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 ME2
Gene summary
Basic gene Info.Gene symbolME2
Gene namemalic enzyme 2, NAD(+)-dependent, mitochondrial
SynonymsODS1
CytomapUCSC genome browser: 18q21
Type of geneprotein-coding
RefGenesNM_001168335.1,
NM_002396.4,
DescriptionNAD-MENAD-dependent malic enzyme, mitochondrialmalate dehydrogenasepyruvic-malic carboxylase
Modification date20141207
dbXrefs MIM : 154270
HGNC : HGNC
HPRD : 01103
ProteinUniProt: P23368
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_ME2
BioGPS: 4200
PathwayNCI Pathway Interaction Database: ME2
KEGG: ME2
REACTOME: ME2
Pathway Commons: ME2
ContextiHOP: ME2
ligand binding site mutation search in PubMed: ME2
UCL Cancer Institute: ME2
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


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Ligand binding site mutations for ME2

Cancer type specific mutLBS sorted by frequency
LBSAAchange of nsSNVCancer type# samples
R245R245GCOAD1
G446S447GCOAD1
R91,L95E93DCOAD1
N482R484QCOAD1
R91R91TLUAD1
E255Q253HLUSC1
R542F541LLUSC1
R542Y543CSTAD1
K156A157VSTAD1
D279D278NUCEC1
R91,L95E93DUCEC1
R67R67QUCEC1
N421T423AUCEC1
R542F541LUCEC1
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 ME2
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
R245R245G-1.8657954
N482R484Q-1.5022941
E255Q253H-1.2911829
G446S447G-1.2435972
R67R67Q-1.0389538
R91R91T-0.86783347
N421T423A-0.74259461
R91E93D-0.71041434
L95E93D-0.71041434
D279D278N-0.70361679
K156A157V-0.66049122
R542Y543C-0.65687365
R542F541L-0.62324647
(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 ME2 from PDB

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Differential gene expression and gene-gene network for ME2
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 ME2 and the right PPI network was created from samples without mutations in the LBS of ME2. 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 ME2
Gene level disease information (DisGeNet)
Disease IDDisease name# PubMedAssociation type
umls:C0270850Epilepsy, Idiopathic Generalized2Biomarker, GeneticVariation
umls:C0017661Glomerulonephritis, IGA1Biomarker

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

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Pharmacological information for ME2
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
NutraceuticalDB00157NADHSmall molecule
ExperimentalDB01677FumarateSmall molecule
ExperimentalDB03499Malate IonSmall molecule
ExperimentalDB03589Alpha-Ketomalonic AcidSmall molecule
ExperimentalDB03680TartronateSmall molecule

