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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)LengthDescriptionGraphical viewFeature identifierActions
Binding sitei93 – 931S-adenosyl-L-methionine; via amide nitrogen and carbonyl oxygenBy similarity
Binding sitei96 – 961S-adenosyl-L-methionine; via carbonyl oxygenBy similarity
Binding sitei173 – 1731S-adenosyl-L-methionine; via amide nitrogen and carbonyl oxygenBy similarity
Binding sitei220 – 2201S-adenosyl-L-methionine; via amide nitrogen and carbonyl oxygenBy similarity

GO - Molecular functioni

GO - Biological processi

Complete GO annotation...

Keywords - Molecular functioni

Methyltransferase, Transferase

Keywords - Ligandi

S-adenosyl-L-methionine

Enzyme and pathway databases

BioCyciAPER272557:GJD6-676-MONOMER.
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)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 294294Diphthine synthasePRO_0000156114Add
BLAST

Interactioni

Subunit structurei

Homodimer.By similarity

Protein-protein interaction databases

STRINGi272557.APE_0931.

Structurei

Secondary structure

1
294
Legend: HelixTurnBeta strand
Show more details
Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Beta strandi9 – 146Combined sources
Beta strandi16 – 183Combined sources
Helixi24 – 329Combined sources
Beta strandi34 – 396Combined sources
Beta strandi41 – 433Combined sources
Helixi48 – 5710Combined sources
Beta strandi59 – 646Combined sources
Helixi67 – 715Combined sources
Helixi74 – 774Combined sources
Beta strandi85 – 928Combined sources
Beta strandi96 – 994Combined sources
Helixi100 – 10910Combined sources
Beta strandi113 – 1175Combined sources
Helixi122 – 1309Combined sources
Helixi134 – 1363Combined sources
Beta strandi137 – 1437Combined sources
Helixi146 – 1483Combined sources
Helixi153 – 16412Combined sources
Beta strandi168 – 1736Combined sources
Helixi184 – 20219Combined sources
Helixi208 – 2103Combined sources
Beta strandi213 – 2175Combined sources
Helixi220 – 2223Combined sources
Beta strandi225 – 2306Combined sources
Helixi232 – 2365Combined sources
Beta strandi246 – 2494Combined sources
Helixi255 – 26410Combined sources
Helixi277 – 28711Combined sources
Turni288 – 2903Combined sources

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
1WDEX-ray2.00A1-294[»]
ProteinModelPortaliQ9YDI2.
SMRiQ9YDI2. Positions 6-294.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiQ9YDI2.

Family & Domainsi

Region

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Regioni121 – 1222S-adenosyl-L-methionine bindingBy similarity

Sequence similaritiesi

Belongs to the diphthine synthase family.Curated

Phylogenomic databases

eggNOGiarCOG04161. Archaea.
COG1798. LUCA.
HOGENOMiHOG000112257.
KOiK00586.
OMAiFYEDYTG.

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.

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
EntryMethodResolution (Å)ChainPositionsPDBsum
1WDEX-ray2.00A1-294[»]
ProteinModelPortaliQ9YDI2.
SMRiQ9YDI2. Positions 6-294.
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.
KOiK00586.
OMAiFYEDYTG.

Enzyme and pathway databases

UniPathwayiUPA00559.
BioCyciAPER272557:GJD6-676-MONOMER.
BRENDAi2.1.1.98. 171.

Miscellaneous databases

EvolutionaryTraceiQ9YDI2.

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. Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: ATCC 700893 / DSM 11879 / JCM 9820 / NBRC 100138 / K1.
  2. "Structures of two archaeal diphthine synthases: insights into the post-translational modification of elongation factor 2."
    Kishishita S., Shimizu K., Murayama K., Terada T., Shirouzu M., Yokoyama S., Kunishima N.
    Acta Crystallogr. D 64:397-406(2008) [PubMed] [Europe PMC] [Abstract]
    Cited for: X-RAY CRYSTALLOGRAPHY (2.0 ANGSTROMS).
    Strain: ATCC 700893 / DSM 11879 / JCM 9820 / NBRC 100138 / K1.

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 11, 2015
This is version 86 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.