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Protein

LIM/homeobox protein Lhx3

Gene

Lhx3

Organism
Mus musculus (Mouse)
Status
Reviewed-Annotation score: Annotation score: 5 out of 5-Experimental evidence at protein leveli

Functioni

Required for the establishment of the specialized cells of the pituitary gland and the nervous system (By similarity). Involved in the development of interneurons and motor neurons in cooperation with LDB1 and ISL1. Acts as a transcriptional activator. Binds to and activates the promoter of the alpha-glycoprotein gene, and synergistically enhances transcription from the prolactin promoter in cooperation with Pou1f1/Pit-1.By similarity2 Publications

Regions

Feature keyPosition(s)DescriptionActionsGraphical viewLength
DNA bindingi160 – 219HomeoboxPROSITE-ProRule annotationAdd BLAST60

GO - Molecular functioni

GO - Biological processi

  • cell differentiation Source: MGI
  • dorsal/ventral pattern formation Source: MGI
  • inner ear development Source: Ensembl
  • lung development Source: Ensembl
  • medial motor column neuron differentiation Source: MGI
  • motor neuron axon guidance Source: MGI
  • negative regulation of apoptotic process Source: MGI
  • pituitary gland development Source: MGI
  • placenta development Source: MGI
  • positive regulation of transcription, DNA-templated Source: UniProtKB
  • positive regulation of transcription from RNA polymerase II promoter Source: MGI
  • spinal cord association neuron differentiation Source: MGI
  • spinal cord motor neuron cell fate specification Source: MGI
  • transcription, DNA-templated Source: UniProtKB-KW
  • ventral spinal cord interneuron specification Source: MGI
Complete GO annotation...

Keywords - Molecular functioni

Activator

Keywords - Biological processi

Transcription, Transcription regulation

Keywords - Ligandi

DNA-binding, Metal-binding, Zinc

Names & Taxonomyi

Protein namesi
Recommended name:
LIM/homeobox protein Lhx3
Short name:
LIM homeobox protein 3
Alternative name(s):
Homeobox protein LIM-3
Homeobox protein P-LIM
Gene namesi
Name:Lhx3
Synonyms:Lim-3, Lim3, Plim
OrganismiMus musculus (Mouse)
Taxonomic identifieri10090 [NCBI]
Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresGliresRodentiaSciurognathiMuroideaMuridaeMurinaeMusMus
Proteomesi
  • UP000000589 Componenti: Chromosome 2

Organism-specific databases

MGIiMGI:102673. Lhx3.

Subcellular locationi

GO - Cellular componenti

  • intracellular Source: MGI
  • nucleus Source: MGI
  • transcription factor complex Source: MGI
Complete GO annotation...

Keywords - Cellular componenti

Nucleus

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_00000757821 – 400LIM/homeobox protein Lhx3Add BLAST400

Amino acid modifications

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Modified residuei74PhosphoserineBy similarity1
Modified residuei230PhosphotyrosineBy similarity1
Modified residuei237PhosphoserineBy similarity1
Modified residuei241PhosphoserineBy similarity1

Keywords - PTMi

Phosphoprotein

Proteomic databases

PaxDbiP50481.
PRIDEiP50481.

PTM databases

PhosphoSitePlusiP50481.

Expressioni

Tissue specificityi

Mostly expressed in the pituitary anterior and intermediate lobes of the adult mouse. It is also expressed in the pineal gland and transiently in the primordia of motor neurons including the spinal cord, pons and medulla oblongata.

Developmental stagei

Expressed throughout pituitary development. Detected on embryonic day 11 (E11) in the primordium of the hypophysis. Following a maximum between E12 and E14, lower levels persisted into adulthood.

Gene expression databases

BgeeiENSMUSG00000026934.
CleanExiMM_LHX3.
ExpressionAtlasiP50481. baseline and differential.
GenevisibleiP50481. MM.

Interactioni

Subunit structurei

Interacts with POU1F1 (By similarity). At neuronal promoters, interacts with LDB1, in motor neurons LDB1 is displaced by ISL1 and a ternary complex is formed in which ISL1 contacts both LHX3 and LDB1 (PubMed:12150931, PubMed:18583962).By similarity2 Publications

Binary interactionsi

WithEntry#Exp.IntActNotes
Isl1P613727EBI-7988290,EBI-7988215
Ldb1P706625EBI-7988290,EBI-6272082

GO - Molecular functioni

Protein-protein interaction databases

IntActiP50481. 2 interactors.
MINTiMINT-7009840.
STRINGi10090.ENSMUSP00000028302.

