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 PCMT1
Gene summary
Basic gene Info.Gene symbolPCMT1
Gene nameprotein-L-isoaspartate (D-aspartate) O-methyltransferase
CytomapUCSC genome browser: 6q25.1
Type of geneprotein-coding
DescriptionL-isoaspartyl protein carboxyl methyltransferaseprotein L-isoaspartyl/D-aspartyl methyltransferaseprotein-L-isoaspartate(D-aspartate) O-methyltransferaseprotein-beta-aspartate methyltransferase
Modification date20141207
dbXrefs MIM : 176851
Ensembl : ENSG00000120265
HPRD : 08908
Vega : OTTHUMG00000015794
ProteinUniProt: P22061
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_PCMT1
BioGPS: 5110
PathwayNCI Pathway Interaction Database: PCMT1
Pathway Commons: PCMT1
ContextiHOP: PCMT1
ligand binding site mutation search in PubMed: PCMT1
UCL Cancer Institute: PCMT1
Assigned class in mutLBSgeneDBC: This gene just belongs to mutLBSgenes.

Gene ontology having evidence of Inferred from Direct Assay (IDA) from Entrez

Ligand binding site mutations for PCMT1

Cancer type specific mutLBS sorted by frequency
LBSAAchange of nsSNVCancer type# samples
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.

Protein structure related information for PCMT1
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
(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 PCMT1 from PDB
PDB IDPDB titlePDB structure
1KR5Crystal structure of human L-isoaspartyl methyltransferase

Differential gene expression and gene-gene network for PCMT1
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 PCMT1 and the right PPI network was created from samples without mutations in the LBS of PCMT1. Only genes with p-value < 0.05 are shown.
Red circle: input gene. Orange circle: LBSgene. Blue circle: other gene.


Phenotype information for PCMT1
Gene level disease information (DisGeNet)
Disease IDDisease name# PubMedAssociation type
umls:C0080178Spinal Dysraphism3Biomarker, GeneticVariation

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

Pharmacological information for PCMT1
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
ExperimentalDB01752S-Adenosyl-L-HomocysteineSmall molecule

Gene-centered ligand-gene interaction network

Ligands binding to mutated ligand binding site of PCMT1 go to BioLip
Ligand IDLigand short nameLigand long namePDB IDPDB namemutLBS

