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 CBS
Gene summary
Basic gene Info.Gene symbolCBS
Gene namecystathionine-beta-synthase
SynonymsHIP4
CytomapUCSC genome browser: 21q22.3
Type of geneprotein-coding
RefGenesNM_000071.2,
NM_001178008.1,NM_001178009.1,
Descriptionbeta-thionasecystathionine beta-synthasemethylcysteine synthaseserine sulfhydrase
Modification date20141222
dbXrefs MIM : 613381
HGNC : HGNC
Ensembl : ENSG00000160200
HPRD : 01994
Vega : OTTHUMG00000086834
ProteinUniProt: P35520
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_CBS
BioGPS: 875
PathwayNCI Pathway Interaction Database: CBS
KEGG: CBS
REACTOME: CBS
Pathway Commons: CBS
ContextiHOP: CBS
ligand binding site mutation search in PubMed: CBS
UCL Cancer Institute: CBS
Assigned class in mutLBSgeneDBA: This gene has a literature evidence and it belongs to targetable_mutLBSgenes.
References showing study about ligand binding site mutation for CBS.1. "Singh S, Madzelan P, Stasser J, Weeks CL, Becker D, Spiro TG, Penner-Hahn J,Banerjee R. Modulation of the heme electronic structure and cystathionine beta-synthase activity by second coordination sphere ligands: The role of heme ligand switching in redox regulation. J Inorg Biochem. 2009 May;103(5):689-97. doi: 10.1016/j.jinorgbio.2009.01.009. Epub 2009 Jan 22. PubMed PMID: 19232736; PubMed Central PMCID: PMC2772092. " 19232736
2. "Smith AT, Su Y, Stevens DJ, Majtan T, Kraus JP, Burstyn JN. Effect of the disease-causing R266K mutation on the heme and PLP environments of human cystathionine β-synthase. Biochemistry. 2012 Aug 14;51(32):6360-70. Epub 2012 Jul 31. PubMed PMID: 22738154; PubMed Central PMCID: PMC3569099. " 22738154

Gene ontology having evidence of Inferred from Direct Assay (IDA) from Entrez
GO IDGO TermPubMed ID
GO:0006563L-serine metabolic process19010420
GO:0006565L-serine catabolic process18776696
GO:0019448L-cysteine catabolic process15520012
GO:0043418homocysteine catabolic process18776696
GO:0050667homocysteine metabolic process19010420
GO:0070814hydrogen sulfide biosynthetic process15520012


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Ligand binding site mutations for CBS
Lollipop-style diagram of mutations at LBS in amino-acid sequence.
We represented ligand binding site mutations only. (You can see big image via clicking.)
 : non-synonymous mutation on LBS, Circle size denotes number of samples.

Cancer type specific mutLBS sorted by frequency
LBSAAchange of nsSNVCancer type# samples
I306G307SBRCA1
D538L540MLUSC1
P49P49SSKCM1
V118V118MSTAD1
R224R224CUCEC1
K119R121HUCEC1
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 CBS
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
D538L540M-1.4839507
P49P49S-1.3705286
K119R121H-1.2461512
I306G307S-0.75261106
R224R224C-0.60724271
V118V118M-0.39603917
(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 CBS from PDB

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Differential gene expression and gene-gene network for CBS
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 CBS and the right PPI network was created from samples without mutations in the LBS of CBS. 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 CBS
Gene level disease information (DisGeNet)
Disease IDDisease name# PubMedAssociation type
umls:C0019880Homocystinuria79Biomarker, GeneticVariation
umls:C0598608Hyperhomocysteinemia44Biomarker, GeneticVariation
umls:C1439329CYSTATHIONINE BETA-SYNTHASE25GeneticVariation
umls:C0007222Cardiovascular Diseases10Biomarker, GeneticVariation
umls:C0024305Lymphoma, Non-Hodgkin3Biomarker, GeneticVariation
umls:C0162429Malnutrition2Biomarker, GeneticVariation
umls:C0011860Diabetes Mellitus, Type 22Biomarker, GeneticVariation
umls:C0020538Hypertension2Biomarker, GeneticVariation

