Human Gene UBA3 (ENST00000361055.9_9) from GENCODE V47lift37
  Description: ubiquitin like modifier activating enzyme 3, transcript variant 1 (from RefSeq NM_003968.4)
Gencode Transcript: ENST00000361055.9_9
Gencode Gene: ENSG00000144744.18_11
Transcript (Including UTRs)
   Position: hg19 chr3:69,103,881-69,129,516 Size: 25,636 Total Exon Count: 18 Strand: -
Coding Region
   Position: hg19 chr3:69,104,588-69,129,504 Size: 24,917 Coding Exon Count: 18 

Page IndexSequence and LinksUniProtKB CommentsPrimersCTDGene Alleles
RNA-Seq ExpressionMicroarray ExpressionRNA StructureProtein StructureOther SpeciesGO Annotations
mRNA DescriptionsPathwaysOther NamesModel InformationMethods
Data last updated at UCSC: 2024-08-22 23:36:26

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr3:69,103,881-69,129,516)mRNA (may differ from genome)Protein (463 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneGene interactionsTable Schema
AlphaFoldBioGPSEnsemblEntrez GeneExonPrimerGeneCards
HGNCMGIOMIMPubMedReactomeUniProtKB
WikipediaBioGrid CRISPR DB

-  Comments and Description Text from UniProtKB
  ID: UBA3_HUMAN
DESCRIPTION: RecName: Full=NEDD8-activating enzyme E1 catalytic subunit; EC=6.3.2.-; AltName: Full=NEDD8-activating enzyme E1C; AltName: Full=Ubiquitin-activating enzyme E1C; AltName: Full=Ubiquitin-like modifier-activating enzyme 3; Short=Ubiquitin-activating enzyme 3;
FUNCTION: Catalytic subunit of the dimeric UBA3-NAE1 E1 enzyme. E1 activates NEDD8 by first adenylating its C-terminal glycine residue with ATP, thereafter linking this residue to the side chain of the catalytic cysteine, yielding a NEDD8-UBA3 thioester and free AMP. E1 finally transfers NEDD8 to the catalytic cysteine of UBE2M. Down-regulates steroid receptor activity. Necessary for cell cycle progression.
ENZYME REGULATION: Binding of TP53BP2 to the regulatory subunit NAE1 decreases activity.
PATHWAY: Protein modification; protein neddylation.
SUBUNIT: Heterodimer of UBA3 and NAE1. Interacts with NEDD8, UBE2F and UBE2M. Binds ESR1 and ESR2 with bound steroid ligand (By similarity). Interacts with TBATA (By similarity).
INTERACTION: P61081:UBE2M; NbExp=2; IntAct=EBI-717567, EBI-1041660;
TISSUE SPECIFICITY: Ubiquitously expressed.
MISCELLANEOUS: Arg-211 acts as a selectivity gate, preventing misactivation of ubiquitin by this NEDD8-specific E1 complex.
SIMILARITY: Belongs to the ubiquitin-activating E1 family. UBA3 subfamily.
SEQUENCE CAUTION: Sequence=AAC27648.1; Type=Erroneous initiation;

-  Primer design for this transcript
 

Primer3Plus can design qPCR Primers that straddle exon-exon-junctions, which amplify only cDNA, not genomic DNA.
Click here to load the transcript sequence and exon structure into Primer3Plus

Exonprimer can design one pair of Sanger sequencing primers around every exon, located in non-genic sequence.
Click here to open Exonprimer with this transcript

To design primers for a non-coding sequence, zoom to a region of interest and select from the drop-down menu: View > In External Tools > Primer3


-  Comparative Toxicogenomics Database (CTD)
  The following chemicals interact with this gene
  • D019327 Copper Sulfate
  • C006780 bisphenol A
  • C539933 ((1S,2S,4R)-4-(4-((1S)-2,3-dihydro-1H-inden-1-ylamino)-7H-pyrrolo(2,3-d)pyrimidin-7-yl)-2-hydroxycyclopentyl)methyl sulphamate
  • C111118 2',3,3',4',5-pentachloro-4-hydroxybiphenyl
  • C016403 2,4-dinitrotoluene
  • C023514 2,6-dinitrotoluene
  • D000643 Ammonium Chloride
  • D001564 Benzo(a)pyrene
  • D006861 Hydrogen Peroxide
  • D058185 Magnetite Nanoparticles
          more ... click here to view the complete list

+  Common Gene Haplotype Alleles
  Press "+" in the title bar above to open this section.

-  RNA-Seq Expression Data from GTEx (53 Tissues, 570 Donors)
  Highest median expression: 36.13 RPKM in Cells - EBV-transformed lymphocytes
Total median expression: 1069.53 RPKM



View in GTEx track of Genome Browser    View at GTEx portal     View GTEx Body Map

+  Microarray Expression Data
  Press "+" in the title bar above to open this section.