Conservation information for LBS of PCMT1
Multiple alignments for P22061 in multiple species
LBSAA sequence# speciesSpecies
A57SIGFQATISAP3Homo sapiens, Bos taurus, Gallus gallus
A57SIGYGVTISAP1Schizosaccharomyces pombe (strain 972 / ATCC 24843)
A57SIGYNVTISAP1Arabidopsis thaliana
A57RIGYNATVSAP1Caenorhabditis elegans
A57PIGGGVTISAP1Drosophila melanogaster
A57SIGYQATISAP1Danio rerio
D110KVIGIDHIKEL3Homo sapiens, Danio rerio, Bos taurus
D110TVKGIEHIPQL1Schizosaccharomyces pombe (strain 972 / ATCC 24843)
D110RAIGVEHIPEL1Arabidopsis thaliana
D110TVVGIEHMPQL1Caenorhabditis elegans
D110RIVGIEHQAEL1Drosophila melanogaster
D110QVVGIDHIKEL1Gallus gallus
D142QLVVGDGRMGY2Homo sapiens, Bos taurus
D142QINVGDGRMGT1Schizosaccharomyces pombe (strain 972 / ATCC 24843)
D142AVHVGDGRQGW1Arabidopsis thaliana
D142IIIEGDGRQGF1Caenorhabditis elegans
D142LIVEGDGRKGY1Drosophila melanogaster
D142KLIVGDGRMGF1Danio rerio
D142KLIVGDGRMGY1Gallus gallus
G141VQLVVGDGRMG2Homo sapiens, Bos taurus
G141LQINVGDGRMG1Schizosaccharomyces pombe (strain 972 / ATCC 24843)
G141LAVHVGDGRQG1Arabidopsis thaliana
G141VIIIEGDGRQG1Caenorhabditis elegans
G141LLIVEGDGRKG1Drosophila melanogaster
G141IKLIVGDGRMG1Danio rerio
G141VKLIVGDGRMG1Gallus gallus
G143LVVGDGRMGYA2Homo sapiens, Bos taurus
G143INVGDGRMGTS1Schizosaccharomyces pombe (strain 972 / ATCC 24843)
G143VHVGDGRQGWA1Arabidopsis thaliana
G143IIEGDGRQGFA1Caenorhabditis elegans
G143IVEGDGRKGYP1Drosophila melanogaster
G143LIVGDGRMGFT1Danio rerio
G143LIVGDGRMGYA1Gallus gallus
G159DAIHVGAAAPV3Homo sapiens, Bos taurus, Gallus gallus
G159DAIHVGASASE1Schizosaccharomyces pombe (strain 972 / ATCC 24843)
G159DAIHVGAAAPE1Arabidopsis thaliana
G159NAIHVGAASKG1Caenorhabditis elegans
G159NAIHVGAAAPD1Drosophila melanogaster
G159DAIHVGAAAPT1Danio rerio
G86KALDVGSGSGI4Homo sapiens, Danio rerio, Bos taurus, Gallus gallus
G86SALDIGSGSGY1Schizosaccharomyces pombe (strain 972 / ATCC 24843)
G86RVLDVGSGTGY1Arabidopsis thaliana
G86KALDVGSGSGY1Caenorhabditis elegans
G86RILDVGSGSGY1Drosophila melanogaster
G88LDVGSGSGILT3Homo sapiens, Bos taurus, Gallus gallus
G88LDVGSGSGYLT2Caenorhabditis elegans, Drosophila melanogaster
G88LDIGSGSGYLV1Schizosaccharomyces pombe (strain 972 / ATCC 24843)
G88LDVGSGTGYLT1Arabidopsis thaliana
G88LDVGSGSGILS1Danio rerio
H111VIGIDHIKELV3Homo sapiens, Danio rerio, Bos taurus
H111VKGIEHIPQLV1Schizosaccharomyces pombe (strain 972 / ATCC 24843)
H111AIGVEHIPELV1Arabidopsis thaliana
H111VVGIEHMPQLV1Caenorhabditis elegans
H111IVGIEHQAELV1Drosophila melanogaster
H111VVGIDHIKELV1Gallus gallus
H65SAPHMHAYALE4Homo sapiens, Danio rerio, Bos taurus, Gallus gallus
H65SAPHMHATALQ1Schizosaccharomyces pombe (strain 972 / ATCC 24843)
H65SAPHMHAMCLQ1Arabidopsis thaliana
H65SAPHMHAAALD1Caenorhabditis elegans
H65SAPHMHAFALE1Drosophila melanogaster
I112IGIDHIKELVD2Homo sapiens, Bos taurus
I112KGIEHIPQLVE1Schizosaccharomyces pombe (strain 972 / ATCC 24843)
I112IGVEHIPELVA1Arabidopsis thaliana
I112VGIEHMPQLVE1Caenorhabditis elegans
I112VGIEHQAELVR1Drosophila melanogaster
I112IGIDHIKELVE1Danio rerio
I112VGIDHIKELVD1Gallus gallus
I59GFQATISAPHM3Homo sapiens, Bos taurus, Gallus gallus
I59GYGVTISAPHM1Schizosaccharomyces pombe (strain 972 / ATCC 24843)
