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Protein

Lactase-phlorizin hydrolase

Gene

LCT

Organism
Homo sapiens (Human)
Status
Reviewed-Annotation score: Annotation score: 5 out of 5-Experimental evidence at protein leveli

Functioni

LPH splits lactose in the small intestine.

Catalytic activityi

Lactose + H2O = D-galactose + D-glucose.
Glycosyl-N-acylsphingosine + H2O = N-acylsphingosine + a sugar.

Sites

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Active sitei1065Proton donorSequence analysis1
Active sitei1273NucleophilePROSITE-ProRule annotation1
Active sitei1538Proton donorSequence analysis1
Active sitei1749NucleophilePROSITE-ProRule annotation1

GO - Molecular functioni

GO - Biological processi

Complete GO annotation...

Keywords - Molecular functioni

Glycosidase, Hydrolase

Enzyme and pathway databases

BioCyciMetaCyc:HS03945-MONOMER.
ZFISH:HS03945-MONOMER.
BRENDAi3.2.1.108. 2681.
3.7.1.4. 2681.
ReactomeiR-HSA-189085. Digestion of dietary carbohydrate.

Protein family/group databases

CAZyiGH1. Glycoside Hydrolase Family 1.

Names & Taxonomyi

Protein namesi
Recommended name:
Lactase-phlorizin hydrolase
Alternative name(s):
Lactase-glycosylceramidase
Including the following 2 domains:
Phlorizin hydrolase (EC:3.2.1.62)
Gene namesi
Name:LCT
Synonyms:LPH
OrganismiHomo sapiens (Human)
Taxonomic identifieri9606 [NCBI]
Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresPrimatesHaplorrhiniCatarrhiniHominidaeHomo
Proteomesi
  • UP000005640 Componenti: Chromosome 2

Organism-specific databases

HGNCiHGNC:6530. LCT.

Subcellular locationi

Topology

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Topological domaini20 – 1882ExtracellularSequence analysisAdd BLAST1863
Transmembranei1883 – 1901HelicalSequence analysisAdd BLAST19
Topological domaini1902 – 1927CytoplasmicSequence analysisAdd BLAST26

GO - Cellular componenti

  • apical plasma membrane Source: UniProtKB-SubCell
  • integral component of plasma membrane Source: ProtInc
  • membrane Source: ProtInc
  • plasma membrane Source: Reactome
Complete GO annotation...

Keywords - Cellular componenti

Cell membrane, Membrane

Pathology & Biotechi

Involvement in diseasei

Congenital lactase deficiency (COLACD)1 Publication
The disease is caused by mutations affecting the gene represented in this entry.
Disease descriptionAutosomal recessive, rare and severe gastrointestinal disorder. It is characterized by watery diarrhea in infants fed with breast milk or other lactose-containing formulas. An almost total lack of LCT activity is found in jejunal biopsy material of patients with congenital lactase deficiency. Opposite to congenital lactase deficiency, also known as lactose intolerance, is the most common enzyme deficiency worldwide. It is caused by developmental down-regulation of lactase activity during childhood or early adulthood. The decline of lactase activity is a normal physiological phenomenon; however, the majority of Northern Europeans have the ability to maintain lactase activity and digest lactose throughout life (lactase persistence). The down-regulation of lactase activity operates at the transcriptional level and it is associated with a noncoding variation in the MCM6 gene, located in the upstream vicinity of LCT.
See also OMIM:223000
Feature keyPosition(s)DescriptionActionsGraphical viewLength
Natural variantiVAR_026706268Q → H in COLACD. 1 PublicationCorresponds to variant rs121908937dbSNPEnsembl.1
Natural variantiVAR_0267081363G → S in COLACD. 1 PublicationCorresponds to variant rs386833833dbSNPEnsembl.1

Keywords - Diseasei

Disease mutation

Organism-specific databases

DisGeNETi3938.
MalaCardsiLCT.
MIMi223000. phenotype.
OpenTargetsiENSG00000115850.
Orphaneti53690. Congenital lactase deficiency.
319681. Lactase non-persistence in adulthood.
PharmGKBiPA30315.

Chemistry databases

ChEMBLiCHEMBL1075131.
DrugBankiDB00126. Vitamin C.

Polymorphism and mutation databases

BioMutaiLCT.
DMDMi311033425.