Gene-centered ligand-gene interaction network

Ligands binding to mutated ligand binding site of ME2 go to BioLip
Ligand IDLigand short nameLigand long namePDB IDPDB namemutLBS
NADNAD ZWITTERION1do8AD279 N421 G446
NADNAD ZWITTERION1efkAD279 N421 G446
NADNAD ZWITTERION1efkBD279 N421 G446
NADNAD ZWITTERION1efkCD279 N421 G446
NADNAD ZWITTERION1efkDD279 N421 G446
NADNAD ZWITTERION1eflAD279 N421 G446
NADNAD ZWITTERION1eflDD279 N421 G446
NAINADH1pj2AD279 N421 G446
NADNAD ZWITTERION1pj3AD279 N421 G446
MNMANGANESE(2+)1do8AE255 D279
MGMAGNESIUM(2+)1efkAE255 D279
MGMAGNESIUM(2+)1efkBE255 D279
MGMAGNESIUM(2+)1efkCE255 D279
MGMAGNESIUM(2+)1efkDE255 D279
MGMAGNESIUM(2+)1eflAE255 D279
MGMAGNESIUM(2+)1eflBE255 D279
MGMAGNESIUM(2+)1eflCE255 D279
MGMAGNESIUM(2+)1eflDE255 D279
MNMANGANESE(2+)1gz3AE255 D279
MNMANGANESE(2+)1gz3BE255 D279
MNMANGANESE(2+)1gz3CE255 D279
MNMANGANESE(2+)1gz3DE255 D279
MNMANGANESE(2+)1gz4AE255 D279
MNMANGANESE(2+)1gz4BE255 D279
MNMANGANESE(2+)1gz4CE255 D279
MNMANGANESE(2+)1gz4DE255 D279
MNMANGANESE(2+)1pj2AE255 D279
MNMANGANESE(2+)1pj3AE255 D279
MNMANGANESE(2+)1pj4AE255 D279
LULUTETIUM(3+)1pjlAE255 D279
OXLOXALATE(2-)1do8AE255 D279 N421
MAKOXOMALONIC ACID1efkAE255 D279 N421
MAKOXOMALONIC ACID1efkBE255 D279 N421
MAKOXOMALONIC ACID1efkCE255 D279 N421
MAKOXOMALONIC ACID1efkDE255 D279 N421
TTNHYDROXYMALONATE(2-)1eflAE255 D279 N421
TTNHYDROXYMALONATE(2-)1eflBE255 D279 N421
TTNHYDROXYMALONATE(2-)1eflCE255 D279 N421
TTNHYDROXYMALONATE(2-)1eflDE255 D279 N421
OXLOXALATE(2-)1gz3AE255 D279 N421
OXLOXALATE(2-)1gz3BE255 D279 N421
OXLOXALATE(2-)1gz3CE255 D279 N421
OXLOXALATE(2-)1gz3DE255 D279 N421
TTNHYDROXYMALONATE(2-)1gz4AE255 D279 N421
TTNHYDROXYMALONATE(2-)1gz4BE255 D279 N421
TTNHYDROXYMALONATE(2-)1gz4CE255 D279 N421
TTNHYDROXYMALONATE(2-)1gz4DE255 D279 N421
MLT(R)-MALATE(2-)1pj2AE255 D279 N421
PYRPYRUVIC ACID1pj3AE255 D279 N421
MLT(R)-MALATE(2-)1pj4AE255 D279 N421
NADNAD ZWITTERION1efkCK156
NADNAD ZWITTERION1eflCK156 N482 R542
ATPATP1gz4AK156 N482 R542
ATPATP1gz4DK156 N482 R542
NADNAD ZWITTERION1qr6AK156 N482 R542
NADNAD ZWITTERION1efkBK156 R542
NADNAD ZWITTERION1eflBK156 R542
ATPATP1gz4BK156 R542
ATPATP1gz4CK156 R542
NADNAD ZWITTERION1eflBN421 G446
NADNAD ZWITTERION1eflCN421 G446
NADNAD ZWITTERION1pjlAN421 G446
NADNAD ZWITTERION1qr6AN421 G446
NADNAD ZWITTERION1do8AN482 R542
NADNAD ZWITTERION1efkAN482 R542
NADNAD ZWITTERION1efkDN482 R542
NADNAD ZWITTERION1eflDN482 R542
NAINADH1pj2AN482 R542
NADNAD ZWITTERION1pj3AN482 R542
NADNAD ZWITTERION1do8AR245
NADNAD ZWITTERION1efkAR245
NADNAD ZWITTERION1efkBR245
NADNAD ZWITTERION1efkDR245
NADNAD ZWITTERION1eflAR245
NADNAD ZWITTERION1eflBR245
NADNAD ZWITTERION1eflDR245
NAINADH1pj2AR245
NADNAD ZWITTERION1pj3AR245
NADNAD ZWITTERION1eflAR542
ATPATP1pj4AR542
NADNAD ZWITTERION1pjlAR542
FUMFUMARIC ACID1gz3CR67 R91
FUMFUMARIC ACID1gz3DR67 R91
FUMFUMARIC ACID1pj2AR67 R91
FUMFUMARIC ACID1gz3AR67 R91 L95
FUMFUMARIC ACID1gz3BR67 R91 L95
FUMFUMARIC ACID1gz4AR67 R91 L95
FUMFUMARIC ACID1gz4BR67 R91 L95
FUMFUMARIC ACID1gz4CR67 R91 L95
FUMFUMARIC ACID1gz4DR67 R91 L95
FUMFUMARIC ACID1pj3AR67 R91 L95
FUMFUMARIC ACID1pj4AR67 R91 L95


