UBE2D1 ubiquitin conjugating enzyme E2 D1 [Homo sapiens (human)] - Gene

Summary

Official Symbol: UBE2D1provided by HGNC
Official Full Name: ubiquitin conjugating enzyme E2 D1provided by HGNC
Primary source: HGNC:HGNC:12474
See related: Ensembl:ENSG00000072401 MIM:602961; AllianceGenome:HGNC:12474
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: SFT; UBCH5; UBC4/5; UBCH5A; E2(17)KB1
Summary: The modification of proteins with ubiquitin is an important cellular mechanism for targeting abnormal or short-lived proteins for degradation. Ubiquitination involves at least three classes of enzymes: ubiquitin-activating enzymes, or E1s, ubiquitin-conjugating enzymes, or E2s, and ubiquitin-protein ligases, or E3s. This gene encodes a member of the E2 ubiquitin-conjugating enzyme family. This enzyme is closely related to a stimulator of iron transport (SFT), and is up-regulated in hereditary hemochromatosis. It also functions in the ubiquitination of the tumor-suppressor protein p53 and the hypoxia-inducible transcription factor HIF1alpha by interacting with the E1 ubiquitin-activating enzyme and the E3 ubiquitin-protein ligases. Two transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Mar 2011]
Expression: Ubiquitous expression in bone marrow (RPKM 16.4), appendix (RPKM 13.7) and 25 other tissues See more
Orthologs: mouse all
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Genomic context

Location:: 10q21.1

Exon count:: 7

Annotation release	Status	Assembly	Chr	Location
RS_2024_08	current	GRCh38.p14 (GCF_000001405.40)	10	NC_000010.11 (58335006..58370748)
RS_2024_08	current	T2T-CHM13v2.0 (GCF_009914755.1)	10	NC_060934.1 (59189115..59224853)
RS_2024_09	previous assembly	GRCh37.p13 (GCF_000001405.25)	10	NC_000010.10 (60094766..60130508)

Chromosome 10 - NC_000010.11 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Go to reference sequence details

Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

Project title: HPA RNA-seq normal tissues 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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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

The E2 ubiquitin-conjugating enzymes UBE2D1 and UBE2D2 regulate VEGFR2 dynamics and endothelial function.
Title: The E2 ubiquitin-conjugating enzymes UBE2D1 and UBE2D2 regulate VEGFR2 dynamics and endothelial function.
B-box1 Domain of MID1 Interacts with the Ube2D1 E2 Enzyme Differently Than RING E3 Ligases.
Title: B-box1 Domain of MID1 Interacts with the Ube2D1 E2 Enzyme Differently Than RING E3 Ligases.
UBCH5 Family Members Differentially Impact Stabilization of Mutant p53 via RNF128 Iso1 During Barrett's Progression to Esophageal Adenocarcinoma.
Title: UBCH5 Family Members Differentially Impact Stabilization of Mutant p53 via RNF128 Iso1 During Barrett's Progression to Esophageal Adenocarcinoma.
Functional interaction of ubiquitin ligase RNF167 with UBE2D1 and UBE2N promotes ubiquitination of AMPA receptor.
Title: Functional interaction of ubiquitin ligase RNF167 with UBE2D1 and UBE2N promotes ubiquitination of AMPA receptor.
S-Nitrosylation at the active site decreases the ubiquitin-conjugating activity of ubiquitin-conjugating enzyme E2 D1 (UBE2D1), an ERAD-associated protein.
Title: S-Nitrosylation at the active site decreases the ubiquitin-conjugating activity of ubiquitin-conjugating enzyme E2 D1 (UBE2D1), an ERAD-associated protein.
Results showed that although UBE2D1 RNA was significantly upregulated in both lung adenocarcinoma (LUAD) and lung squamous cell carcinoma (LUSC) tissues; its expression was even higher in LUAD tissues than in LUSC. UBE2D1 RNA upregulation was associated with poor survival in LUAD patients, but not in LUSC suggesting it as an independent indicator of unfavorable prognosis in LUAD, but not in LUSC.
Title: UBE2D1 RNA Expression Was an Independent Unfavorable Prognostic Indicator in Lung Adenocarcinoma, but Not in Lung Squamous Cell Carcinoma.
Upregulation of UBE2D1 promoted HCC growth in vitro and in vivo by decreasing the p53 in ubiquitination-dependent pathway. High expression of UBE2D1 was attributed to the recurrent genomic copy number gain, which was associated with high serum IL-6 level of HCC patients.
Title: Gain of UBE2D1 facilitates hepatocellular carcinoma progression and is associated with DNA damage caused by continuous IL-6.
March-I undergoes lysine-independent ubiquitination by an as yet unidentified E3 ubiquitin ligase that, together with Ube2D1, regulates March-I expression
Title: Ubiquitin-conjugating enzyme E2 D1 (Ube2D1) mediates lysine-independent ubiquitination of the E3 ubiquitin ligase March-I.
The anaphase-promoting complex/cyclosome C activity in human cells is tuned by the combinatorial use of three E2 ubiquitin-conjugating enzymes, namely UBE2C, UBE2S, and UBE2D.
Title: The Spindle Assembly Checkpoint Is Not Essential for Viability of Human Cells with Genetically Lowered APC/C Activity.
Data show that ubiquitin E2 enzymes UBE2D1/2/3 and E3 ligase RNF138 accumulate at DNA-damage sites and act at early resection stages by promoting CtIP protein ubiquitylation and accrual.
Title: Systematic E2 screening reveals a UBE2D-RNF138-CtIP axis promoting DNA repair.

