mutLBSgeneDB

mutLBSgeneDB
mutated Ligand Binding Site gene DataBase

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Bioinformatics and Systems Medicine Laboratory Bioinformatics and Systems Medicine Laboratory

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 CTH
Gene summary
Basic gene Info.Gene symbolCTH
Gene namecystathionine gamma-lyase
Synonyms-
CytomapUCSC genome browser: 1p31.1
Type of geneprotein-coding
RefGenesNM_001190463.1,
NM_001902.5,NM_153742.4,
Descriptioncystathionase (cystathionine gamma-lyase)cysteine desulfhydrasecysteine-protein sulfhydrasegamma-cystathionasehomoserine deaminasehomoserine dehydratase
Modification date20141222
dbXrefs MIM : 607657
HGNC : HGNC
Ensembl : ENSG00000116761
HPRD : 09633
Vega : OTTHUMG00000009352
ProteinUniProt: P32929
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_CTH
BioGPS: 1491
PathwayNCI Pathway Interaction Database: CTH
KEGG: CTH
REACTOME: CTH
Pathway Commons: CTH
ContextiHOP: CTH
ligand binding site mutation search in PubMed: CTH
UCL Cancer Institute: CTH
Assigned class in mutLBSgeneDBB: This gene belongs to targetable_mutLBSgenes.

Gene ontology having evidence of Inferred from Direct Assay (IDA) from Entrez
GO IDGO TermPubMed ID
GO:0018272protein-pyridoxal-5-phosphate linkage via peptidyl-N6-pyridoxal phosphate-L-lysine19019829
GO:0019344cysteine biosynthetic process10212249
GO:0070814hydrogen sulfide biosynthetic process19019829


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Ligand binding site mutations for CTH

Cancer type specific mutLBS sorted by frequency
LBSAAchange of nsSNVCancer type# samples
D187V186ACOAD1
D187V186MCOAD1
R62R62LGBM1
E339E339DHNSC1
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 CTH
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
D187V186A-1.4834468
D187V186M-0.99312956
E339E339D-0.97456941
R62R62L-0.61055849
(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 CTH from PDB

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Differential gene expression and gene-gene network for CTH
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 CTH and the right PPI network was created from samples without mutations in the LBS of CTH. 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 CTH
Gene level disease information (DisGeNet)
Disease IDDisease name# PubMedAssociation type
umls:C0220993Cystathioninuria4Biomarker, GeneticVariation
umls:C0268616Gamma-cystathionase deficiency3Biomarker, GeneticVariation

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

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Pharmacological information for CTH
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
NutraceuticalDB00114Pyridoxal PhosphateSmall molecule
Approved|nutraceuticalDB00151L-CysteineSmall molecule
ExperimentalDB023282-[(3-Hydroxy-2-Methyl-5-Phosphonooxymethyl-Pyridin-4-Ylmethyl)-Imino]-5-Phosphono-Pent-3-Enoic AcidSmall molecule
ExperimentalDB03928Carboxymethylthio-3-(3-Chlorophenyl)-1,2,4-OxadiazolSmall molecule
ExperimentalDB04217L-2-amino-3-butynoic acidSmall molecule

Gene-centered ligand-gene interaction network

Ligands binding to mutated ligand binding site of CTH go to BioLip
Ligand IDLigand short nameLigand long namePDB IDPDB namemutLBS
PLPPYRIDOXAL 5'-PHOSPHATE2nmpAD187
PLPPYRIDOXAL 5'-PHOSPHATE2nmpCD187
PLPPYRIDOXAL 5'-PHOSPHATE2nmpDD187
PLPPYRIDOXAL 5'-PHOSPHATE3cogAD187
PLPPYRIDOXAL 5'-PHOSPHATE3cogCD187
PLPPYRIDOXAL 5'-PHOSPHATE3cogDD187
2AGL-ALLYLGLYCINE3cogAE339
2AGL-ALLYLGLYCINE3cogCE339
2AGL-ALLYLGLYCINE3cogDE339
PLPPYRIDOXAL 5'-PHOSPHATE2nmpBR62
PLPPYRIDOXAL 5'-PHOSPHATE2nmpCR62
PLPPYRIDOXAL 5'-PHOSPHATE2nmpDR62
PLPPYRIDOXAL 5'-PHOSPHATE3cogBR62
2AGL-ALLYLGLYCINE3cogBR62
PLPPYRIDOXAL 5'-PHOSPHATE3cogCR62
2AGL-ALLYLGLYCINE3cogCR62
PLPPYRIDOXAL 5'-PHOSPHATE3cogDR62
2AGL-ALLYLGLYCINE3cogDR62


