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 SARS

Gene summary

Basic gene Info.	Gene symbol	SARS
	Gene name	seryl-tRNA synthetase
	Synonyms	SERRS\|SERS
	Cytomap	UCSC genome browser: 1p13.3
	Type of gene	protein-coding
	RefGenes	NM_006513.3, NR_034072.1,NR_034073.1,
	Description	Seryl-tRNA Ser/Sec synthetaseserine tRNA ligase 1, cytoplasmicserine--tRNA ligase, cytoplasmicseryl-tRNA synthetase, cytoplasmicseryl-tRNA(Ser/Sec) synthetase
	Modification date	20141207
dbXrefs	MIM : 607529
	HGNC : HGNC
	Ensembl : ENSG00000031698
	HPRD : 09605
	Vega : OTTHUMG00000011726
Protein	UniProt: P49591 go to UniProt's Cross Reference DB Table
Expression	CleanEX: HS_SARS
	BioGPS: 6301
Pathway	NCI Pathway Interaction Database: SARS
	KEGG: SARS
	REACTOME: SARS
	Pathway Commons: SARS
Context	iHOP: SARS
	ligand binding site mutation search in PubMed: SARS
	UCL Cancer Institute: SARS
Assigned class in mutLBSgeneDB	C: This gene just belongs to mutLBSgenes.

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

GO ID

GO Term

PubMed ID

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Ligand binding site mutations for SARS

Cancer type specific mutLBS sorted by frequency

LBS	AAchange of nsSNV	Cancer type	# samples
W43	E42Q	BLCA	1
D378	D378Y	BRCA	1
E246	D244V	BRCA	1
F48	R47S	LUAD	1
R44	R45Q	LUSC	1
R44	R45Q	OV	1
A432	A432T	STAD	1
N58	K57N	UCEC	1

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 SARS

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.

LBS	AAchange of nsSNV	Relative stability change
E246	D244V	0.18401516
R44	R45Q	-0.92539706
A432	A432T	-0.88080958
N58	K57N	-0.81133723
W43	E42Q	-0.79543364
F48	R47S	-0.79300174
D378	D378Y	-0.46856392

(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 SARS from PDB

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Differential gene expression and gene-gene network for SARS

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 SARS and the right PPI network was created from samples without mutations in the LBS of SARS. 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 SARS

Gene level disease information (DisGeNet)

Disease ID

Disease name

# PubMed

Association type

Mutation level pathogenic information (ClinVar annotation)

Allele ID

AA change

Clinical significance

Origin

Phenotype IDs

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Pharmacological information for SARS

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 status	DrugBank ID	Name	Type	Drug structure
Approved\|nutraceutical	DB00133	L-Serine	Small molecule

Gene-centered ligand-gene interaction network

Ligands binding to mutated ligand binding site of SARS go to BioLip

Ligand ID	Ligand short name	Ligand long name	PDB ID	PDB name	mutLBS
SSA		5'-O-(N-(L-SERYL)-SULFAMOYL)ADENOSINE	4l87	A	A432
ANP		AMP-PNP	4rqe	A	A432
ANP		AMP-PNP	4rqe	C	A432
ANP		AMP-PNP	4rqf	A	A432
ANP		AMP-PNP	4rqf	B	A432
MG		MAGNESIUM(2+)	4l87	A	D378
MG		MAGNESIUM(2+)	4l87	A	E246
NUC		Nucleic Acids	4rqe	C	R44 F48 N58
NUC		Nucleic Acids	4rqe	A	R44 N58
NUC		Nucleic Acids	4rqf	A	W43 R44 F48 N58

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Conservation information for LBS of SARS