I59GYNVTISAPHM1Arabidopsis thaliana
I59GYNATVSAPHM1Caenorhabditis elegans
I59GGGVTISAPHM1Drosophila melanogaster
I59GYQATISAPHM1Danio rerio
L115DHIKELVDDSI2Bos taurus, Gallus gallus
L115DHIKELVDDSV1Homo sapiens
L115EHIPQLVETSK1Schizosaccharomyces pombe (strain 972 / ATCC 24843)
L115EHIPELVASSV1Arabidopsis thaliana
L115EHMPQLVELSE1Caenorhabditis elegans
L115EHQAELVRRSK1Drosophila melanogaster
L115DHIKELVEDSI1Danio rerio
L216VIYVPLTDKEK3Homo sapiens, Bos taurus, Gallus gallus
L216VRYVPLTDSPD1Schizosaccharomyces pombe (strain 972 / ATCC 24843)
L216VRYVPLTSREA1Arabidopsis thaliana
L216VIYVPLTSREE1Caenorhabditis elegans
L216VMYVPLTDLRS1Drosophila melanogaster
L216VIYVPLTDKDK1Danio rerio
P215GVIYVPLTDKE3Homo sapiens, Bos taurus, Gallus gallus
P215PVRYVPLTDSP1Schizosaccharomyces pombe (strain 972 / ATCC 24843)
P215SVRYVPLTSRE1Arabidopsis thaliana
P215HVIYVPLTSRE1Caenorhabditis elegans
P215GVMYVPLTDLR1Drosophila melanogaster
P215GVIYVPLTDKD1Danio rerio
Q222TDKEKQWSRWK2Homo sapiens, Bos taurus
Q222TDSPDDSSDY-1Schizosaccharomyces pombe (strain 972 / ATCC 24843)
Q222TSREAQLRGD-1Arabidopsis thaliana
Q222TSREEQWNRN-1Caenorhabditis elegans
Q222TDLRS------1Drosophila melanogaster
Q222TDKDKQWSRDE1Danio rerio
Q222TDKEKQWSRDE1Gallus gallus
R144VVGDGRMGYAE1Homo sapiens
R144NVGDGRMGTSE1Schizosaccharomyces pombe (strain 972 / ATCC 24843)
R144HVGDGRQGWAE1Arabidopsis thaliana
R144IEGDGRQGFAE1Caenorhabditis elegans
R144VEGDGRKGYPP1Drosophila melanogaster
R144IVGDGRMGFTE1Danio rerio
R144VVGDGRMGYAA1Bos taurus
R144IVGDGRMGYAE1Gallus gallus
S60FQATISAPHMH3Homo sapiens, Bos taurus, Gallus gallus
S60YGVTISAPHMH1Schizosaccharomyces pombe (strain 972 / ATCC 24843)
S60YNVTISAPHMH1Arabidopsis thaliana
S60YNATVSAPHMH1Caenorhabditis elegans
S60GGVTISAPHMH1Drosophila melanogaster
S60YQATISAPHMH1Danio rerio
S87ALDVGSGSGIL4Homo sapiens, Danio rerio, Bos taurus, Gallus gallus
S87ALDIGSGSGYL1Schizosaccharomyces pombe (strain 972 / ATCC 24843)
S87VLDVGSGTGYL1Arabidopsis thaliana
S87ALDVGSGSGYL1Caenorhabditis elegans
S87ILDVGSGSGYL1Drosophila melanogaster
S89DVGSGSGILTA3Homo sapiens, Bos taurus, Gallus gallus
S89DIGSGSGYLVA1Schizosaccharomyces pombe (strain 972 / ATCC 24843)
S89DVGSGTGYLTA1Arabidopsis thaliana
S89DVGSGSGYLTV1Caenorhabditis elegans
S89DVGSGSGYLTA1Drosophila melanogaster
S89DVGSGSGILSV1Danio rerio
T217IYVPLTDKEKQ3Homo sapiens, Bos taurus, Gallus gallus
T217RYVPLTDSPDD1Schizosaccharomyces pombe (strain 972 / ATCC 24843)
T217RYVPLTSREAQ1Arabidopsis thaliana
T217IYVPLTSREEQ1Caenorhabditis elegans
T217MYVPLTDLRS-1Drosophila melanogaster
T217IYVPLTDKDKQ1Danio rerio
T58IGFQATISAPH3Homo sapiens, Bos taurus, Gallus gallus
T58IGYGVTISAPH1Schizosaccharomyces pombe (strain 972 / ATCC 24843)
T58IGYNVTISAPH1Arabidopsis thaliana
T58IGYNATVSAPH1Caenorhabditis elegans
T58IGGGVTISAPH1Drosophila melanogaster
T58IGYQATISAPH1Danio rerio
V214MGVIYVPLTDK4Homo sapiens, Danio rerio, Bos taurus, Gallus gallus
V214FPVRYVPLTDS1Schizosaccharomyces pombe (strain 972 / ATCC 24843)
V214TSVRYVPLTSR1Arabidopsis thaliana
V214EHVIYVPLTSR1Caenorhabditis elegans
V214MGVMYVPLTDL1Drosophila melanogaster

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