Structurei

Secondary structure

1400
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details
Feature keyPosition(s)DescriptionActionsGraphical viewLength
Beta strandi33 – 40Combined sources8
Beta strandi43 – 45Combined sources3
Turni56 – 58Combined sources3
Turni62 – 64Combined sources3
Beta strandi73 – 77Combined sources5
Helixi82 – 89Combined sources8
Turni94 – 96Combined sources3
Beta strandi104 – 109Combined sources6
Beta strandi112 – 115Combined sources4
Helixi116 – 118Combined sources3
Turni122 – 124Combined sources3
Beta strandi133 – 136Combined sources4
Beta strandi142 – 144Combined sources3
Helixi145 – 147Combined sources3
Helixi148 – 153Combined sources6

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
2JTNNMR-A28-153[»]
2RGTX-ray2.05A/B28-153[»]
ProteinModelPortaliP50481.
SMRiP50481.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiP50481.

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Domaini34 – 84LIM zinc-binding 1PROSITE-ProRule annotationAdd BLAST51
Domaini93 – 147LIM zinc-binding 2PROSITE-ProRule annotationAdd BLAST55

Domaini

The LIM domain specifically interacts with the Pit-1 POU domain and is required for synergistic interactions with Pit-1, but not for basal transcriptional activation events.

Sequence similaritiesi

Contains 1 homeobox DNA-binding domain.PROSITE-ProRule annotation
Contains 2 LIM zinc-binding domains.PROSITE-ProRule annotation

Keywords - Domaini

Homeobox, LIM domain, Repeat

Phylogenomic databases

eggNOGiKOG4577. Eukaryota.
ENOG410XPDC. LUCA.
GeneTreeiENSGT00760000118921.
HOGENOMiHOG000231629.
HOVERGENiHBG006263.
InParanoidiP50481.
KOiK09374.
OMAiSQDQFHD.
TreeFamiTF315442.

Family and domain databases

Gene3Di1.10.10.60. 1 hit.
2.10.110.10. 2 hits.
InterProiIPR017970. Homeobox_CS.
IPR001356. Homeobox_dom.
IPR009057. Homeodomain-like.
IPR001781. Znf_LIM.
[Graphical view]
PfamiPF00046. Homeobox. 1 hit.
PF00412. LIM. 2 hits.
[Graphical view]
SMARTiSM00389. HOX. 1 hit.
SM00132. LIM. 2 hits.
[Graphical view]
SUPFAMiSSF46689. SSF46689. 1 hit.
PROSITEiPS00027. HOMEOBOX_1. 1 hit.
PS50071. HOMEOBOX_2. 1 hit.
PS00478. LIM_DOMAIN_1. 2 hits.
PS50023. LIM_DOMAIN_2. 2 hits.
[Graphical view]

Sequences (2)i

Sequence statusi: Complete.

This entry describes 2 isoformsi produced by alternative splicing. AlignAdd to basket

Note: Additional isoforms seem to exist.
Isoform LIM3A (identifier: P50481-1) [UniParc]FASTAAdd to basket

This isoform has been chosen as the 'canonical' sequence. All positional information in this entry refers to it. This is also the sequence that appears in the downloadable versions of the entry.

« Hide

        10         20         30         40         50
MLLEAELDCH RERPGAPGAS ALCTFSRTPE IPMCAGCDQH ILDRFILKAL
60 70 80 90 100
DRHWHSKCLK CSDCHVPLAE RCFSRGESVY CKDDFFKRFG TKCAACQLGI
110 120 130 140 150
PPTQVVRRAQ DFVYHLHCFA CVVCKRQLAT GDEFYLMEDS RLVCKADYET
160 170 180 190 200
AKQREAEATA KRPRTTITAK QLETLKSAYN TSPKPARHVR EQLSSETGLD
210 220 230 240 250
MRVVQVWFQN RRAKEKRLKK DAGRQRWGQY FRNMKRSRGS SKSDKDSIQE
260 270 280 290 300
GQDSDAEVSF TDEPSMADMG PANGLYSSLG EPAPALGRPV GGLGSFTLDH
310 320 330 340 350
GGLTGPEQYR ELRPGSPYGI PPSPAAPQSL PGPQPLLSSL VYPDTNLSLV
360 370 380 390 400
PSGPPGGPPP MRVLAGNGPS SDLSTESSSG YPDFPASPAS WLDEVDHAQF
Length:400
Mass (Da):44,010
Last modified:October 1, 1996 - v1
Checksum:iAD7A9453CFACC730
GO
Isoform LIM3B (identifier: P50481-2) [UniParc]FASTAAdd to basket

The sequence of this isoform differs from the canonical sequence as follows:
     1-29: MLLEAELDCHRERPGAPGASALCTFSRTP → MEARGELDPSRESAGGDLLLALLARRADLRR

Show »
Length:402
Mass (Da):44,289
Checksum:i45942CCDADC72080
GO

Experimental Info

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Sequence conflicti26S → N in AAA98998 (PubMed:7626792).Curated1
Sequence conflicti76G → R in AAA73902 (PubMed:7708713).Curated1
Sequence conflicti311 – 312EL → DV in AAA73902 (PubMed:7708713).Curated2
Sequence conflicti351 – 378PSGPP…STESS → LQGPQVDPGPTHEGCWLEMA RTCPQRAG (PubMed:7708713).CuratedAdd BLAST28