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Conservation information for LBS of CTH
Multiple alignments for P32929 in multiple species
LBSAA sequence# speciesSpecies
D187IILVVDNTFMS4Homo sapiens, Mus musculus, Rattus norvegicus, Bos taurus
D187VILVVDNTFLS1Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
D187IVVVVDNTFMS1Caenorhabditis elegans
E157KLVWIETPTNP5Homo sapiens, Saccharomyces cerevisiae (strain ATCC 204508 / S288c), Mus musculus, Rattus norvegicus, Bos taurus
E157KMVWFESPSNP1Caenorhabditis elegans
E339LFTLAESLGGY2Mus musculus, Bos taurus
E339LFTLAESLGGF1Homo sapiens
E339LFTLAESLGGI1Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
E339VFTLAESLGGY1Caenorhabditis elegans
E339LFALAESLGGY1Rattus norvegicus
G90LAFASGLAATV2Homo sapiens, Bos taurus
G90LAFSSGSATTA1Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
G90QVFSSGLAATS1Caenorhabditis elegans
G90LAFASGLAATI1Mus musculus
G90LTFARGLAATT1Rattus norvegicus
K212MCSATKYMNGH2Mus musculus, Rattus norvegicus
K212MYSATKYMNGH1Homo sapiens
K212VHSATKYINGH1Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
K212VHSITKYINGH1Caenorhabditis elegans
K212MYSATKYMNGY1Bos taurus
L91AFASGLAATVT2Homo sapiens, Bos taurus
L91AFSSGSATTAT1Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
L91VFSSGLAATSA1Caenorhabditis elegans
L91AFASGLAATIT1Mus musculus
L91TFARGLAATTT1Rattus norvegicus
N161IETPTNPTLKL2Mus musculus, Rattus norvegicus
N161IETPTNPTQKV1Homo sapiens
N161IETPTNPTLKV1Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
N161FESPSNPLLKV1Caenorhabditis elegans
N161IETPTNPSLKM1Bos taurus
R119YGGTNRYFRQV2Homo sapiens, Bos taurus
R119YGGTNRYFRRV2Mus musculus, Rattus norvegicus
R119YGGTHRYFTKV1Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
R119YGGTQRYIRRV1Caenorhabditis elegans
R62-FEYSRSGNPT3Homo sapiens, Mus musculus, Bos taurus
R62TYEYSRSQNPN1Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
R62-HDYSRAGNPT1Caenorhabditis elegans
R62-FVYSRSGNPT1Rattus norvegicus
S209DICMCSATKYM2Mus musculus, Rattus norvegicus
S209DISMYSATKYM1Homo sapiens
S209DIVVHSATKYI1Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
S209DVVVHSITKYI1Caenorhabditis elegans
S209DICMYSATKYM1Bos taurus
S89SLAFASGLAAT2Mus musculus, Bos taurus
S89CLAFASGLAAT1Homo sapiens
S89GLAFSSGSATT1Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
S89CQVFSSGLAAT1Caenorhabditis elegans
S89CLTFARGLAAT1Rattus norvegicus
T189LVVDNTFMSAY3Mus musculus, Rattus norvegicus, Bos taurus
T189LVVDNTFMSPY1Homo sapiens
T189LVVDNTFLSPY1Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
T189VVVDNTFMSPY1Caenorhabditis elegans
T211CMCSATKYMNG2Mus musculus, Rattus norvegicus
T211SMYSATKYMNG1Homo sapiens
T211VVHSATKYING1Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
T211VVHSITKYING1Caenorhabditis elegans
T211CMYSATKYMNG1Bos taurus
Y114CMDDVYGGTNR2Homo sapiens, Bos taurus
Y114CMDEVYGGTNR2Mus musculus, Rattus norvegicus
Y114SIGDVYGGTHR1Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
Y114CSDDVYGGTQR1Caenorhabditis elegans
Y60SG-FEYSRSGN3Homo sapiens, Mus musculus, Bos taurus
Y60IGTYEYSRSQN1Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
Y60KG-HDYSRAGN1Caenorhabditis elegans
Y60SG-FVYSRSGN1Rattus norvegicus


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