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 PNPO
Gene summary
Basic gene Info.Gene symbolPNPO
Gene namepyridoxamine 5'-phosphate oxidase
SynonymsHEL-S-302|PDXPO
CytomapUCSC genome browser: 17q21.32
Type of geneprotein-coding
RefGenesNM_018129.3,
Descriptionepididymis secretory protein Li 302pyridoxal 5'-phosphate synthasepyridoxamine-phosphate oxidasepyridoxine 5'-phosphate oxidasepyridoxine-5'-phosphate oxidase
Modification date20141207
dbXrefs MIM : 603287
HGNC : HGNC
HPRD : 04476
ProteinUniProt: Q9NVS9
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_PNPO
BioGPS: 55163
PathwayNCI Pathway Interaction Database: PNPO
KEGG: PNPO
REACTOME: PNPO
Pathway Commons: PNPO
ContextiHOP: PNPO
ligand binding site mutation search in PubMed: PNPO
UCL Cancer Institute: PNPO
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 PNPO
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
Y157Y157HBLCA1
M96M96IBRCA1
E251R249CCOAD1
G101G103WLUAD1
Q174Q174HSTAD1
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 PNPO
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
M96M96I0.27215888
Y157Y157H-0.87894165
Q174Q174H-0.79288507
E251R249C-0.37132064
G101G103W-0.32011937
(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 PNPO from PDB

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Differential gene expression and gene-gene network for PNPO
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 PNPO and the right PPI network was created from samples without mutations in the LBS of PNPO. 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 PNPO
Gene level disease information (DisGeNet)
Disease IDDisease name# PubMedAssociation type
umls:C1864723Pyridoxamine 5-Prime-Phosphate Oxidase Deficiency1Biomarker, GeneticVariation
umls:C0038220Status Epilepticus1Biomarker

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

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Pharmacological information for PNPO
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
ExperimentalDB03247Riboflavin MonophosphateSmall molecule
ExperimentalDB03345Beta-MercaptoethanolSmall molecule

Gene-centered ligand-gene interaction network

Ligands binding to mutated ligand binding site of PNPO go to BioLip
Ligand IDLigand short nameLigand long namePDB IDPDB namemutLBS
PO4PHOSPHATE ION3hy8AE251
PO4PHOSPHATE ION3hy8AG101 Y157
FMNFLAVIN MONONUCLEOTIDE1nrgAM96 Q174
FMNFLAVIN MONONUCLEOTIDE3hy8AM96 Q174
PO4PHOSPHATE ION1nrgAQ174
PLPPYRIDOXAL 5'-PHOSPHATE1nrgAY157 Q174