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Conservation information for LBS of ME2
Multiple alignments for P23368 in multiple species
LBSAA sequence# speciesSpecies
A312ILFLGAGEAAL2Homo sapiens, Mus musculus
A312FLFLGAGEAGT2Arabidopsis thaliana, Arabidopsis thaliana
A315LGAGEAALGIA2Homo sapiens, Mus musculus
A315LGAGEAGTGIA2Arabidopsis thaliana, Arabidopsis thaliana
A393TIIGVAGAGRL1Homo sapiens
A393VLIGTSGVGKT1Arabidopsis thaliana
A393VLIGTSGVGQT1Arabidopsis thaliana
A393VIIGVAGAGPL1Mus musculus
A395IGVAGAGRLFT1Homo sapiens
A395IGTSGVGKTFT1Arabidopsis thaliana
A395IGTSGVGQTFT1Arabidopsis thaliana
A395IGVAGAGPLFT1Mus musculus
D244MKAITDRYGRN2Homo sapiens, Mus musculus
D244MCAVKQNYGEK2Arabidopsis thaliana, Arabidopsis thaliana
D256LIQFEDFGNHN2Homo sapiens, Mus musculus
D256LVQFEDFANHH1Arabidopsis thaliana
D256LVQFEDFANHN1Arabidopsis thaliana
D279CTFNDDIQGTA2Homo sapiens, Mus musculus
D279LVFNDDIQGTA2Arabidopsis thaliana, Arabidopsis thaliana
D345KIWLVDSKGLI2Arabidopsis thaliana, Arabidopsis thaliana
D345KIWMFDKYGLL1Homo sapiens
D345KIWMFDKSGLL1Mus musculus
E255TLIQFEDFGNH2Homo sapiens, Mus musculus
E255VLVQFEDFANH2Arabidopsis thaliana, Arabidopsis thaliana
E314FLGAGEAALGI2Homo sapiens, Mus musculus
E314FLGAGEAGTGI2Arabidopsis thaliana, Arabidopsis thaliana
F127QYGHIFRRPKG2Homo sapiens, Mus musculus
F127KYGSIYRRPQG1Arabidopsis thaliana
F127KYGSIFRKPQG1Arabidopsis thaliana
G168GERILGLGDLG4Homo sapiens, Arabidopsis thaliana, Arabidopsis thaliana, Mus musculus
G192YTALGGIRPSA2Arabidopsis thaliana, Arabidopsis thaliana
G192YTACAGIRPDR1Homo sapiens
G192YTACAGIQPEK1Mus musculus
G247ITDRYGRNTLI2Homo sapiens, Mus musculus
G247VKQNYGEKVLV2Arabidopsis thaliana, Arabidopsis thaliana
G311KILFLGAGEAA2Homo sapiens, Mus musculus
G311TFLFLGAGEAG2Arabidopsis thaliana, Arabidopsis thaliana
G313LFLGAGEAALG2Homo sapiens, Mus musculus
G313LFLGAGEAGTG2Arabidopsis thaliana, Arabidopsis thaliana
G394IIGVAGAGRLF1Homo sapiens
G394LIGTSGVGKTF1Arabidopsis thaliana
G394LIGTSGVGQTF1Arabidopsis thaliana
G394IIGVAGAGPLF1Mus musculus
G446CLFASGSPFGP1Homo sapiens
G446AIFASGSPFDP1Arabidopsis thaliana
G446AIFGSGSPFDP1Arabidopsis thaliana
G446CLFASGSPFEP1Mus musculus
G465FTPGQGNNVYI1Homo sapiens
G465FTPGQANNCYI1Arabidopsis thaliana
G465YLPGQANNCYI1Arabidopsis thaliana
G465FTPGQGNNAYI1Mus musculus
H154NWPENHVKAVV2Homo sapiens, Mus musculus
H154NWPQRGIQVIV2Arabidopsis thaliana, Arabidopsis thaliana
I193TALGGIRPSAC2Arabidopsis thaliana, Arabidopsis thaliana
I193TACAGIRPDRC1Homo sapiens
I193TACAGIQPEKC1Mus musculus
I479LGLGLIMSGAI2Arabidopsis thaliana, Arabidopsis thaliana
I479VALAVILCNTR1Homo sapiens
I479VALAVILCEAR1Mus musculus
I88IYIMGIQERNE2Homo sapiens, Mus musculus
I88MALMDLQERNE2Arabidopsis thaliana, Arabidopsis thaliana
K156PENHVKAVVVT2Homo sapiens, Mus musculus
K156PQRGIQVIVVT2Arabidopsis thaliana, Arabidopsis thaliana
K183GIPVGKLCLYT2Homo sapiens, Mus musculus
K183GIPVGKLSLYT2Arabidopsis thaliana, Arabidopsis thaliana
K346IWLVDSKGLIV2Arabidopsis thaliana, Arabidopsis thaliana
K346IWMFDKYGLLV1Homo sapiens
K346IWMFDKSGLLV1Mus musculus
L167DGERILGLGDL4Homo sapiens, Arabidopsis thaliana, Arabidopsis thaliana, Mus musculus
L310HKILFLGAGEA2Homo sapiens, Mus musculus
