EGLX-ray1.80A/B1-265[»]
2EGSX-ray1.90A/B1-265[»]
2EH2X-ray2.00A/B1-265[»]
2EH4X-ray2.10A/B1-265[»]
2EH5X-ray2.30A/B1-265[»]
2EHCX-ray1.80A/B1-265[»]
2EHLX-ray1.60A/B1-265[»]
2EJJX-ray2.10A/B1-265[»]
2EJKX-ray2.40A/B1-265[»]
2EJZX-ray1.85A/B1-265[»]
2EK2X-ray2.20A/B1-265[»]
2EK3X-ray2.80A/B1-265[»]
2EK4X-ray2.20A/B1-265[»]
2EK7X-ray2.00A/B1-265[»]
2EKAX-ray2.30A/B1-265[»]
2EL0X-ray2.40A/B1-265[»]
2EL1X-ray2.20A/B1-265[»]
2EL2X-ray2.30A/B1-265[»]
2EL3X-ray2.40A/B1-265[»]
2ELDX-ray2.30A/B1-265[»]
2ELEX-ray2.40A/B1-265[»]
2EMRX-ray2.40A/B1-265[»]
2EMUX-ray2.20A/B1-265[»]
2EN5X-ray1.90A/B1-265[»]
2ENIX-ray2.50A/B1-265[»]
2HR8X-ray2.80A/B1-265[»]
2HUQX-ray2.20A/B1-265[»]
2HUTX-ray2.40A/B1-265[»]
2HUVX-ray2.10A/B1-265[»]
2HUXX-ray2.40A/B1-265[»]
2OWFX-ray2.20A1-265[»]
2OWGX-ray2.10A/B1-265[»]
2OWKX-ray2.00A/B1-265[»]
2OWUX-ray2.20A/B1-265[»]
2OWVX-ray2.80A/B1-265[»]
2P2XX-ray2.90A/B1-265[»]
2P5CX-ray2.40A/B1-265[»]
2P5FX-ray2.50A/B1-265[»]
2P6DX-ray2.40A/B1-265[»]
2P6IX-ray2.20A/B1-265[»]
2P6KX-ray2.10A/B1-265[»]
2P6LX-ray2.00A/B1-265[»]
2P9DX-ray2.10A/B1-265[»]
2PB4X-ray2.10A/B1-265[»]
2PB5X-ray2.10A/B1-265[»]
2PB6X-ray2.20A/B1-265[»]
2PCAX-ray2.00A/B1-265[»]
2PCGX-ray2.20A/B1-265[»]
2PCHX-ray2.00A/B1-265[»]
2PCIX-ray2.00A/B1-265[»]
2PCKX-ray2.60A/B1-265[»]
2PCMX-ray2.40A/B1-265[»]
2Z6RX-ray1.50A/B1-265[»]
ProteinModelPortaliO58456.
SMRiO58456.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

STRINGi70601.PH0725.

Proteomic databases

PRIDEiO58456.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiBAA29816; BAA29816; BAA29816.
GeneIDi1443058.
KEGGipho:PH0725.

Phylogenomic databases

eggNOGiarCOG04161. Archaea.
COG1798. LUCA.
HOGENOMiHOG000205302.
KOiK20215.
OMAiMTANEGL.

Enzyme and pathway databases

UniPathwayiUPA00559.
BioCyciMetaCyc:MONOMER-18825.
BRENDAi2.1.1.98. 5244.

Miscellaneous databases

EvolutionaryTraceiO58456.

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.
InterProiIPR000878. 4pyrrol_Mease.
IPR014777. 4pyrrole_Mease_sub1.
IPR014776. 4pyrrole_Mease_sub2.
IPR004551. Dphthn_synthase.
[Graphical view]
PANTHERiPTHR10882:SF0. PTHR10882:SF0. 1 hit.
PfamiPF00590. TP_methylase. 1 hit.
[Graphical view]
PIRSFiPIRSF036432. Diphthine_synth. 1 hit.
SUPFAMiSSF53790. SSF53790. 1 hit.
TIGRFAMsiTIGR00522. dph5. 1 hit.
ProtoNetiSearch...

Entry informationi

Entry nameiDPHB_PYRHO
AccessioniPrimary (citable) accession number: O58456
Entry historyi
Integrated into UniProtKB/Swiss-Prot: October 10, 2003
Last sequence update: August 1, 1998
Last modified: November 2, 2016
This is version 98 of the entry and version 1 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programProkaryotic Protein Annotation Program

Miscellaneousi

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.

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

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.