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Conservation information for LBS of PNPO
Multiple alignments for Q9NVS9 in multiple species
LBSAA sequence# speciesSpecies
E114FTNF-ESRKGK2Homo sapiens, Bos taurus
E114FTNY-ESRKGK2Mus musculus, Rattus norvegicus
E114YSNWGTSRKAH1Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
E114FTNLGTSKKAK1Schizosaccharomyces pombe (strain 972 / ATCC 24843)
E114YTNY-TSRKGN1Caenorhabditis elegans
E153KLPEEEAECYF2Homo sapiens, Bos taurus
E153KLPEKEAENYF2Mus musculus, Rattus norvegicus
E153HVNRETSERYF1Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
E153RLSREETEEYF1Schizosaccharomyces pombe (strain 972 / ATCC 24843)
E153KLPDEMAVAYW1Caenorhabditis elegans
E251MTHHGEEDWVY2Mus musculus, Rattus norvegicus
E251MTHRGEEDWLY1Homo sapiens
E251--------WKV1Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
E251-----DEDYEL1Schizosaccharomyces pombe (strain 972 / ATCC 24843)
E251--------WLL1Caenorhabditis elegans
E251MTHRGEEDWVY1Bos taurus
E77DIG--EANAMC3Homo sapiens, Mus musculus, Rattus norvegicus
E77RET--LPEAIT1Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
E77GIK--SPESTT1Schizosaccharomyces pombe (strain 972 / ATCC 24843)
E77DLTFEEINAVS1Caenorhabditis elegans
E77DIM--EANAMC1Bos taurus
F110DGFRFFTNF-E2Homo sapiens, Bos taurus
F110DGFRFFTNY-E2Mus musculus, Rattus norvegicus
F110RGFTIYSNWGT1Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
F110RGFIIFTNLGT1Schizosaccharomyces pombe (strain 972 / ATCC 24843)
F110TGFSFYTNY-T1Caenorhabditis elegans
G101MLLLKGFGKDG3Homo sapiens, Mus musculus, Rattus norvegicus
G101ILLFKELDHRG1Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
G101LVLLKELDHRG1Schizosaccharomyces pombe (strain 972 / ATCC 24843)
G101MVLLKAYTPTG1Caenorhabditis elegans
G101MVLLKGFGKDG1Bos taurus
K100RMLLLKGFGKD3Homo sapiens, Mus musculus, Rattus norvegicus
K100RILLFKELDHR1Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
K100RLVLLKELDHR1Schizosaccharomyces pombe (strain 972 / ATCC 24843)
K100RMVLLKAYTPT1Caenorhabditis elegans
K100RMVLLKGFGKD1Bos taurus
K117F-ESRKGKELD2Homo sapiens, Bos taurus
K117Y-ESRKGKELD2Mus musculus, Rattus norvegicus
K117WGTSRKAHDIA1Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
K117LGTSKKAKDLK1Schizosaccharomyces pombe (strain 972 / ATCC 24843)
K117Y-TSRKGNQLE1Caenorhabditis elegans
K119ESRKGKELDSN4Homo sapiens, Mus musculus, Rattus norvegicus, Bos taurus
K119TSRKAHDIATN1Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
K119TSKKAKDLKSN1Schizosaccharomyces pombe (strain 972 / ATCC 24843)
K119TSRKGNQLEEN1Caenorhabditis elegans
K60SLDPVKQFAAW2Homo sapiens, Bos taurus
K60SLDPMKQFASW2Mus musculus, Rattus norvegicus
K60D-DPIDLFTKW1Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
K60GKDPLVLFNQW1Schizosaccharomyces pombe (strain 972 / ATCC 24843)
K60TTSPFELFDIW1Caenorhabditis elegans
L97PSARMLLLKGF3Homo sapiens, Mus musculus, Rattus norvegicus
L97VSSRILLFKEL1Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
L97VSSRLVLLKEL1Schizosaccharomyces pombe (strain 972 / ATCC 24843)
L97PSSRMVLLKAY1Caenorhabditis elegans
L97PSARMVLLKGF1Bos taurus
L98SARMLLLKGFG3Homo sapiens, Mus musculus, Rattus norvegicus
L98SSRILLFKELD1Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
L98SSRLVLLKELD1Schizosaccharomyces pombe (strain 972 / ATCC 24843)
L98SSRMVLLKAYT1Caenorhabditis elegans
L98SARMVLLKGFG1Bos taurus
M96KPSARMLLLKG3Homo sapiens, Mus musculus, Rattus norvegicus