L310HTFLFLGAGEA2Arabidopsis thaliana, Arabidopsis thaliana
L398AGAGRLFTPDV1Homo sapiens
L398SGVGKTFTKEV1Arabidopsis thaliana
L398SGVGQTFTKEV1Arabidopsis thaliana
L398AGAGPLFTHGV1Mus musculus
L419PLILALSNPTS2Arabidopsis thaliana, Arabidopsis thaliana
L419PVIFALSNPTA1Homo sapiens
L419PIIFALSNPTA1Mus musculus
L480GLGLIMSGAIR2Arabidopsis thaliana, Arabidopsis thaliana
L480ALAVILCNTRH1Homo sapiens
L480ALAVILCEARH1Mus musculus
L95ERNEKLFYRIL2Homo sapiens, Mus musculus
L95ERNERLFYKLL2Arabidopsis thaliana, Arabidopsis thaliana
N249DRYGRNTLIQF2Homo sapiens, Mus musculus
N249QNYGEKVLVQF2Arabidopsis thaliana, Arabidopsis thaliana
N259FEDFGNHNAFR2Homo sapiens, Mus musculus
N259FEDFANHHAFE1Arabidopsis thaliana
N259FEDFANHNAFD1Arabidopsis thaliana
N421IFALSNPTAQA2Homo sapiens, Mus musculus
N421ILALSNPTSQA2Arabidopsis thaliana, Arabidopsis thaliana
N466TPGQGNNVYIF1Homo sapiens
N466TPGQANNCYIF1Arabidopsis thaliana
N466LPGQANNCYIF1Arabidopsis thaliana
N466TPGQGNNAYIF1Mus musculus
N467PGQANNCYIFP2Arabidopsis thaliana, Arabidopsis thaliana
N467PGQGNNVYIFP1Homo sapiens
N467PGQGNNAYIFP1Mus musculus
N482GLIMSGAIRVR2Arabidopsis thaliana, Arabidopsis thaliana
N482AVILCNTRHIS1Homo sapiens
N482AVILCEARHIS1Mus musculus
Q64ETQDIQALRFH2Homo sapiens, Mus musculus
Q64LSQDVQERKVM2Arabidopsis thaliana, Arabidopsis thaliana
R128YGHIFRRPKGL2Homo sapiens, Mus musculus
R128YGSIYRRPQGL1Arabidopsis thaliana
R128YGSIFRKPQGL1Arabidopsis thaliana
R165VTDGERILGLG4Homo sapiens, Arabidopsis thaliana, Arabidopsis thaliana, Mus musculus
R194ALGGIRPSACL2Arabidopsis thaliana, Arabidopsis thaliana
R194ACAGIRPDRCL1Homo sapiens
R194ACAGIQPEKCL1Mus musculus
R197GIRPSACLPIT2Arabidopsis thaliana, Arabidopsis thaliana
R197GIRPDRCLPVC1Homo sapiens
R197GIQPEKCLPVC1Mus musculus
R245KAITDRYGRNT2Homo sapiens, Mus musculus
R245CAVKQNYGEKV2Arabidopsis thaliana, Arabidopsis thaliana
R248TDRYGRNTLIQ2Homo sapiens, Mus musculus
R248KQNYGEKVLVQ2Arabidopsis thaliana, Arabidopsis thaliana
R542NKMAFRYPEPE2Homo sapiens, Mus musculus
R542LGLASNLPRPK1Arabidopsis thaliana
R542LGLASNLPRAK1Arabidopsis thaliana
R556KYVKERTWRSE1Homo sapiens
R556KMAESCMYSPV1Arabidopsis thaliana
R556KFAESSMYSPV1Arabidopsis thaliana
R556RYVRERIWRSN1Mus musculus
R67DIQALRFHRNL2Homo sapiens, Mus musculus
R67DVQERKVMHNL2Arabidopsis thaliana, Arabidopsis thaliana
R91MGIQERNEKLF2Homo sapiens, Mus musculus
R91MDLQERNERLF2Arabidopsis thaliana, Arabidopsis thaliana
S420LILALSNPTSQ2Arabidopsis thaliana, Arabidopsis thaliana
S420VIFALSNPTAQ1Homo sapiens
S420IIFALSNPTAQ1Mus musculus
T113MPIVYTPTVGL2Homo sapiens, Mus musculus
T113LPVVYTPTVGE2Arabidopsis thaliana, Arabidopsis thaliana
T283DDIQGTAAVAL2Homo sapiens, Mus musculus
T283DDIQGTASVVL2Arabidopsis thaliana, Arabidopsis thaliana
V392STIIGVAGAGR1Homo sapiens
V392TVLIGTSGVGK1Arabidopsis thaliana
V392TVLIGTSGVGQ1Arabidopsis thaliana
V392SVIIGVAGAGP1Mus musculus
Y112LMPIVYTPTVG2Homo sapiens, Mus musculus
Y112LLPVVYTPTVG2Arabidopsis thaliana, Arabidopsis thaliana
Y246AITDRYGRNTL2Homo sapiens, Mus musculus
Y246AVKQNYGEKVL2Arabidopsis thaliana, Arabidopsis thaliana
Y552EDKAKYVKERT1Homo sapiens
Y552KDLVKMAESCM1Arabidopsis thaliana
Y552KDLVKFAESSM1Arabidopsis thaliana
Y552EDKARYVRERI1Mus musculus


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