Mutation level pathogenic information (ClinVar annotation)
Allele IDAA changeClinical significanceOriginPhenotype IDs
15156G307SPathogenicGermlineGeneReviews:NBK1524
MedGen:C3150344
OMIM:236200
Orphanet:ORPHA394
MedGen:CN068393
MedGen:CN221809
187059R121HLikely pathogenic;PathogenicGermline;unknownGeneReviews:NBK1524
MedGen:C3150344
OMIM:236200
Orphanet:ORPHA394
MedGen:CN221809
210431R224CLikely pathogenicGermlineMedGen:CN221809

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Pharmacological information for CBS
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|nutraceuticalDB00118S-AdenosylmethionineSmall molecule
Approved|nutraceuticalDB00133L-SerineSmall molecule
Approved|nutraceuticalDB00151L-CysteineSmall molecule

Gene-centered ligand-gene interaction network

Ligands binding to mutated ligand binding site of CBS go to BioLip
Ligand IDLigand short nameLigand long namePDB IDPDB namemutLBS
SAMS-ADENOSYL-L-METHIONINE4uuuAD538
SAMS-ADENOSYL-L-METHIONINE4uuuBD538
SAMS-ADENOSYL-L-METHIONINE4pcuAD538
SAMS-ADENOSYL-L-METHIONINE4pcuBD538
PLPPYRIDOXAL 5'-PHOSPHATE1jbqAK119 I306
PLPPYRIDOXAL 5'-PHOSPHATE1jbqBK119 I306
PLPPYRIDOXAL 5'-PHOSPHATE1jbqCK119 I306
PLPPYRIDOXAL 5'-PHOSPHATE1jbqDK119 I306
PLPPYRIDOXAL 5'-PHOSPHATE1jbqEK119 I306
PLPPYRIDOXAL 5'-PHOSPHATE1jbqFK119 I306
PLPPYRIDOXAL 5'-PHOSPHATE1m54AK119 I306
PLPPYRIDOXAL 5'-PHOSPHATE1m54BK119 I306
PLPPYRIDOXAL 5'-PHOSPHATE1m54DK119 I306
PLPPYRIDOXAL 5'-PHOSPHATE1m54EK119 I306
PLPPYRIDOXAL 5'-PHOSPHATE1m54FK119 I306
PLPPYRIDOXAL 5'-PHOSPHATE4l0dAK119 I306
PLPPYRIDOXAL 5'-PHOSPHATE4l0dBK119 I306
PLPPYRIDOXAL 5'-PHOSPHATE4l27BK119 I306
PLPPYRIDOXAL 5'-PHOSPHATE4l27DK119 I306
PLPPYRIDOXAL 5'-PHOSPHATE4l27AK119 I306
PLPPYRIDOXAL 5'-PHOSPHATE4l27CK119 I306
PLPPYRIDOXAL 5'-PHOSPHATE4l28AK119 I306
PLPPYRIDOXAL 5'-PHOSPHATE4l28BK119 I306
PLPPYRIDOXAL 5'-PHOSPHATE4l28CK119 I306
PLPPYRIDOXAL 5'-PHOSPHATE4l28DK119 I306
PLPPYRIDOXAL 5'-PHOSPHATE4l3vBK119 I306
PLPPYRIDOXAL 5'-PHOSPHATE4l3vAK119 I306
PLPPYRIDOXAL 5'-PHOSPHATE4l3vCK119 I306
PLPPYRIDOXAL 5'-PHOSPHATE4cooAK119 I306
PLPPYRIDOXAL 5'-PHOSPHATE4cooBK119 I306
PLPPYRIDOXAL 5'-PHOSPHATE4pcuAK119 I306
PLPPYRIDOXAL 5'-PHOSPHATE4pcuBK119 I306
HEMHEME B1m54DP49
HEMHEME B4pcuAP49
HEMHEME B1m54BP49 R224
HEMHEME B4pcuBP49 R224
HEMHEME B1jbqAR224
HEMHEME B1jbqBR224
HEMHEME B1jbqCR224
HEMHEME B1jbqDR224
HEMHEME B1jbqER224
HEMHEME B1jbqFR224
HEMHEME B1m54FR224
HEMHEME B4l27BR224
HEMHEME B4l27DR224
HEMHEME B4l27CR224
PLPPYRIDOXAL 5'-PHOSPHATE1m54CV118 K119 I306


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Conservation information for LBS of CBS
Multiple alignments for P35520 in multiple species
LBSAA sequence# speciesSpecies


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