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DPH5 diphthamide biosynthesis 5 [ Homo sapiens (human) ]

Gene ID: 51611, updated on 11-Apr-2024

Summary

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Official Symbol
DPH5provided by HGNC
Official Full Name
diphthamide biosynthesis 5provided by HGNC
Primary source
HGNC:HGNC:24270
See related
Ensembl:ENSG00000117543 MIM:611075; AllianceGenome:HGNC:24270
Gene type
protein coding
RefSeq status
REVIEWED
Organism
Homo sapiens
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as
AD-018; CGI-30; NEDSFF; NPD015; HSPC143
Summary
This gene encodes a component of the diphthamide synthesis pathway. Diphthamide is a post-translationally modified histidine residue found only on translation elongation factor 2. It is conserved from archaebacteria to humans, and is targeted by diphtheria toxin and Pseudomonas exotoxin A to halt cellular protein synthesis. The yeast and Chinese hamster homologs of this protein catalyze the trimethylation of the histidine residue on elongation factor 2, resulting in a diphthine moiety that is subsequently amidated to yield diphthamide. Multiple transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Jul 2008]
Expression
Ubiquitous expression in ovary (RPKM 15.2), thyroid (RPKM 9.2) and 25 other tissues See more
Orthologs
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Genomic context

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Location:
1p21.2
Exon count:
8
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 1 NC_000001.11 (100989623..101025784, complement)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 1 NC_060925.1 (100838455..100874670, complement)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 1 NC_000001.10 (101455179..101491340, complement)

Chromosome 1 - NC_000001.11Genomic Context describing neighboring genes Neighboring gene Sharpr-MPRA regulatory region 5467 Neighboring gene MPRA-validated peak338 silencer Neighboring gene H3K27ac hESC enhancer GRCh37_chr1:101359730-101360453 Neighboring gene H3K27ac hESC enhancer GRCh37_chr1:101360454-101361176 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 1388 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 1389 Neighboring gene exostosin like glycosyltransferase 2 Neighboring gene solute carrier family 30 member 7 Neighboring gene heterogeneous nuclear ribonucleoprotein A1 pseudogene 68 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 1390 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr1:101490870-101492069 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 1122 Neighboring gene DPH5 divergent transcript Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:101519189-101519689 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 1123 Neighboring gene Sharpr-MPRA regulatory region 5182 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 1124 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 1392 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 1393 Neighboring gene small Cajal body-specific RNA 16

Genomic regions, transcripts, and products

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Go to nucleotide: Graphics FASTA GenBank

Expression

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  • Project title: HPA RNA-seq normal tissues
  • Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
  • BioProject: PRJEB4337
  • Publication: PMID 24309898
  • Analysis date: Wed Apr 4 07:08:55 2018

Bibliography

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Related articles in PubMed

  1. A modified form of diphthamide causes immunotoxin resistance in a lymphoma cell line with a deletion of the WDR85 gene. Wei H, et al. J Biol Chem, 2013 Apr 26. PMID 23486472, Free PMC Article
  2. The post-translational trimethylation of diphthamide studied in vitro. Moehring JM, et al. J Biol Chem, 1988 Mar 15. PMID 3346227
  3. Identification of the proteins required for biosynthesis of diphthamide, the target of bacterial ADP-ribosylating toxins on translation elongation factor 2. Liu S, et al. Mol Cell Biol, 2004 Nov. PMID 15485916, Free PMC Article
  4. Drug-gene interactions and the search for missing heritability: a cross-sectional pharmacogenomics study of the QT interval. Avery CL, et al. Pharmacogenomics J, 2014 Feb. PMID 23459443, Free PMC Article
  5. Gene expression profiling in the human hypothalamus-pituitary-adrenal axis and full-length cDNA cloning. Hu RM, et al. Proc Natl Acad Sci U S A, 2000 Aug 15. PMID 10931946, Free PMC Article

See all (23) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. The yeast and Chinese hamster homologs of human DPH5 catalyze the trimethylation step in the biosynthesis of diphthamide
    Title: Identification of the proteins required for biosynthesis of diphthamide, the target of bacterial ADP-ribosylating toxins on translation elongation factor 2.
Submit: New GeneRIF Correction

Phenotypes

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Find tests for this gene in the NIH Genetic Testing Registry (GTR)

Review eQTL and phenotype association data in this region using PheGenI

Associated conditions

Description Tests
Neurodevelopmental disorder with short stature, prominent forehead, and feeding difficulties
MedGen: C5774228 OMIM: 620070 GeneReviews: Not available
not available

EBI GWAS Catalog

Description
Drug-gene interactions and the search for missing heritability: a cross-sectional pharmacogenomics study of the QT interval.
EBI GWAS Catalog

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

Genotypes

Pathways from PubChem

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Interactions

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Products Interactant Other Gene Complex Source Pubs Description

General gene information

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Markers

Homology

Clone Names

  • MGC61450

Gene Ontology Provided by GOA

Function Evidence Code Pubs
enables diphthine methyl ester synthase activity NAS
Non-traceable Author Statement
more info
 PubMed 
enables diphthine synthase activity EXP
Inferred from Experiment
more info
 PubMed 
Process Evidence Code Pubs
involved_in methylation IEA
Inferred from Electronic Annotation
more info
  
involved_in protein histidyl modification to diphthamide IEA
Inferred from Electronic Annotation
more info
  
involved_in protein histidyl modification to diphthamide ISS
Inferred from Sequence or Structural Similarity
more info
  
involved_in protein histidyl modification to diphthamide NAS
Non-traceable Author Statement
more info
 PubMed 
involved_in protein histidyl modification to diphthamide TAS
Traceable Author Statement
more info
  