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Signal peptidei1 – 19Add BLAST19
PropeptideiPRO_000001176720 – 868Beta-glucosidaseBy similarityAdd BLAST849
ChainiPRO_0000011768869 – 1927Lactase-phlorizin hydrolaseAdd BLAST1059

Keywords - PTMi

Zymogen

Proteomic databases

EPDiP09848.
MaxQBiP09848.
PaxDbiP09848.
PeptideAtlasiP09848.
PRIDEiP09848.

PTM databases

iPTMnetiP09848.
PhosphoSitePlusiP09848.

Expressioni

Tissue specificityi

Intestine.

Gene expression databases

BgeeiENSG00000115850.
CleanExiHS_LCT.
ExpressionAtlasiP09848. baseline and differential.
GenevisibleiP09848. HS.

Organism-specific databases

HPAiHPA007408.

Interactioni

Protein-protein interaction databases

BioGridi110130. 2 interactors.
IntActiP09848. 1 interactor.
MINTiMINT-3380713.
STRINGi9606.ENSP00000264162.

Chemistry databases

BindingDBiP09848.

Structurei

3D structure databases

ProteinModelPortaliP09848.
SMRiP09848.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Repeati87 – 1721Add BLAST86
Repeati363 – 8482Add BLAST486
Repeati884 – 13653Add BLAST482
Repeati1370 – 18414Add BLAST472

Region

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Regioni87 – 18414 X approximate repeatsAdd BLAST1755

Domaini

The sequence exhibits 4 regions (I-IV) of internal homology; therefore LPH might have evolved by two cycles of partial gene duplication.

Sequence similaritiesi

Belongs to the glycosyl hydrolase 1 family.Curated

Keywords - Domaini

Repeat, Signal, Transmembrane, Transmembrane helix

Phylogenomic databases

eggNOGiKOG0626. Eukaryota.
COG2723. LUCA.
GeneTreeiENSGT00550000074452.
HOGENOMiHOG000024957.
HOVERGENiHBG006290.
InParanoidiP09848.
KOiK01229.
OMAiKSAYFFT.
OrthoDBiEOG091G0035.
PhylomeDBiP09848.
TreeFamiTF314803.

Family and domain databases

Gene3Di3.20.20.80. 4 hits.
InterProiIPR001360. Glyco_hydro_1.
IPR018120. Glyco_hydro_1_AS.
IPR033132. Glyco_hydro_1_N_CS.
IPR013781. Glyco_hydro_catalytic_dom.
IPR017853. Glycoside_hydrolase_SF.
[Graphical view]
PANTHERiPTHR10353. PTHR10353. 2 hits.
PfamiPF00232. Glyco_hydro_1. 4 hits.
[Graphical view]
PRINTSiPR00131. GLHYDRLASE1.
SUPFAMiSSF51445. SSF51445. 4 hits.
PROSITEiPS00572. GLYCOSYL_HYDROL_F1_1. 2 hits.
PS00653. GLYCOSYL_HYDROL_F1_2. 3 hits.
[Graphical view]

Sequencei

Sequence statusi: Complete.

Sequence processingi: The displayed sequence is further processed into a mature form.

