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Protein

Diphthine synthase

Gene

dphB

Organism
Aeropyrum pernix (strain ATCC 700893 / DSM 11879 / JCM 9820 / NBRC 100138 / K1)
Status
Reviewed-Annotation score: Annotation score: 3 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 (By similarity).By similarity

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].

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)DescriptionActionsGraphical viewLength
Binding sitei93S-adenosyl-L-methionine; via amide nitrogen and carbonyl oxygenBy similarity1
Binding sitei96S-adenosyl-L-methionine; via carbonyl oxygenBy similarity1
Binding sitei173S-adenosyl-L-methionine; via amide nitrogen and carbonyl oxygenBy similarity1
Binding sitei220S-adenosyl-L-methionine; via amide nitrogen and carbonyl oxygenBy similarity1

GO - Molecular functioni

GO - Biological processi

Complete GO annotation...

Keywords - Molecular functioni

Methyltransferase, Transferase

Keywords - Ligandi

S-adenosyl-L-methionine

Enzyme and pathway databases

BRENDAi2.1.1.98. 171.
UniPathwayiUPA00559.

Names & Taxonomyi

Protein namesi
Recommended name:
Diphthine synthase (EC:2.1.1.98)
Alternative name(s):
Diphthamide biosynthesis methyltransferase
Gene namesi
Name:dphB
Ordered Locus Names:APE_0931
OrganismiAeropyrum pernix (strain ATCC 700893 / DSM 11879 / JCM 9820 / NBRC 100138 / K1)
Taxonomic identifieri272557 [NCBI]
Taxonomic lineageiArchaeaCrenarchaeotaThermoproteiDesulfurococcalesDesulfurococcaceaeAeropyrum
Proteomesi
  • UP000002518 Componenti: Chromosome

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_00001561141 – 294Diphthine synthaseAdd BLAST294

Interactioni

Subunit structurei

Homodimer.By similarity

Protein-protein interaction databases

STRINGi272557.APE_0931.

Structurei

Secondary structure

1294
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details
Feature keyPosition(s)DescriptionActionsGraphical viewLength
Beta strandi9 – 14Combined sources6
Beta strandi16 – 18Combined sources3
Helixi24 – 32Combined sources9
Beta strandi34 – 39Combined sources6
Beta strandi41 – 43Combined sources3
Helixi48 – 57Combined sources10
Beta strandi59 – 64Combined sources6
Helixi67 – 71Combined sources5
Helixi74 – 77Combined sources4
Beta strandi85 – 92Combined sources8
Beta strandi96 – 99Combined sources4
Helixi100 – 109Combined sources10
Beta strandi113 – 117Combined sources5
Helixi122 – 130Combined sources9
Helixi134 – 136Combined sources3
Beta strandi137 – 143Combined sources7
Helixi146 – 148Combined sources3
Helixi153 – 164Combined sources12
Beta strandi168 – 173Combined sources6
Helixi184 – 202Combined sources19
Helixi208 – 210Combined sources3
Beta strandi213 – 217Combined sources5
Helixi220 – 222Combined sources3
Beta strandi225 – 230Combined sources6
Helixi232 – 236Combined sources5
Beta strandi246 – 249Combined sources4
Helixi255 – 264Combined sources10
Helixi277 – 287Combined sources11
Turni288 – 290Combined sources3

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
1WDEX-ray2.00A1-294[»]
ProteinModelPortaliQ9YDI2.
SMRiQ9YDI2.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiQ9YDI2.

Family & Domainsi

Region

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Regioni121 – 122S-adenosyl-L-methionine bindingBy similarity2

Sequence similaritiesi

Belongs to the diphthine synthase family.Curated

Phylogenomic databases

eggNOGiarCOG04161. Archaea.
COG1798. LUCA.
HOGENOMiHOG000112257.
KOiK20215.
OMAiYDICIAT.

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.

Q9YDI2-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MARGREAVTL LLVGWGYAPG MQTLEALDAV RRADVVYVES YTMPGSSWLY
60 70 80 90 100
KSVVEAAGEA RVVEASRRDL EERSREIVSR ALDAVVAVVT AGDPMVATTH
110 120 130 140 150
SSLAAEALEA GVAVRYIPGV SGVQAARGAT MLSFYRFGGT VTLPGPWRGV
160 170 180 190 200
TPISVARRIY LNLCAGLHTT ALLDVDERGV QLSPGQGVSL LLEADREYAR
210 220 230 240 250
EAGAPALLAR LPSVLVEAGA GGGHRVLYWS SLERLSTADV EGGVYSIVIP
260 270 280 290
ARLSGVEEWL LAAASGQRRP LEYDRSVYET VEENCKKGVY MEPV
Length:294
Mass (Da):31,451
Last modified:November 1, 1999 - v1
Checksum:i521C3A3C2B206C90
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
BA000002 Genomic DNA. Translation: BAA79915.1.
PIRiC72689.

Genome annotation databases

EnsemblBacteriaiBAA79915; BAA79915; APE_0931.
KEGGiape:APE_0931.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
BA000002 Genomic DNA. Translation: BAA79915.1.
PIRiC72689.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
1WDEX-ray2.00A1-294[»]
ProteinModelPortaliQ9YDI2.
SMRiQ9YDI2.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

STRINGi272557.APE_0931.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiBAA79915; BAA79915; APE_0931.
KEGGiape:APE_0931.

Phylogenomic databases

eggNOGiarCOG04161. Archaea.
COG1798. LUCA.
HOGENOMiHOG000112257.
KOiK20215.
OMAiYDICIAT.

Enzyme and pathway databases

UniPathwayiUPA00559.
BRENDAi2.1.1.98. 171.

Miscellaneous databases

EvolutionaryTraceiQ9YDI2.

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_AERPE
AccessioniPrimary (citable) accession number: Q9YDI2
Entry historyi
Integrated into UniProtKB/Swiss-Prot: October 10, 2003
Last sequence update: November 1, 1999
Last modified: November 2, 2016
This is version 89 of the entry and version 1 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programProkaryotic Protein Annotation Program

Miscellaneousi

Keywords - Technical termi

3D-structure, Complete proteome, Reference 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.