Multiple alignments for P49591 in multiple species

LBS	AA sequence	# species	Species
A428	VHMLNATMCAT	4	Homo sapiens, Caenorhabditis elegans, Bos taurus, Rattus norvegicus
A428	VHMLNSTLTAT	1	Arabidopsis thaliana
A428	VHCLNSTLAAT	1	Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
A428	VHCLNSTLCAT	1	Schizosaccharomyces pombe (strain 972 / ATCC 24843)
A432	NATMCATTRTI	3	Homo sapiens, Bos taurus, Rattus norvegicus
A432	NATMCATTRVI	1	Caenorhabditis elegans
A432	NSTLTATERTI	1	Arabidopsis thaliana
A432	NSTLAATQRAL	1	Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
A432	NSTLCATERAL	1	Schizosaccharomyces pombe (strain 972 / ATCC 24843)
D378	ASKKLDLEAWF	3	Homo sapiens, Bos taurus, Rattus norvegicus
D378	AAKKYDLEAWF	3	Arabidopsis thaliana, Saccharomyces cerevisiae (strain ATCC 204508 / S288c), Schizosaccharomyces pombe (strain 972 / ATCC 24843)
D378	AAKKFDLEAWF	1	Caenorhabditis elegans
D51	CRFRADNLNKL	3	Homo sapiens, Bos taurus, Rattus norvegicus
D51	ERFVADQLNRQ	1	Caenorhabditis elegans
D51	RQFEVDSFRKE	1	Arabidopsis thaliana
D51	TRFELDELNKK	1	Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
D51	LRFELDNTNKS	1	Schizosaccharomyces pombe (strain 972 / ATCC 24843)
E246	SQFDEELYKVI	3	Homo sapiens, Bos taurus, Rattus norvegicus
E246	SQFDDELYKVS	1	Caenorhabditis elegans
E246	AQFDEELYKVT	1	Arabidopsis thaliana
E246	SEFDEELYKVI	1	Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
E246	EQFDEELYKVI	1	Schizosaccharomyces pombe (strain 972 / ATCC 24843)
E273	LIATSEQPIAA	4	Homo sapiens, Caenorhabditis elegans, Bos taurus, Rattus norvegicus
E273	LIATSEQPISA	2	Saccharomyces cerevisiae (strain ATCC 204508 / S288c), Schizosaccharomyces pombe (strain 972 / ATCC 24843)
E273	LIATAEQPLCA	1	Arabidopsis thaliana
E304	TCFRQEVGSHG	4	Homo sapiens, Caenorhabditis elegans, Bos taurus, Rattus norvegicus
E304	SCFRKEAGSHG	1	Arabidopsis thaliana
E304	SCFRREAGSHG	1	Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
E304	TCYRREAGSHG	1	Schizosaccharomyces pombe (strain 972 / ATCC 24843)
E325	QFEKIEQFVYS	3	Homo sapiens, Bos taurus, Rattus norvegicus
E325	QFEKIEQFVLC	1	Caenorhabditis elegans
E325	QFEKIEQFCIT	1	Arabidopsis thaliana
E325	AFEKIEQFVIT	1	Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
E325	AFEKIEQFVLT	1	Schizosaccharomyces pombe (strain 972 / ATCC 24843)
E391	SGAFRELVSCS	3	Homo sapiens, Bos taurus, Rattus norvegicus
E391	SGAYRELVSCS	1	Caenorhabditis elegans
E391	SETFRELVSCS	1	Arabidopsis thaliana
E391	QKEYKELVSCS	1	Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
E391	QGEYKELVSCS	1	Schizosaccharomyces pombe (strain 972 / ATCC 24843)
F316	DTRGIFRVHQF	4	Homo sapiens, Caenorhabditis elegans, Bos taurus, Rattus norvegicus
F316	DTLGIFRVHQF	1	Arabidopsis thaliana
F316	DAWGVFRVHAF	1	Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
F316	DAWGIFRVHAF	1	Schizosaccharomyces pombe (strain 972 / ATCC 24843)
F321	FRVHQFEKIEQ	5	Homo sapiens, Caenorhabditis elegans, Bos taurus, Rattus norvegicus, Arabidopsis thaliana
F321	FRVHAFEKIEQ	2	Saccharomyces cerevisiae (strain ATCC 204508 / S288c), Schizosaccharomyces pombe (strain 972 / ATCC 24843)