P09848-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MELSWHVVFI ALLSFSCWGS DWESDRNFIS TAGPLTNDLL HNLSGLLGDQ
60 70 80 90 100
SSNFVAGDKD MYVCHQPLPT FLPEYFSSLH ASQITHYKVF LSWAQLLPAG
110 120 130 140 150
STQNPDEKTV QCYRRLLKAL KTARLQPMVI LHHQTLPAST LRRTEAFADL
160 170 180 190 200
FADYATFAFH SFGDLVGIWF TFSDLEEVIK ELPHQESRAS QLQTLSDAHR
210 220 230 240 250
KAYEIYHESY AFQGGKLSVV LRAEDIPELL LEPPISALAQ DTVDFLSLDL
260 270 280 290 300
SYECQNEASL RQKLSKLQTI EPKVKVFIFN LKLPDCPSTM KNPASLLFSL
310 320 330 340 350
FEAINKDQVL TIGFDINEFL SCSSSSKKSM SCSLTGSLAL QPDQQQDHET
360 370 380 390 400
TDSSPASAYQ RIWEAFANQS RAERDAFLQD TFPEGFLWGA STGAFNVEGG
410 420 430 440 450
WAEGGRGVSI WDPRRPLNTT EGQATLEVAS DSYHKVASDV ALLCGLRAQV
460 470 480 490 500
YKFSISWSRI FPMGHGSSPS LPGVAYYNKL IDRLQDAGIE PMATLFHWDL
510 520 530 540 550
PQALQDHGGW QNESVVDAFL DYAAFCFSTF GDRVKLWVTF HEPWVMSYAG
560 570 580 590 600
YGTGQHPPGI SDPGVASFKV AHLVLKAHAR TWHHYNSHHR PQQQGHVGIV
610 620 630 640 650
LNSDWAEPLS PERPEDLRAS ERFLHFMLGW FAHPVFVDGD YPATLRTQIQ
660 670 680 690 700
QMNRQCSHPV AQLPEFTEAE KQLLKGSADF LGLSHYTSRL ISNAPQNTCI
710 720 730 740 750
PSYDTIGGFS QHVNHVWPQT SSSWIRVVPW GIRRLLQFVS LEYTRGKVPI
760 770 780 790 800
YLAGNGMPIG ESENLFDDSL RVDYFNQYIN EVLKAIKEDS VDVRSYIARS
810 820 830 840 850
LIDGFEGPSG YSQRFGLHHV NFSDSSKSRT PRKSAYFFTS IIEKNGFLTK
860 870 880 890 900
GAKRLLPPNT VNLPSKVRAF TFPSEVPSKA KVVWEKFSSQ PKFERDLFYH
910 920 930 940 950
GTFRDDFLWG VSSSAYQIEG AWDADGKGPS IWDNFTHTPG SNVKDNATGD
960 970 980 990 1000
IACDSYHQLD ADLNMLRALK VKAYRFSISW SRIFPTGRNS SINSHGVDYY
1010 1020 1030 1040 1050
NRLINGLVAS NIFPMVTLFH WDLPQALQDI GGWENPALID LFDSYADFCF
1060 1070 1080 1090 1100
QTFGDRVKFW MTFNEPMYLA WLGYGSGEFP PGVKDPGWAP YRIAHAVIKA
1110 1120 1130 1140 1150
HARVYHTYDE KYRQEQKGVI SLSLSTHWAE PKSPGVPRDV EAADRMLQFS
1160 1170 1180 1190 1200
LGWFAHPIFR NGDYPDTMKW KVGNRSELQH LATSRLPSFT EEEKRFIRAT
1210 1220 1230 1240 1250
ADVFCLNTYY SRIVQHKTPR LNPPSYEDDQ EMAEEEDPSW PSTAMNRAAP
1260 1270 1280 1290 1300
WGTRRLLNWI KEEYGDIPIY ITENGVGLTN PNTEDTDRIF YHKTYINEAL
1310 1320 1330 1340 1350
KAYRLDGIDL RGYVAWSLMD NFEWLNGYTV KFGLYHVDFN NTNRPRTARA
1360 1370 1380 1390 1400
SARYYTEVIT NNGMPLARED EFLYGRFPEG FIWSAASAAY QIEGAWRADG
1410 1420 1430 1440 1450
KGLSIWDTFS HTPLRVENDA IGDVACDSYH KIAEDLVTLQ NLGVSHYRFS
1460 1470 1480 1490 1500
ISWSRILPDG TTRYINEAGL NYYVRLIDTL LAASIQPQVT IYHWDLPQTL
1510 1520 1530 1540 1550
QDVGGWENET IVQRFKEYAD VLFQRLGDKV KFWITLNEPF VIAYQGYGYG
1560 1570 1580 1590 1600
TAAPGVSNRP GTAPYIVGHN LIKAHAEAWH LYNDVYRASQ GGVISITISS
1610 1620 1630 1640 1650
DWAEPRDPSN QEDVEAARRY VQFMGGWFAH PIFKNGDYNE VMKTRIRDRS
1660 1670 1680 1690 1700
LAAGLNKSRL PEFTESEKRR INGTYDFFGF NHYTTVLAYN LNYATAISSF
1710 1720 1730 1740 1750
DADRGVASIA DRSWPDSGSF WLKMTPFGFR RILNWLKEEY NDPPIYVTEN
1760 1770 1780 1790 1800
GVSQREETDL NDTARIYYLR TYINEALKAV QDKVDLRGYT VWSAMDNFEW
1810 1820 1830 1840 1850
ATGFSERFGL HFVNYSDPSL PRIPKASAKF YASVVRCNGF PDPATGPHAC
1860 1870 1880 1890 1900
LHQPDAGPTI SPVRQEEVQF LGLMLGTTEA QTALYVLFSL VLLGVCGLAF
1910 1920
LSYKYCKRSK QGKTQRSQQE LSPVSSF
Length:1,927
Mass (Da):218,587
Last modified:November 2, 2010 - v3
Checksum:i2FCD55CB47BBA35A
GO