M96RVSSRILLFKE1Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
M96RVSSRLVLLKE1Schizosaccharomyces pombe (strain 972 / ATCC 24843)
M96RPSSRMVLLKA1Caenorhabditis elegans
M96KPSARMVLLKG1Bos taurus
P162YFHSRPKSSQI4Homo sapiens, Mus musculus, Rattus norvegicus, Bos taurus
P162YFKTRPRGSKI1Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
P162YFKTRPRNSRI1Schizosaccharomyces pombe (strain 972 / ATCC 24843)
P162YWNSRPVASRI1Caenorhabditis elegans
Q174AVVSHQSSVIP2Homo sapiens, Bos taurus
Q174AVVSRQSSVIP2Mus musculus, Rattus norvegicus
Q174AWASRQSDVIK1Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
Q174AWASPQSEVIA1Schizosaccharomyces pombe (strain 972 / ATCC 24843)
Q174SKSSDQSKVVP1Caenorhabditis elegans
R108GKDGFRFFTNF2Homo sapiens, Bos taurus
R108GKDGFRFFTNY2Mus musculus, Rattus norvegicus
R108DHRGFTIYSNW1Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
R108DHRGFIIFTNL1Schizosaccharomyces pombe (strain 972 / ATCC 24843)
R108TPTGFSFYTNY1Caenorhabditis elegans
R116NF-ESRKGKEL2Homo sapiens, Bos taurus
R116NY-ESRKGKEL2Mus musculus, Rattus norvegicus
R116NWGTSRKAHDI1Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
R116NLGTSKKAKDL1Schizosaccharomyces pombe (strain 972 / ATCC 24843)
R116NY-TSRKGNQL1Caenorhabditis elegans
R161CYFHSRPKSSQ2Homo sapiens, Bos taurus
R161NYFHSRPKSSQ2Mus musculus, Rattus norvegicus
R161RYFKTRPRGSK1Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
R161EYFKTRPRNSR1Schizosaccharomyces pombe (strain 972 / ATCC 24843)
R161AYWNSRPVASR1Caenorhabditis elegans
R95GKPSARMLLLK3Homo sapiens, Mus musculus, Rattus norvegicus
R95GRVSSRILLFK1Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
R95GRVSSRLVLLK1Schizosaccharomyces pombe (strain 972 / ATCC 24843)
R95LRPSSRMVLLK1Caenorhabditis elegans
R95GKPSARMVLLK1Bos taurus
S115TNF-ESRKGKE2Homo sapiens, Bos taurus
S115TNY-ESRKGKE2Mus musculus, Rattus norvegicus
S115SNWGTSRKAHD1Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
S115TNLGTSKKAKD1Schizosaccharomyces pombe (strain 972 / ATCC 24843)
S115TNY-TSRKGNQ1Caenorhabditis elegans
S165SRPKSSQIGAV4Homo sapiens, Mus musculus, Rattus norvegicus, Bos taurus
S165TRPRGSKIGAW1Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
S165TRPRNSRIGAW1Schizosaccharomyces pombe (strain 972 / ATCC 24843)
S165SRPVASRIGSK1Caenorhabditis elegans
S175VVSHQSSVIPD2Homo sapiens, Bos taurus
S175VVSRQSSVIPD2Mus musculus, Rattus norvegicus
S175WASRQSDVIKN1Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
S175WASPQSEVIAD1Schizosaccharomyces pombe (strain 972 / ATCC 24843)
S175KSSDQSKVVPD1Caenorhabditis elegans
S55ETHLTSLDPVK2Homo sapiens, Bos taurus
S55EKQLTD-DPID1Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
S55RDALMGKDPLV1Schizosaccharomyces pombe (strain 972 / ATCC 24843)
S55ESKLPTTSPFE1Caenorhabditis elegans
S55ETHLTSLDPMK1Mus musculus
S55EAHLTSLDPMK1Rattus norvegicus
T111GFRFFTNF-ES2Homo sapiens, Bos taurus
T111GFRFFTNY-ES2Mus musculus, Rattus norvegicus
T111GFTIYSNWGTS1Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
T111GFIIFTNLGTS1Schizosaccharomyces pombe (strain 972 / ATCC 24843)
T111GFSFYTNY-TS1Caenorhabditis elegans
Y157EEAECYFHSRP2Homo sapiens, Bos taurus
Y157KEAENYFHSRP2Mus musculus, Rattus norvegicus
Y157ETSERYFKTRP1Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
Y157EETEEYFKTRP1Schizosaccharomyces pombe (strain 972 / ATCC 24843)
Y157EMAVAYWNSRP1Caenorhabditis elegans


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