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 SRR
Gene summary
Basic gene Info.Gene symbolSRR
Gene nameserine racemase
SynonymsILV1|ISO1
CytomapUCSC genome browser: 17p13
Type of geneprotein-coding
RefGenesNM_021947.1,
DescriptionD-serine ammonia-lyaseD-serine dehydrataseL-serine ammonia-lyaseL-serine dehydratase
Modification date20141207
dbXrefs MIM : 606477
HGNC : HGNC
Ensembl : ENSG00000167720
HPRD : 10451
Vega : OTTHUMG00000090583
ProteinUniProt: Q9GZT4
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_SRR
BioGPS: 63826
PathwayNCI Pathway Interaction Database: SRR
KEGG: SRR
REACTOME: SRR
Pathway Commons: SRR
ContextiHOP: SRR
ligand binding site mutation search in PubMed: SRR
UCL Cancer Institute: SRR
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:0006563L-serine metabolic process11054547
GO:0042866pyruvate biosynthetic process18812225
GO:0070178D-serine metabolic process20106978
GO:0070179D-serine biosynthetic process11054547


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Ligand binding site mutations for SRR
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
E283I282TCOAD1
S242I244TSTAD1
K56R58CUCEC1
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 SRR
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
E283I282T-1.2912101
S242I244T-0.82478064
K56R58C-0.75163916
(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 SRR from PDB

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Differential gene expression and gene-gene network for SRR
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 SRR and the right PPI network was created from samples without mutations in the LBS of SRR. 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 SRR
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 SRR
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|nutraceuticalDB00133L-SerineSmall molecule

Gene-centered ligand-gene interaction network

Ligands binding to mutated ligand binding site of SRR go to BioLip
Ligand IDLigand short nameLigand long namePDB IDPDB namemutLBS
PLPPYRIDOXAL 5'-PHOSPHATE3l6bAK56 E283
MLIMALONATE(2-)3l6bAK56 S242
MLIMALONATE(2-)3l6rAK56 S242