Experimental Info

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Sequence conflicti1096A → T in CAA30801 (PubMed:2460343).Curated1

Natural variant

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Natural variantiVAR_055882190S → L.Corresponds to variant rs35156533dbSNPEnsembl.1
Natural variantiVAR_026705219V → I.1 PublicationCorresponds to variant rs3754689dbSNPEnsembl.1
Natural variantiVAR_026706268Q → H in COLACD. 1 PublicationCorresponds to variant rs121908937dbSNPEnsembl.1
Natural variantiVAR_026707362I → V.2 PublicationsCorresponds to variant rs4954449dbSNPEnsembl.1
Natural variantiVAR_0267081363G → S in COLACD. 1 PublicationCorresponds to variant rs386833833dbSNPEnsembl.1
Natural variantiVAR_0558831593V → M.Corresponds to variant rs35891837dbSNPEnsembl.1
Natural variantiVAR_0267091639N → S.1 PublicationCorresponds to variant rs2322659dbSNPEnsembl.1

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
X07994 mRNA. Translation: CAA30801.1.
M61850
, M61834, M61835, M61836, M61837, M61838, M61839, M61840, M61841, M61842, M61843, M61844, M61845, M61846, M61847, M61848, M61849 Genomic DNA. Translation: AAA59504.1.
AC011893 Genomic DNA. Translation: AAX88924.1.
CCDSiCCDS2178.1.
PIRiS01168.
RefSeqiNP_002290.2. NM_002299.3.
UniGeneiHs.551506.

Genome annotation databases

EnsembliENST00000264162; ENSP00000264162; ENSG00000115850.
GeneIDi3938.
KEGGihsa:3938.
UCSCiuc002tuu.2. human.

Keywords - Coding sequence diversityi

Polymorphism

Cross-referencesi

Web resourcesi

Wikipedia

Lactase entry

Protein Spotlight

Darwin's dessert - Issue 111 of November 2009

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
X07994 mRNA. Translation: CAA30801.1.
M61850
, M61834, M61835, M61836, M61837, M61838, M61839, M61840, M61841, M61842, M61843, M61844, M61845, M61846, M61847, M61848, M61849 Genomic DNA. Translation: AAA59504.1.
AC011893 Genomic DNA. Translation: AAX88924.1.
CCDSiCCDS2178.1.
PIRiS01168.
RefSeqiNP_002290.2. NM_002299.3.
UniGeneiHs.551506.

3D structure databases

ProteinModelPortaliP09848.
SMRiP09848.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi110130. 2 interactors.
IntActiP09848. 1 interactor.
MINTiMINT-3380713.
STRINGi9606.ENSP00000264162.

Chemistry databases

BindingDBiP09848.
ChEMBLiCHEMBL1075131.
DrugBankiDB00126. Vitamin C.

Protein family/group databases

CAZyiGH1. Glycoside Hydrolase Family 1.

PTM databases

iPTMnetiP09848.
PhosphoSitePlusiP09848.

Polymorphism and mutation databases

BioMutaiLCT.
DMDMi311033425.

Proteomic databases

EPDiP09848.
MaxQBiP09848.
PaxDbiP09848.
PeptideAtlasiP09848.
PRIDEiP09848.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsembliENST00000264162; ENSP00000264162; ENSG00000115850.
GeneIDi3938.
KEGGihsa:3938.
UCSCiuc002tuu.2. human.