-  mRNA Secondary Structure of 3' and 5' UTRs
 
RegionFold EnergyBasesEnergy/Base
Display As
3' UTR -141.40707-0.200 Picture PostScript Text

The RNAfold program from the Vienna RNA Package is used to perform the secondary structure predictions and folding calculations. The estimated folding energy is in kcal/mol. The more negative the energy, the more secondary structure the RNA is likely to have.

-  Protein Domain and Structure Information
  InterPro Domains: Graphical view of domain structure
IPR014929 - E2_binding
IPR009036 - Molybdenum_cofac_synth_MoeB
IPR016040 - NAD(P)-bd_dom
IPR000594 - ThiF_NAD_FAD-bd
IPR023318 - Ub_act_enz_dom_a
IPR000127 - UBact_repeat
IPR019572 - Ubiquitin-activating_enzyme
IPR018074 - UBQ-activ_enz_E1_AS

Pfam Domains:
PF00899 - ThiF family
PF08825 - E2 binding domain

SCOP Domains:
69572 - Activating enzymes of the ubiquitin-like proteins
51735 - NAD(P)-binding Rossmann-fold domains
51905 - FAD/NAD(P)-binding domain
51971 - Nucleotide-binding domain
51984 - MurCD N-terminal domain

Protein Data Bank (PDB) 3-D Structure
MuPIT help
1R4M - X-ray MuPIT 1R4N - X-ray MuPIT 1TT5 - X-ray MuPIT 1Y8X - X-ray MuPIT 1YOV - X-ray MuPIT 2LQ7 - NMR MuPIT 2NVU - X-ray MuPIT 3DBH - X-ray MuPIT 3DBL - X-ray MuPIT 3DBR - X-ray MuPIT 3FN1 - X-ray MuPIT 3GZN - X-ray MuPIT


ModBase Predicted Comparative 3D Structure on Q8TBC4
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The pictures above may be empty if there is no ModBase structure for the protein. The ModBase structure frequently covers just a fragment of the protein. You may be asked to log onto ModBase the first time you click on the pictures. It is simplest after logging in to just click on the picture again to get to the specific info on that model.

-  Orthologous Genes in Other Species
  Orthologies between human, mouse, and rat are computed by taking the best BLASTP hit, and filtering out non-syntenic hits. For more distant species reciprocal-best BLASTP hits are used. Note that the absence of an ortholog in the table below may reflect incomplete annotations in the other species rather than a true absence of the orthologous gene.
MouseRatZebrafishD. melanogasterC. elegansS. cerevisiae
No orthologNo orthologNo orthologNo orthologNo orthologGenome Browser
Gene DetailsGene Details Gene Details Gene Details
Gene SorterGene Sorter Gene Sorter Gene Sorter
 RGDEnsembl  SGD
     Protein Sequence
     Alignment

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0000166 nucleotide binding
GO:0005515 protein binding
GO:0005524 ATP binding
GO:0008641 small protein activating enzyme activity
GO:0016874 ligase activity
GO:0016881 acid-amino acid ligase activity
GO:0016922 ligand-dependent nuclear receptor binding
GO:0019781 NEDD8 activating enzyme activity
GO:0019788 NEDD8 transferase activity
GO:0042802 identical protein binding
GO:0046982 protein heterodimerization activity

Biological Process:
GO:0000278 mitotic cell cycle
GO:0006464 cellular protein modification process
GO:0006508 proteolysis
GO:0007049 cell cycle
GO:0007113 endomitotic cell cycle
GO:0043687 post-translational protein modification
GO:0045116 protein neddylation
GO:0045892 negative regulation of transcription, DNA-templated
GO:0051726 regulation of cell cycle