Alternative sequence

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Alternative sequenceiVSP_0031081 – 29MLLEA…FSRTP → MEARGELDPSRESAGGDLLL ALLARRADLRR in isoform LIM3B. CuratedAdd BLAST29

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
L33776 Genomic DNA. Translation: AAA62369.1.
L38857 mRNA. Translation: AAA73902.1.
L38249 mRNA. Translation: AAA98998.1.
L38248 mRNA. Translation: AAB64178.1.
CCDSiCCDS38081.1. [P50481-2]
CCDS71004.1. [P50481-1]
PIRiI59360.
RefSeqiNP_001034742.1. NM_001039653.2. [P50481-2]
NP_034841.2. NM_010711.2. [P50481-1]
UniGeneiMm.386765.

Genome annotation databases

EnsembliENSMUST00000028302; ENSMUSP00000028302; ENSMUSG00000026934. [P50481-2]
ENSMUST00000054099; ENSMUSP00000056822; ENSMUSG00000026934. [P50481-1]
GeneIDi16871.
KEGGimmu:16871.
UCSCiuc008iug.1. mouse. [P50481-1]

Keywords - Coding sequence diversityi

Alternative splicing

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
L33776 Genomic DNA. Translation: AAA62369.1.
L38857 mRNA. Translation: AAA73902.1.
L38249 mRNA. Translation: AAA98998.1.
L38248 mRNA. Translation: AAB64178.1.
CCDSiCCDS38081.1. [P50481-2]
CCDS71004.1. [P50481-1]
PIRiI59360.
RefSeqiNP_001034742.1. NM_001039653.2. [P50481-2]
NP_034841.2. NM_010711.2. [P50481-1]
UniGeneiMm.386765.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
2JTNNMR-A28-153[»]
2RGTX-ray2.05A/B28-153[»]
ProteinModelPortaliP50481.
SMRiP50481.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

IntActiP50481. 2 interactors.
MINTiMINT-7009840.
STRINGi10090.ENSMUSP00000028302.

PTM databases

PhosphoSitePlusiP50481.

Proteomic databases

PaxDbiP50481.
PRIDEiP50481.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsembliENSMUST00000028302; ENSMUSP00000028302; ENSMUSG00000026934. [P50481-2]
ENSMUST00000054099; ENSMUSP00000056822; ENSMUSG00000026934. [P50481-1]
GeneIDi16871.
KEGGimmu:16871.
UCSCiuc008iug.1. mouse. [P50481-1]

Organism-specific databases

CTDi8022.
MGIiMGI:102673. Lhx3.

Phylogenomic databases

eggNOGiKOG4577. Eukaryota.
ENOG410XPDC. LUCA.
GeneTreeiENSGT00760000118921.
HOGENOMiHOG000231629.
HOVERGENiHBG006263.
InParanoidiP50481.
KOiK09374.
OMAiSQDQFHD.
TreeFamiTF315442.

Miscellaneous databases

EvolutionaryTraceiP50481.
PROiP50481.
SOURCEiSearch...

Gene expression databases

BgeeiENSMUSG00000026934.
CleanExiMM_LHX3.
ExpressionAtlasiP50481. baseline and differential.
GenevisibleiP50481. MM.

Family and domain databases

Gene3Di1.10.10.60. 1 hit.
2.10.110.10. 2 hits.
InterProiIPR017970. Homeobox_CS.
IPR001356. Homeobox_dom.
IPR009057. Homeodomain-like.
IPR001781. Znf_LIM.
[Graphical view]
PfamiPF00046. Homeobox. 1 hit.
PF00412. LIM. 2 hits.
[Graphical view]
SMARTiSM00389. HOX. 1 hit.
SM00132. LIM. 2 hits.
[Graphical view]
SUPFAMiSSF46689. SSF46689. 1 hit.
PROSITEiPS00027. HOMEOBOX_1. 1 hit.
PS50071. HOMEOBOX_2. 1 hit.
PS00478. LIM_DOMAIN_1. 2 hits.
PS50023. LIM_DOMAIN_2. 2 hits.
[Graphical view]
ProtoNetiSearch...

Entry informationi

Entry nameiLHX3_MOUSE
AccessioniPrimary (citable) accession number: P50481
Secondary accession number(s): Q61800, Q61801
Entry historyi
Integrated into UniProtKB/Swiss-Prot: October 1, 1996
Last sequence update: October 1, 1996
Last modified: November 2, 2016
This is version 147 of the entry and version 1 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programChordata Protein Annotation Program

Miscellaneousi

Keywords - Technical termi

3D-structure, Complete proteome, Reference proteome

Documents

  1. MGD cross-references
    Mouse Genome Database (MGD) cross-references in UniProtKB/Swiss-Prot
  2. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
  3. 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.