Organism-specific databases

CTDi3938.
DisGeNETi3938.
GeneCardsiLCT.
H-InvDBHIX0030024.
HIX0117702.
HGNCiHGNC:6530. LCT.
HPAiHPA007408.
MalaCardsiLCT.
MIMi223000. phenotype.
603202. gene.
neXtProtiNX_P09848.
OpenTargetsiENSG00000115850.
Orphaneti53690. Congenital lactase deficiency.
319681. Lactase non-persistence in adulthood.
PharmGKBiPA30315.
GenAtlasiSearch...

Phylogenomic databases

eggNOGiKOG0626. Eukaryota.
COG2723. LUCA.
GeneTreeiENSGT00550000074452.
HOGENOMiHOG000024957.
HOVERGENiHBG006290.
InParanoidiP09848.
KOiK01229.
OMAiKSAYFFT.
OrthoDBiEOG091G0035.
PhylomeDBiP09848.
TreeFamiTF314803.

Enzyme and pathway databases

BioCyciMetaCyc:HS03945-MONOMER.
ZFISH:HS03945-MONOMER.
BRENDAi3.2.1.108. 2681.
3.7.1.4. 2681.
ReactomeiR-HSA-189085. Digestion of dietary carbohydrate.

Miscellaneous databases

ChiTaRSiLCT. human.
GenomeRNAii3938.
PROiP09848.
SOURCEiSearch...

Gene expression databases

BgeeiENSG00000115850.
CleanExiHS_LCT.
ExpressionAtlasiP09848. baseline and differential.
GenevisibleiP09848. HS.

Family and domain databases

Gene3Di3.20.20.80. 4 hits.
InterProiIPR001360. Glyco_hydro_1.
IPR018120. Glyco_hydro_1_AS.
IPR033132. Glyco_hydro_1_N_CS.
IPR013781. Glyco_hydro_catalytic_dom.
IPR017853. Glycoside_hydrolase_SF.
[Graphical view]
PANTHERiPTHR10353. PTHR10353. 2 hits.
PfamiPF00232. Glyco_hydro_1. 4 hits.
[Graphical view]
PRINTSiPR00131. GLHYDRLASE1.
SUPFAMiSSF51445. SSF51445. 4 hits.
PROSITEiPS00572. GLYCOSYL_HYDROL_F1_1. 2 hits.
PS00653. GLYCOSYL_HYDROL_F1_2. 3 hits.
[Graphical view]
ProtoNetiSearch...

Entry informationi

Entry nameiLPH_HUMAN
AccessioniPrimary (citable) accession number: P09848
Secondary accession number(s): Q4ZG58
Entry historyi
Integrated into UniProtKB/Swiss-Prot: July 1, 1989
Last sequence update: November 2, 2010
Last modified: November 30, 2016
This is version 170 of the entry and version 3 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programChordata Protein Annotation Program
DisclaimerAny medical or genetic information present in this entry is provided for research, educational and informational purposes only. It is not in any way intended to be used as a substitute for professional medical advice, diagnosis, treatment or care.

Miscellaneousi

Keywords - Technical termi

Complete proteome, Multifunctional enzyme, Reference proteome

Documents

  1. Glycosyl hydrolases
    Classification of glycosyl hydrolase families and list of entries
  2. Human chromosome 2
    Human chromosome 2: entries, gene names and cross-references to MIM
  3. Human entries with polymorphisms or disease mutations
    List of human entries with polymorphisms or disease mutations
  4. Human polymorphisms and disease mutations
    Index of human polymorphisms and disease mutations
  5. MIM cross-references
    Online Mendelian Inheritance in Man (MIM) cross-references in UniProtKB/Swiss-Prot
  6. Protein Spotlight
    Protein Spotlight articles and cited UniProtKB/Swiss-Prot entries
  7. SIMILARITY comments
    Index of protein domains and families

Similar proteinsi

Links to similar proteins from the UniProt Reference Clusters (UniRef) at 100%, 90% and 50% sequence identity:
100%UniRef100 combines identical sequences and sub-fragments with 11 or more residues from any organism into one UniRef entry.
90%UniRef90 is built by clustering UniRef100 sequences that have at least 90% sequence identity to, and 80% overlap with, the longest sequence (a.k.a seed sequence).
50%UniRef50 is built by clustering UniRef90 seed sequences that have at least 50% sequence identity to, and 80% overlap with, the longest sequence in the cluster.