Cellular Component:
GO:0005634 nucleus
GO:0005737 cytoplasm
GO:0005829 cytosol


-  Descriptions from all associated GenBank mRNAs
  AL117566 - Homo sapiens mRNA; cDNA DKFZp566J164 (from clone DKFZp566J164).
AF046024 - Homo sapiens UBA3 (UBA3) mRNA, complete cds.
AK002159 - Homo sapiens cDNA FLJ11297 fis, clone PLACE1009763, highly similar to NEDD8-activating enzyme E1 catalytic subunit (EC 6.3.2.-).
JD114369 - Sequence 95393 from Patent EP1572962.
JD350361 - Sequence 331385 from Patent EP1572962.
BC022853 - Homo sapiens ubiquitin-like modifier activating enzyme 3, mRNA (cDNA clone MGC:22384 IMAGE:4073511), complete cds.
JD565892 - Sequence 546916 from Patent EP1572962.
CR533537 - Homo sapiens full open reading frame cDNA clone RZPDo834E0519D for gene UBE1C, ubiquitin-activating enzyme E1C (UBA3 homolog, yeast); complete cds, incl. stopcodon.
AK316540 - Homo sapiens cDNA, FLJ79439 complete cds, highly similar to NEDD8-activating enzyme E1 catalytic subunit (EC 6.3.2.-).
AK298878 - Homo sapiens cDNA FLJ58044 complete cds, highly similar to NEDD8-activating enzyme E1 catalytic subunit (EC 6.3.2.-).
AK289392 - Homo sapiens cDNA FLJ78055 complete cds, highly similar to Homo sapiens ubiquitin-activating enzyme E1C (UBA3 homolog, yeast) (UBE1C), transcript variant 1, mRNA.
JD110060 - Sequence 91084 from Patent EP1572962.
AB012190 - Homo sapiens mRNA for Nedd8-activating enzyme hUba3, complete cds.
AK314751 - Homo sapiens cDNA, FLJ95615, highly similar to Homo sapiens ubiquitin-activating enzyme E1C (UBA3 homolog, yeast)(UBE1C), mRNA.
DQ893167 - Synthetic construct clone IMAGE:100005797; FLH194567.01X; RZPDo839C0980D ubiquitin-activating enzyme E1C (UBA3 homolog, yeast) (UBE1C) gene, encodes complete protein.
DQ896465 - Synthetic construct Homo sapiens clone IMAGE:100010925; FLH194563.01L; RZPDo839C0970D ubiquitin-activating enzyme E1C (UBA3 homolog, yeast) (UBE1C) gene, encodes complete protein.
AB463332 - Synthetic construct DNA, clone: pF1KB8668, Homo sapiens UBE1C gene for ubiquitin-like modifier activating enzyme 3, without stop codon, in Flexi system.
AM392893 - Synthetic construct Homo sapiens clone IMAGE:100001962 for hypothetical protein (UBE1C gene).
AM393088 - Synthetic construct Homo sapiens clone IMAGE:100001725 for hypothetical protein (UBE1C gene).
CU692738 - Synthetic construct Homo sapiens gateway clone IMAGE:100021968 5' read UBE1C mRNA.

-  Biochemical and Signaling Pathways
  BioCyc Knowledge Library
PWY-7511 - protein ubiquitination
PWY-7899 - protein NEDDylation

Reactome (by CSHL, EBI, and GO)

Protein Q8TBC4 (Reactome details) participates in the following event(s):

R-HSA-8951648 NEDD8 covalently binds catalytic cysteine of UBA3:NAE1
R-HSA-983153 E1 mediated ubiquitin activation
R-HSA-983152 Transfer of ubiquitin from E1 to E2
R-HSA-8951656 NEDD8-UBA3:NAE1 binds a second NEDD8
R-HSA-8951661 Transfer of NEDD8 to AcM-UBE2M
R-HSA-8951764 Transfer of NEDD8 to AcM-UBE2F
R-HSA-8951751 Doubly neddylated UBA3:NAE1 binds AcM-UBE2M
R-HSA-8951766 Doubly neddylated UBA3:NAE1 binds AcM-UBE2F
R-HSA-5607761 Dectin-1 mediated noncanonical NF-kB signaling
R-HSA-5676590 NIK-->noncanonical NF-kB signaling
R-HSA-8951664 Neddylation
R-HSA-983168 Antigen processing: Ubiquitination & Proteasome degradation
R-HSA-5607764 CLEC7A (Dectin-1) signaling
R-HSA-5668541 TNFR2 non-canonical NF-kB pathway
R-HSA-597592 Post-translational protein modification
R-HSA-983169 Class I MHC mediated antigen processing & presentation
R-HSA-5621481 C-type lectin receptors (CLRs)
R-HSA-1280215 Cytokine Signaling in Immune system
R-HSA-392499 Metabolism of proteins
R-HSA-1280218 Adaptive Immune System
R-HSA-168249 Innate Immune System
R-HSA-168256 Immune System

-  Other Names for This Gene
  Alternate Gene Symbols: A6NLB5, A8K027, ENST00000361055.1, ENST00000361055.2, ENST00000361055.3, ENST00000361055.4, ENST00000361055.5, ENST00000361055.6, ENST00000361055.7, ENST00000361055.8, NM_003968, O76088, Q8TBC4, Q9NTU3, UBA3_HUMAN, UBE1C, uc318bvt.1, uc318bvt.2
UCSC ID: ENST00000361055.9_9
RefSeq Accession: NM_003968.4
Protein: Q8TBC4 (aka UBA3_HUMAN)

-  Gene Model Information
  Click here for a detailed description of the fields of the table above.

-  Methods, Credits, and Use Restrictions
  Click here for details on how this gene model was made and data restrictions if any.