F48	WRRCRFRADNL	3	Homo sapiens, Bos taurus, Rattus norvegicus
F48	WRKERFVADQL	1	Caenorhabditis elegans
F48	WRQRQFEVDSF	1	Arabidopsis thaliana
F48	WVKTRFELDEL	1	Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
F48	WVSLRFELDNT	1	Schizosaccharomyces pombe (strain 972 / ATCC 24843)
I64	LCSKTIGEKMK	3	Homo sapiens, Bos taurus, Rattus norvegicus
I64	AISKAIGEKMK	1	Caenorhabditis elegans
I64	KLNKQVAQLKI	1	Arabidopsis thaliana
I64	KLQKDIGLKFK	1	Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
I64	RVQKEIGLKMK	1	Schizosaccharomyces pombe (strain 972 / ATCC 24843)
K323	VHQFEKIEQFV	4	Homo sapiens, Caenorhabditis elegans, Bos taurus, Rattus norvegicus
K323	VHAFEKIEQFV	2	Saccharomyces cerevisiae (strain ATCC 204508 / S288c), Schizosaccharomyces pombe (strain 972 / ATCC 24843)
K323	VHQFEKIEQFC	1	Arabidopsis thaliana
K376	HAASKKLDLEA	3	Homo sapiens, Bos taurus, Rattus norvegicus
K376	NAAAKKYDLEA	2	Saccharomyces cerevisiae (strain ATCC 204508 / S288c), Schizosaccharomyces pombe (strain 972 / ATCC 24843)
K376	NAAAKKFDLEA	1	Caenorhabditis elegans
K376	DAAAKKYDLEA	1	Arabidopsis thaliana
K55	ADNLNKLKNLC	3	Homo sapiens, Bos taurus, Rattus norvegicus
K55	ADQLNRQKNAI	1	Caenorhabditis elegans
K55	VDSFRKEFNKL	1	Arabidopsis thaliana
K55	LDELNKKFNKL	1	Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
K55	LDNTNKSINRV	1	Schizosaccharomyces pombe (strain 972 / ATCC 24843)
L392	GAFRELVSCSN	3	Homo sapiens, Bos taurus, Rattus norvegicus
L392	GAYRELVSCSN	1	Caenorhabditis elegans
L392	ETFRELVSCSN	1	Arabidopsis thaliana
L392	KEYKELVSCSN	1	Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
L392	GEYKELVSCSN	1	Schizosaccharomyces pombe (strain 972 / ATCC 24843)
N427	FVHMLNATMCA	4	Homo sapiens, Caenorhabditis elegans, Bos taurus, Rattus norvegicus
N427	YVHMLNSTLTA	1	Arabidopsis thaliana
N427	YVHCLNSTLAA	1	Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
N427	YVHCLNSTLCA	1	Schizosaccharomyces pombe (strain 972 / ATCC 24843)
N54	RADNLNKLKNL	3	Homo sapiens, Bos taurus, Rattus norvegicus
N54	VADQLNRQKNA	1	Caenorhabditis elegans
N54	EVDSFRKEFNK	1	Arabidopsis thaliana
N54	ELDELNKKFNK	1	Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
N54	ELDNTNKSINR	1	Schizosaccharomyces pombe (strain 972 / ATCC 24843)
N58	LNKLKNLCSKT	3	Homo sapiens, Bos taurus, Rattus norvegicus
N58	LNRQKNAISKA	1	Caenorhabditis elegans
N58	FRKEFNKLNKQ	1	Arabidopsis thaliana
N58	LNKKFNKLQKD	1	Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
N58	TNKSINRVQKE	1	Schizosaccharomyces pombe (strain 972 / ATCC 24843)
R302	LSTCFRQEVGS	2	Homo sapiens, Bos taurus
R302	VSTCFRQEVGS	1	Caenorhabditis elegans
R302	FSTCFRQEVGS	1	Rattus norvegicus
R302	YSSCFRKEAGS	1	Arabidopsis thaliana
R302	YSSCFRREAGS	1	Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
R302	YSTCYRREAGS	1	Schizosaccharomyces pombe (strain 972 / ATCC 24843)
R317	TRGIFRVHQFE	4	Homo sapiens, Caenorhabditis elegans, Bos taurus, Rattus norvegicus
R317	TLGIFRVHQFE	1	Arabidopsis thaliana
R317	AWGVFRVHAFE	1	Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