Component Evidence Code Pubs
located_in cytosol TAS
Traceable Author Statement
more info
  

General protein information

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Preferred Names
diphthine methyl ester synthase
Names
DPH5 homolog
diphthamide biosynthesis methyltransferase
diphthine synthase
protein x 0011
NP_001070862.1
NP_001070863.1
NP_057042.2
XP_005270995.1
XP_011539872.1
XP_024303368.1
XP_047278469.1
XP_047278470.1
XP_047278471.1
XP_054192957.1
XP_054192958.1
XP_054192959.1
XP_054192960.1
XP_054192961.1
XP_054192962.1

NCBI Reference Sequences (RefSeq)

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RefSeqs maintained independently of Annotated Genomes

These reference sequences exist independently of genome builds. Explain

These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

mRNA and Protein(s)

  1. NM_001077394.2 → NP_001070862.1  diphthine methyl ester synthase isoform a

    See identical proteins and their annotated locations for NP_001070862.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (1) represents the longest transcript. Variants 1 and 2 encode the longer isoform (a).
    Source sequence(s)
    AK125485, BI907367, BM808505, CK002046
    Consensus CDS
    CCDS41358.1
    UniProtKB/Swiss-Prot
    A8JZY6, D3DT62, Q9H2P9, Q9P017, Q9P0I4, Q9Y319
    Related
    ENSP00000418282.1, ENST00000488176.1
    Conserved Domains (1) summary
    PTZ00175
    Location:1 → 272
    PTZ00175; diphthine synthase; Provisional

  2. NM_001077395.2 → NP_001070863.1  diphthine methyl ester synthase isoform b

    See identical proteins and their annotated locations for NP_001070863.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (3) differs in the 5' UTR and uses an alternate in-frame splice site in the 3' coding region, compared to variant 1. The resulting protein (isoform b) is one amino acid shorter than isoform a.
    Source sequence(s)
    AC093157, AK125485, AK225469, BM808505
    Consensus CDS
    CCDS41359.1
    UniProtKB/Swiss-Prot
    Q9H2P9
    UniProtKB/TrEMBL
    B3KWP1
    Related
    ENSP00000339630.7, ENST00000342173.11
    Conserved Domains (1) summary
    PTZ00175
    Location:1 → 271
    PTZ00175; diphthine synthase; Provisional

  3. NM_015958.3 → NP_057042.2  diphthine methyl ester synthase isoform a

    See identical proteins and their annotated locations for NP_057042.2

    Status: REVIEWED

    Description
    Transcript Variant: This variant (2) differs in the 5' UTR compared to variant 1. Variants 1 and 2 encode the same isoform (a).
    Source sequence(s)
    AK125485, BC053857, BM808505, DA133565
    Consensus CDS
    CCDS41358.1
    UniProtKB/Swiss-Prot
    A8JZY6, D3DT62, Q9H2P9, Q9P017, Q9P0I4, Q9Y319
    Related
    ENSP00000359127.3, ENST00000370109.8
    Conserved Domains (1) summary
    PTZ00175
    Location:1 → 272
    PTZ00175; diphthine synthase; Provisional

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2023_10

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCh38.p14 Primary Assembly

Genomic

  1. NC_000001.11 Reference GRCh38.p14 Primary Assembly

    Range
    100989623..101025784 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_047422514.1 → XP_047278470.1  diphthine methyl ester synthase isoform X3

  2. XM_005270938.3 → XP_005270995.1  diphthine methyl ester synthase isoform X2

    Conserved Domains (1) summary
    cl00304
    Location:1 → 177
    TP_methylase; S-AdoMet dependent tetrapyrrole methylases

  3. XM_024447600.2 → XP_024303368.1  diphthine methyl ester synthase isoform X2

    Conserved Domains (1) summary
    cl00304
    Location:1 → 177
    TP_methylase; S-AdoMet dependent tetrapyrrole methylases

  4. XM_047422513.1 → XP_047278469.1  diphthine methyl ester synthase isoform X1

  5. XM_047422515.1 → XP_047278471.1  diphthine methyl ester synthase isoform X5

  6. XM_011541570.4 → XP_011539872.1  diphthine methyl ester synthase isoform X4

    See identical proteins and their annotated locations for XP_011539872.1

    UniProtKB/TrEMBL
    B3KWP1, D3DT65
    Conserved Domains (1) summary
    cl00304
    Location:1 → 159
    TP_methylase; S-AdoMet dependent tetrapyrrole methylases

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060925.1 Alternate T2T-CHM13v2.0

    Range
    100838455..100874670 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_054336987.1 → XP_054192962.1  diphthine methyl ester synthase isoform X5

  2. XM_054336986.1 → XP_054192961.1  diphthine methyl ester synthase isoform X4

    UniProtKB/TrEMBL
    B3KWP1, D3DT65

  3. XM_054336985.1 → XP_054192960.1  diphthine methyl ester synthase isoform X3

  4. XM_054336983.1 → XP_054192958.1  diphthine methyl ester synthase isoform X2

  5. XM_054336984.1 → XP_054192959.1  diphthine methyl ester synthase isoform X2

  6. XM_054336982.1 → XP_054192957.1  diphthine methyl ester synthase isoform X1

Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
Q9H2P9.2 GenPept UniProtKB/Swiss-Prot:Q9H2P9

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