Submit: New GeneRIF Correction See all GeneRIFs (25)

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

EBI GWAS Catalog

Description
Genome-wide meta-analysis increases to 71 the number of confirmed Crohn's disease susceptibility loci. EBI GWAS Catalog EBI GWAS CatalogPubMed

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

HIV-1 interactions

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Protein interactions

Protein	Gene	Interaction	Pubs
Tat	tat	Ubiquitination of HIV-1 Tat by Hdm2 requires ubiquitin-conjugating enzyme E2D 1 (UbcH5)	PubMed

Go to the HIV-1, Human Interaction Database

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

SHGC-14566 (e-PCR)
- UniSTS:790

D7S2050E (e-PCR)
- UniSTS:151113

Gene Ontology Provided by GOA

Function	Evidence Code	Pubs
enables ATP binding	IEA Inferred from Electronic Annotation more info
enables protein binding	IPI Inferred from Physical Interaction more info	PubMed
enables ubiquitin conjugating enzyme activity	IBA Inferred from Biological aspect of Ancestor more info
enables ubiquitin conjugating enzyme activity	IDA Inferred from Direct Assay more info	PubMed
enables ubiquitin protein ligase activity	IDA Inferred from Direct Assay more info	PubMed
enables ubiquitin-protein transferase activity	IDA Inferred from Direct Assay more info	PubMed
enables ubiquitin-protein transferase activity	TAS Traceable Author Statement more info

Process	Evidence Code	Pubs
involved_in negative regulation of BMP signaling pathway	TAS Traceable Author Statement more info
involved_in negative regulation of TORC1 signaling	IDA Inferred from Direct Assay more info	PubMed
involved_in negative regulation of transcription by RNA polymerase II	TAS Traceable Author Statement more info
involved_in positive regulation of protein polyubiquitination	IEA Inferred from Electronic Annotation more info
involved_in positive regulation of protein ubiquitination	IDA Inferred from Direct Assay more info	PubMed
involved_in proteasome-mediated ubiquitin-dependent protein catabolic process	IDA Inferred from Direct Assay more info	PubMed
involved_in protein K48-linked ubiquitination	IBA Inferred from Biological aspect of Ancestor more info
involved_in protein K48-linked ubiquitination	IDA Inferred from Direct Assay more info	PubMed
involved_in protein polyubiquitination	IDA Inferred from Direct Assay more info	PubMed
involved_in ubiquitin-dependent protein catabolic process	IBA Inferred from Biological aspect of Ancestor more info
involved_in ubiquitin-dependent protein catabolic process	IDA Inferred from Direct Assay more info	PubMed

Component	Evidence Code	Pubs
located_in cytoplasm	IDA Inferred from Direct Assay more info	PubMed
located_in cytosol	TAS Traceable Author Statement more info
located_in nucleoplasm	TAS Traceable Author Statement more info
is_active_in nucleus	IBA Inferred from Biological aspect of Ancestor more info
part_of protein-containing complex	IDA Inferred from Direct Assay more info	PubMed

General protein information

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Preferred Names: ubiquitin-conjugating enzyme E2 D1

Names: (E3-independent) E2 ubiquitin-conjugating enzyme D1; E2 ubiquitin-conjugating enzyme D1; UBC4/5 homolog; stimulator of Fe transport; ubiquitin carrier protein D1; ubiquitin conjugating enzyme E2D 1; ubiquitin-conjugating enzyme E2(17)KB 1; ubiquitin-conjugating enzyme E2-17 kDa 1; ubiquitin-conjugating enzyme E2D 1 (UBC4/5 homolog, yeast); ubiquitin-protein ligase D1

NP_001191809.1

EC 2.3.2.23

EC 2.3.2.24

NP_003329.1

EC 2.3.2.23

EC 2.3.2.24

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)

NM_001204880.2 → NP_001191809.1 ubiquitin-conjugating enzyme E2 D1 isoform 2

See identical proteins and their annotated locations for NP_001191809.1

Status: REVIEWED

Description

Transcript Variant: This variant (2) lacks an alternate coding exon compared to variant 1. The resulting isoform (2) uses a downstream start site and has a shorter and distinct N-terminus compared to isoform 1.

Source sequence(s)

AC023170, DA618122

Consensus CDS

CCDS73139.1

UniProtKB/TrEMBL

A0A087WW00

Related

ENSP00000479814.1, ENST00000615793.1

Conserved Domains (1) summary

COG5078
Location:3 → 109

COG5078; Ubiquitin-protein ligase [Posttranslational modification, protein turnover, chaperones]
NM_003338.5 → NP_003329.1 ubiquitin-conjugating enzyme E2 D1 isoform 1

See identical proteins and their annotated locations for NP_003329.1

Status: REVIEWED

Description

Transcript Variant: This variant (1) represents the longer transcript and encodes the longer isoform (1).

Source sequence(s)

AC023170, BC005980, DA677507

Consensus CDS

CCDS7252.1

UniProtKB/Swiss-Prot

A6NLF6, A8K786, P51668

Related

ENSP00000363019.3, ENST00000373910.9

Conserved Domains (1) summary

cl00154
Location:1 → 146

UBCc; Ubiquitin-conjugating enzyme E2, catalytic (UBCc) domain. This is part of the ubiquitin-mediated protein degradation pathway in which a thiol-ester linkage forms between a conserved cysteine and the C-terminus of ubiquitin and complexes with ubiquitin ...