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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)LengthDescriptionGraphical viewFeature identifierActions
Binding sitei10 – 101S-adenosyl-L-methionine; via carbonyl oxygenUniRule annotation2 Publications
Binding sitei87 – 871S-adenosyl-L-methionine; via amide nitrogen and carbonyl oxygenUniRule annotation2 Publications
Binding sitei90 – 901S-adenosyl-L-methionine; via carbonyl oxygenUniRule annotation2 Publications
Binding sitei166 – 1661S-adenosyl-L-methionine; via amide nitrogen and carbonyl oxygenUniRule annotation2 Publications
Binding sitei209 – 2091S-adenosyl-L-methionine; via amide nitrogen and carbonyl oxygenUniRule annotation2 Publications
Binding sitei234 – 2341S-adenosyl-L-methionine; via carbonyl oxygenUniRule annotation2 Publications

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

BioCyciPHOR70601:GJWR-724-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)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 265265Diphthine synthasePRO_0000156126Add
BLAST

Interactioni

Subunit structurei

Homodimer.UniRule annotation2 Publications

Protein-protein interaction databases

STRINGi70601.PH0725.

Structurei

Secondary structure

1
265
Legend: HelixTurnBeta strand
Show more details
Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Beta strandi3 – 75Combined sources
Beta strandi9 – 124Combined sources
Helixi13 – 153Combined sources
Helixi18 – 269Combined sources
Beta strandi28 – 336Combined sources
Beta strandi35 – 373Combined sources
Helixi44 – 518Combined sources
Beta strandi56 – 583Combined sources
Helixi60 – 7011Combined sources
Helixi72 – 754Combined sources
Beta strandi80 – 867Combined sources
Beta strandi90 – 934Combined sources
Helixi95 – 1039Combined sources
Beta strandi108 – 1114Combined sources
Helixi116 – 1194Combined sources
Helixi120 – 1234Combined sources
Helixi127 – 1293Combined sources
Beta strandi134 – 1363Combined sources
Beta strandi141 – 1433Combined sources
Helixi147 – 15711Combined sources
Beta strandi161 – 1666Combined sources
Helixi170 – 1723Combined sources
Helixi178 – 19215Combined sources
Beta strandi195 – 1973Combined sources
Beta strandi202 – 2087Combined sources
Beta strandi211 – 2133Combined sources
Beta strandi215 – 2206Combined sources
Helixi221 – 2244Combined sources
Beta strandi234 – 2385Combined sources
Helixi244 – 25411Combined sources
Helixi258 – 2614Combined sources

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
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. Positions 1-265.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiO58456.

Family & Domainsi

Region

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Regioni115 – 1162S-adenosyl-L-methionine bindingUniRule annotation2 Publications

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
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. Positions 1-265.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

STRINGi70601.PH0725.

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.
BioCyciPHOR70601:GJWR-724-MONOMER.
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: September 7, 2016
This is version 96 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.