R317	AWGIFRVHAFE	1	Schizosaccharomyces pombe (strain 972 / ATCC 24843)
R435	MCATTRTICAI	3	Homo sapiens, Bos taurus, Rattus norvegicus
R435	MCATTRVICAI	1	Caenorhabditis elegans
R435	LTATERTICCI	1	Arabidopsis thaliana
R435	LAATQRALCCI	1	Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
R435	LCATERALCCI	1	Schizosaccharomyces pombe (strain 972 / ATCC 24843)
R44	ADSEWRRCRFR	3	Homo sapiens, Bos taurus, Rattus norvegicus
R44	LDEKWRKERFV	1	Caenorhabditis elegans
R44	LDKEWRQRQFE	1	Arabidopsis thaliana
R44	DYKDWVKTRFE	1	Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
R44	MYKEWVSLRFE	1	Schizosaccharomyces pombe (strain 972 / ATCC 24843)
R9	DLDLFRVDKGG	3	Homo sapiens, Bos taurus, Rattus norvegicus
R9	DIDMFRTEKGG	1	Caenorhabditis elegans
R9	DINLFREEKGN	1	Arabidopsis thaliana
R9	DINQFIEDKGG	1	Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
R9	DINLFQVEKGG	1	Schizosaccharomyces pombe (strain 972 / ATCC 24843)
S394	FRELVSCSNCT	4	Homo sapiens, Bos taurus, Rattus norvegicus, Arabidopsis thaliana
S394	YKELVSCSNCT	2	Saccharomyces cerevisiae (strain ATCC 204508 / S288c), Schizosaccharomyces pombe (strain 972 / ATCC 24843)
S394	YRELVSCSNCL	1	Caenorhabditis elegans
S61	LKNLCSKTIGE	3	Homo sapiens, Bos taurus, Rattus norvegicus
S61	QKNAISKAIGE	1	Caenorhabditis elegans
S61	EFNKLNKQVAQ	1	Arabidopsis thaliana
S61	KFNKLQKDIGL	1	Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
S61	SINRVQKEIGL	1	Schizosaccharomyces pombe (strain 972 / ATCC 24843)
T271	KYLIATSEQPI	5	Homo sapiens, Caenorhabditis elegans, Bos taurus, Rattus norvegicus, Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
T271	KYLIATAEQPL	1	Arabidopsis thaliana
T271	RYLIATSEQPI	1	Schizosaccharomyces pombe (strain 972 / ATCC 24843)
T429	HMLNATMCATT	4	Homo sapiens, Caenorhabditis elegans, Bos taurus, Rattus norvegicus
T429	HMLNSTLTATE	1	Arabidopsis thaliana
T429	HCLNSTLAATQ	1	Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
T429	HCLNSTLCATE	1	Schizosaccharomyces pombe (strain 972 / ATCC 24843)
T434	TMCATTRTICA	3	Homo sapiens, Bos taurus, Rattus norvegicus
T434	TMCATTRVICA	1	Caenorhabditis elegans
T434	TLTATERTICC	1	Arabidopsis thaliana
T434	TLAATQRALCC	1	Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
T434	TLCATERALCC	1	Schizosaccharomyces pombe (strain 972 / ATCC 24843)
V318	RGIFRVHQFEK	4	Homo sapiens, Caenorhabditis elegans, Bos taurus, Rattus norvegicus
V318	LGIFRVHQFEK	1	Arabidopsis thaliana
V318	WGVFRVHAFEK	1	Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
V318	WGIFRVHAFEK	1	Schizosaccharomyces pombe (strain 972 / ATCC 24843)
V393	AFRELVSCSNC	3	Homo sapiens, Bos taurus, Rattus norvegicus
V393	EYKELVSCSNC	2	Saccharomyces cerevisiae (strain ATCC 204508 / S288c), Schizosaccharomyces pombe (strain 972 / ATCC 24843)
V393	AYRELVSCSNC	1	Caenorhabditis elegans
V393	TFRELVSCSNC	1	Arabidopsis thaliana
W43	KADSEWRRCRF	3	Homo sapiens, Bos taurus, Rattus norvegicus
W43	ELDEKWRKERF	1	Caenorhabditis elegans
W43	KLDKEWRQRQF	1	Arabidopsis thaliana
W43	SDYKDWVKTRF	1	Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
W43	EMYKEWVSLRF	1	Schizosaccharomyces pombe (strain 972 / ATCC 24843)