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Conservation information for LBS of SRR
Multiple alignments for Q9GZT4 in multiple species
LBSAA sequence# speciesSpecies
E283MKLLIEPTAGV4Homo sapiens, Bos taurus, Mus musculus, Rattus norvegicus
E283MKVVVEPTACL1Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
E283MKIVVEPTGCL1Schizosaccharomyces pombe (strain 972 / ATCC 24843)
E283LKVSVEPSGAI1Arabidopsis thaliana
E283LKVAVEPSGAI1Oryza sativa subsp. japonica
F55QKTGSFKIRGA4Homo sapiens, Bos taurus, Mus musculus, Rattus norvegicus
F55QRVGAFKFRGA1Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
F55QKMGAFKFRGA1Schizosaccharomyces pombe (strain 972 / ATCC 24843)
F55QKGGAFKFRGA1Arabidopsis thaliana
F55QKAGAFKIRGA1Oryza sativa subsp. japonica
G185LVVPVGGGGML2Homo sapiens, Bos taurus
G185LVVPVGGGGMV2Mus musculus, Rattus norvegicus
G185LFVPLGGGGLL1Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
G185LFVCLGGGGLL1Schizosaccharomyces pombe (strain 972 / ATCC 24843)
G185IVVPISGGGLI1Arabidopsis thaliana
G185IIVPISGGGLI1Oryza sativa subsp. japonica
G186VVPVGGGGMLA2Homo sapiens, Bos taurus
G186VVPVGGGGMVA2Mus musculus, Rattus norvegicus
G186FVPLGGGGLLS1Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
G186FVCLGGGGLLS1Schizosaccharomyces pombe (strain 972 / ATCC 24843)
G186VVPISGGGLIS1Arabidopsis thaliana
G186IVPISGGGLIS1Oryza sativa subsp. japonica
G187VPVGGGGMLAG2Homo sapiens, Bos taurus
G187VPVGGGGMVAG2Mus musculus, Rattus norvegicus
G187VPISGGGLISG2Arabidopsis thaliana, Oryza sativa subsp. japonica
G187VPLGGGGLLSG1Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
G187VCLGGGGLLSG1Schizosaccharomyces pombe (strain 972 / ATCC 24843)
G188PVGGGGMLAGI2Homo sapiens, Bos taurus
G188PVGGGGMVAGI2Mus musculus, Rattus norvegicus
G188PISGGGLISGV2Arabidopsis thaliana, Oryza sativa subsp. japonica
G188PLGGGGLLSGS1Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
G188CLGGGGLLSGS1Schizosaccharomyces pombe (strain 972 / ATCC 24843)
G239ETIADGVKS-S3Homo sapiens, Mus musculus, Rattus norvegicus
G239KTIADGAQTQH2Saccharomyces cerevisiae (strain ATCC 204508 / S288c), Schizosaccharomyces pombe (strain 972 / ATCC 24843)
G239ETIADGIKS-S1Bos taurus
G239NTIADGLRA-S1Arabidopsis thaliana
G239NTIADGLRA-F1Oryza sativa subsp. japonica
G314CIVLSGGNVDL4Homo sapiens, Bos taurus, Mus musculus, Rattus norvegicus
G314GIILSGGNVDM1Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
G314GIIISGGNVDI1Schizosaccharomyces pombe (strain 972 / ATCC 24843)
G314GIVLSGGNVDL1Arabidopsis thaliana
G314GIIVSGGNVDL1Oryza sativa subsp. japonica
H87HSSGNHGQALT3Homo sapiens, Mus musculus, Rattus norvegicus
H87FSSGNHAQAIA2Saccharomyces cerevisiae (strain ATCC 204508 / S288c), Schizosaccharomyces pombe (strain 972 / ATCC 24843)
H87HSSGNHGQALS1Bos taurus
H87HSSGNHAAALS1Arabidopsis thaliana
H87HSSGNHAAAVA1Oryza sativa subsp. japonica
K56KTGSFKIRGAL4Homo sapiens, Bos taurus, Mus musculus, Rattus norvegicus
K56RVGAFKFRGAM1Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
K56KMGAFKFRGAL1Schizosaccharomyces pombe (strain 972 / ATCC 24843)
K56KGGAFKFRGAC1Arabidopsis thaliana
K56KAGAFKIRGAS1Oryza sativa subsp. japonica
M189VGGGGMLAGIA2Homo sapiens, Bos taurus
M189LGGGGLLSGSA2Saccharomyces cerevisiae (strain ATCC 204508 / S288c), Schizosaccharomyces pombe (strain 972 / ATCC 24843)
M189VGGGGMVAGIA2Mus musculus, Rattus norvegicus
M189ISGGGLISGVA2Arabidopsis thaliana, Oryza sativa subsp. japonica
N86THSSGNHGQAL3Homo sapiens, Mus musculus, Rattus norvegicus
N86AFSSGNHAQAI1Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
N86TFSSGNHAQAI1Schizosaccharomyces pombe (strain 972 / ATCC 24843)
N86AHSSGNHGQAL1Bos taurus
N86THSSGNHAAAL1Arabidopsis thaliana
N86THSSGNHAAAV1Oryza sativa subsp. japonica
P183DALVVPVGGGG4Homo sapiens, Bos taurus, Mus musculus, Rattus norvegicus
P183DALFVPLGGGG1Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
P183DALFVCLGGGG1Schizosaccharomyces pombe (strain 972 / ATCC 24843)
P183DAIVVPISGGG1Arabidopsis thaliana
P183DTIIVPISGGG1Oryza sativa subsp. japonica
R135PSDESRENVAK1Homo sapiens
R135RYTEDREQIGR1Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
R135RYKDDREKMAK1Schizosaccharomyces pombe (strain 972 / ATCC 24843)
R135QSEESRENITK1Bos taurus
R135PSDESREKVTQ1Mus musculus
R135PSDESRENVAQ1Rattus norvegicus
R135ATMSSREEIAS1Arabidopsis thaliana
R135VSIESRESVAK1Oryza sativa subsp. japonica
S242ADGVKS-SIGL3Homo sapiens, Mus musculus, Rattus norvegicus
S242ADGAQTQHLGE1Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
S242ADGAQTQHLGN1Schizosaccharomyces pombe (strain 972 / ATCC 24843)
S242ADGIKS-SIGL1Bos taurus
S242ADGLRA-SLGD1Arabidopsis thaliana
S242ADGLRA-FLGD1Oryza sativa subsp. japonica
S313ICIVLSGGNVD3Homo sapiens, Bos taurus, Rattus norvegicus
S313VGIILSGGNVD1Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
S313IGIIISGGNVD1Schizosaccharomyces pombe (strain 972 / ATCC 24843)
S313VCIVLSGGNVD1Mus musculus
S313IGIVLSGGNVD1Arabidopsis thaliana
S313IGIIVSGGNVD1Oryza sativa subsp. japonica
S83AVVTHSSGNHG3Homo sapiens, Mus musculus, Rattus norvegicus
S83GVVTHSSGNHA2Arabidopsis thaliana, Oryza sativa subsp. japonica
S83GVIAFSSGNHA1Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
S83GVLTFSSGNHA1Schizosaccharomyces pombe (strain 972 / ATCC 24843)
S83AVVAHSSGNHG1Bos taurus
S84VVTHSSGNHGQ3Homo sapiens, Mus musculus, Rattus norvegicus
S84VVTHSSGNHAA2Arabidopsis thaliana, Oryza sativa subsp. japonica
S84VIAFSSGNHAQ1Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
S84VLTFSSGNHAQ1Schizosaccharomyces pombe (strain 972 / ATCC 24843)
S84VVAHSSGNHGQ1Bos taurus
T285LLIEPTAGVGV2Homo sapiens, Bos taurus
T285VVVEPTACLGF1Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
T285IVVEPTGCLSF1Schizosaccharomyces pombe (strain 972 / ATCC 24843)
T285LLIEPTAGVAL1Mus musculus
T285LLIEPTAGVGL1Rattus norvegicus
T285VSVEPSGAIGL1Arabidopsis thaliana
T285VAVEPSGAIGL1Oryza sativa subsp. japonica
V240TIADGVKS-SI3Homo sapiens, Mus musculus, Rattus norvegicus
V240TIADGAQTQHL2Saccharomyces cerevisiae (strain ATCC 204508 / S288c), Schizosaccharomyces pombe (strain 972 / ATCC 24843)
V240TIADGIKS-SI1Bos taurus
V240TIADGLRA-SL1Arabidopsis thaliana
V240TIADGLRA-FL1Oryza sativa subsp. japonica


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