mutLBSgeneDB

mutLBSgeneDB
mutated Ligand Binding Site gene DataBase

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Gene Summary

Ligand Binding Site Mutation Information

Protein Structure Related Information

Gene Expression and Gene-Gene Network

Phenotype Information

Pharmacological Information

Conservation Information for LBS

Gene summary for UBE2D2
Gene summary
Basic gene Info.Gene symbolUBE2D2
Gene nameubiquitin-conjugating enzyme E2D 2
SynonymsE2(17)KB2|PUBC1|UBC4|UBC4/5|UBCH4|UBCH5B
CytomapUCSC genome browser: 5q31.2
Type of geneprotein-coding
RefGenesNM_003339.2,
NM_181838.1,
Descriptionp53-regulated ubiquitin-conjugating enzyme 1ubiquitin carrier protein D2ubiquitin-conjugating enzyme E2 D2ubiquitin-conjugating enzyme E2-17 kDa 2ubiquitin-conjugating enzyme E2D 2 (homologous to yeast UBC4/5)ubiquitin-protein ligase D2
Modification date20141207
dbXrefs MIM : 602962
HGNC : HGNC
Ensembl : ENSG00000131508
HPRD : 04268
Vega : OTTHUMG00000163282
ProteinUniProt: P62837
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_UBE2D2
BioGPS: 7322
PathwayNCI Pathway Interaction Database: UBE2D2
KEGG: UBE2D2
REACTOME: UBE2D2
Pathway Commons: UBE2D2
ContextiHOP: UBE2D2
ligand binding site mutation search in PubMed: UBE2D2
UCL Cancer Institute: UBE2D2
Assigned class in mutLBSgeneDBC: This gene just belongs to mutLBSgenes.

Gene ontology having evidence of Inferred from Direct Assay (IDA) from Entrez
GO IDGO TermPubMed ID
GO:0000209protein polyubiquitination15247280
GO:0016567protein ubiquitination9990509
GO:0070936protein K48-linked ubiquitination20061386


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Ligand binding site mutations for UBE2D2

Cancer type specific mutLBS sorted by frequency
LBSAAchange of nsSNVCancer type# samples
W141T142AKIRC1
cf) Cancer type abbreviation. BLCA: Bladder urothelial carcinoma, BRCA: Breast invasive carcinoma, CESC: Cervical squamous cell carcinoma and endocervical adenocarcinoma, COAD: Colon adenocarcinoma, GBM: Glioblastoma multiforme, LGG: Brain lower grade glioma, HNSC: Head and neck squamous cell carcinoma, KICH: Kidney chromophobe, KIRC: Kidney renal clear cell carcinoma, KIRP: Kidney renal papillary cell carcinoma, LAML: Acute myeloid leukemia, LUAD: Lung adenocarcinoma, LUSC: Lung squamous cell carcinoma, OV: Ovarian serous cystadenocarcinoma, PAAD: Pancreatic adenocarcinoma, PRAD: Prostate adenocarcinoma, SKCM: Skin cutaneous melanoma, STAD: Stomach adenocarcinoma, THCA: Thyroid carcinoma, UCEC: Uterine corpus endometrial carcinoma.


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Protein structure related information for UBE2D2
Relative protein structure stability change (ΔΔE) using Mupro 1.1
Mupro score denotes assessment of the effect of mutations on thermodynamic stability.
  (ΔΔE<0: mutation decreases stability, ΔΔE>0: mutation increases stability)
: nsSNV at non-LBS: nsSNV at LBS

nsSNVs sorted by the relative stability change of protein structure by each mutation
Blue: mutations of positive stability change. and red : the most recurrent mutation for this gene.
LBSAAchange of nsSNVRelative stability change
W141T142A-0.88195824
(MuPro1.1: Jianlin Cheng et al., Prediction of Protein Stability Changes for Single-Site Mutations Using Support Vector Machines, PROTEINS: Structure, Function, and Bioinformatics. 2006, 62:1125-1132)

Structure image for UBE2D2 from PDB

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Differential gene expression and gene-gene network for UBE2D2
Differential gene expression between mutated and non-mutated LBS samples in all 16 major cancer types

Differential co-expressed gene network based on protein-protein interaction data (CePIN)
* Left PPI network was created from samples with mutations in the LBS of UBE2D2 and the right PPI network was created from samples without mutations in the LBS of UBE2D2. Only genes with p-value < 0.05 are shown.
Red circle: input gene. Orange circle: LBSgene. Blue circle: other gene.


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Phenotype information for UBE2D2
Gene level disease information (DisGeNet)
Disease IDDisease name# PubMedAssociation type

Mutation level pathogenic information (ClinVar annotation)
Allele IDAA changeClinical significanceOriginPhenotype IDs

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Pharmacological information for UBE2D2
Gene expression profile of anticancer drug treated cell-lines (CCLE)
Heatmap showing the correlation between gene expression and drug response across all the cell-lines. We chose the top 20 among 138 drugs.We used Pearson's correlation coefficient.

Gene-centered drug-gene interaction network
Drug information targeting mutLBSgene (Approved drugs only)
Drug statusDrugBank IDNameTypeDrug structure
ExperimentalDB02418(R,R)-2,3-ButanediolSmall molecule

Gene-centered ligand-gene interaction network

Ligands binding to mutated ligand binding site of UBE2D2 go to BioLip
Ligand IDLigand short nameLigand long namePDB IDPDB namemutLBS
OXLOXALATE(2-)5d1kAW141
OXLOXALATE(2-)5d1lAW141
OXLOXALATE(2-)5d1mAW141


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Conservation information for LBS of UBE2D2
Multiple alignments for P62837 in multiple species
LBSAA sequence# speciesSpecies
K144REWTQKYAM5Homo sapiens, Bos taurus, Mus musculus, Rattus norvegicus, Caenorhabditis elegans
K144REWTRKYAI2Schizosaccharomyces pombe (strain 972 / ATCC 24843), Magnaporthe oryzae (strain 70-15 / ATCC MYA-4617 / FGSC 8958)
K144REWTKKYAV1Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
K144REWTRKYAM1Drosophila melanogaster
W141RIAREWTQKYA4Homo sapiens, Bos taurus, Mus musculus, Rattus norvegicus
W141ATAREWTKKYA1Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
W141ELAREWTRKYA1Drosophila melanogaster
W141QLAREWTQKYA1Caenorhabditis elegans
W141LSAREWTRKYA1Schizosaccharomyces pombe (strain 972 / ATCC 24843)
W141STAREWTRKYA1Magnaporthe oryzae (strain 70-15 / ATCC MYA-4617 / FGSC 8958)
Y145EWTQKYAM5Homo sapiens, Bos taurus, Mus musculus, Rattus norvegicus, Caenorhabditis elegans
Y145EWTRKYAI2Schizosaccharomyces pombe (strain 972 / ATCC 24843), Magnaporthe oryzae (strain 70-15 / ATCC MYA-4617 / FGSC 8958)
Y145EWTKKYAV1Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
Y145EWTRKYAM1Drosophila melanogaster


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