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Protein

LIM and cysteine-rich domains protein 1

Gene

LMCD1

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

Functioni

Transcriptional cofactor that restricts GATA6 function by inhibiting DNA-binding, resulting in repression of GATA6 transcriptional activation of downstream target genes. Represses GATA6-mediated trans activation of lung- and cardiac tissue-specific promoters. Inhibits DNA-binding by GATA4 and GATA1 to the cTNC promoter (By similarity). Plays a critical role in the development of cardiac hypertrophy via activation of calcineurin/nuclear factor of activated T-cells signaling pathway.By similarity1 Publication

GO - Molecular functioni

GO - Biological processi

  • cellular protein metabolic process Source: Reactome
  • negative regulation of transcription from RNA polymerase II promoter Source: Ensembl
  • positive regulation of calcineurin-NFAT signaling cascade Source: UniProtKB
  • regulation of cardiac muscle hypertrophy Source: UniProtKB
  • transcription, DNA-templated Source: UniProtKB-KW
Complete GO annotation...

Keywords - Molecular functioni

Repressor

Keywords - Biological processi

Transcription, Transcription regulation

Keywords - Ligandi

Metal-binding, Zinc

Enzyme and pathway databases

BioCyciZFISH:ENSG00000071282-MONOMER.
ReactomeiR-HSA-5683826. Surfactant metabolism.

Names & Taxonomyi

Protein namesi
Recommended name:
LIM and cysteine-rich domains protein 1
Alternative name(s):
Dyxin
Gene namesi
Name:LMCD1
OrganismiHomo sapiens (Human)
Taxonomic identifieri9606 [NCBI]
Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresPrimatesHaplorrhiniCatarrhiniHominidaeHomo
Proteomesi
  • UP000005640 Componenti: Chromosome 3

Organism-specific databases

HGNCiHGNC:6633. LMCD1.

Subcellular locationi

  • Cytoplasm By similarity
  • Nucleus By similarity

  • Note: May shuttle between the cytoplasm and the nucleus.By similarity

GO - Cellular componenti

  • cytoplasm Source: UniProtKB-SubCell
  • extracellular space Source: BHF-UCL
  • nucleoplasm Source: Reactome
  • nucleus Source: GO_Central
Complete GO annotation...

Keywords - Cellular componenti

Cytoplasm, Nucleus

Pathology & Biotechi

Organism-specific databases

DisGeNETi29995.
OpenTargetsiENSG00000071282.
PharmGKBiPA30401.

Polymorphism and mutation databases

DMDMi20978521.

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_00000758151 – 365LIM and cysteine-rich domains protein 1Add BLAST365

Amino acid modifications

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Modified residuei16PhosphoserineCombined sources1

Keywords - PTMi

Phosphoprotein

Proteomic databases

EPDiQ9NZU5.
MaxQBiQ9NZU5.
PaxDbiQ9NZU5.
PeptideAtlasiQ9NZU5.
PRIDEiQ9NZU5.

PTM databases

iPTMnetiQ9NZU5.
PhosphoSitePlusiQ9NZU5.

Expressioni

Tissue specificityi

Expressed in the heart (at protein level). Expressed in many tissues with highest abundance in skeletal muscle.1 Publication

Gene expression databases

BgeeiENSG00000071282.
CleanExiHS_LMCD1.
ExpressionAtlasiQ9NZU5. baseline and differential.
GenevisibleiQ9NZU5. HS.

Organism-specific databases

HPAiHPA024059.

Interactioni

Subunit structurei

Interacts with GATA1 and GATA4 (By similarity). Interacts with beta-dystroglycan. Interacts with GATA6.By similarity1 Publication

Protein-protein interaction databases

BioGridi119020. 8 interactors.
IntActiQ9NZU5. 5 interactors.
MINTiMINT-6492974.
STRINGi9606.ENSP00000157600.

Structurei

3D structure databases

ProteinModelPortaliQ9NZU5.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Domaini99 – 206PETPROSITE-ProRule annotationAdd BLAST108
Domaini241 – 306LIM zinc-binding 1PROSITE-ProRule annotationAdd BLAST66
Domaini307 – 365LIM zinc-binding 2PROSITE-ProRule annotationAdd BLAST59

Compositional bias

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Compositional biasi28 – 58Cys-richAdd BLAST31

Domaini

The LIM zinc-binding domains and the Cys-rich region mediate interaction with GATA6.By similarity

Sequence similaritiesi

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

Keywords - Domaini

LIM domain, Repeat

Phylogenomic databases

eggNOGiENOG410INGI. Eukaryota.
ENOG410ZPX3. LUCA.
GeneTreeiENSGT00550000074438.
HOGENOMiHOG000231628.
HOVERGENiHBG001038.
InParanoidiQ9NZU5.
OMAiAGYSKQW.
OrthoDBiEOG091G07C5.
PhylomeDBiQ9NZU5.
TreeFamiTF313265.

Family and domain databases

CDDicd09829. PET_testin. 1 hit.
Gene3Di2.10.110.10. 2 hits.
InterProiIPR010442. PET_domain.
IPR033724. PET_testin.
IPR001781. Znf_LIM.
[Graphical view]
PfamiPF00412. LIM. 2 hits.
PF06297. PET. 1 hit.
[Graphical view]
SMARTiSM00132. LIM. 2 hits.
[Graphical view]
PROSITEiPS00478. LIM_DOMAIN_1. 2 hits.
PS50023. LIM_DOMAIN_2. 2 hits.
PS51303. PET. 1 hit.
[Graphical view]

Sequences (2)i

Sequence statusi: Complete.

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

Isoform 1 (identifier: Q9NZU5-1) [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
MAKVAKDLNP GVKKMSLGQL QSARGVACLG CKGTCSGFEP HSWRKICKSC
60 70 80 90 100
KCSQEDHCLT SDLEDDRKIG RLLMDSKYST LTARVKGGDG IRIYKRNRMI
110 120 130 140 150
MTNPIATGKD PTFDTITYEW APPGVTQKLG LQYMELIPKE KQPVTGTEGA
160 170 180 190 200
FYRRRQLMHQ LPIYDQDPSR CRGLLENELK LMEEFVKQYK SEALGVGEVA
210 220 230 240 250
LPGQGGLPKE EGKQQEKPEG AETTAATTNG SLSDPSKEVE YVCELCKGAA
260 270 280 290 300
PPDSPVVYSD RAGYNKQWHP TCFVCAKCSE PLVDLIYFWK DGAPWCGRHY
310 320 330 340 350
CESLRPRCSG CDEIIFAEDY QRVEDLAWHR KHFVCEGCEQ LLSGRAYIVT
360
KGQLLCPTCS KSKRS
Length:365
Mass (Da):40,833
Last modified:October 1, 2000 - v1
Checksum:iD84BFD53C43D2DD7
GO
Isoform 2 (identifier: Q9NZU5-2) [UniParc]FASTAAdd to basket

The sequence of this isoform differs from the canonical sequence as follows:
     1-73: Missing.

Note: No experimental confirmation available.
Show »
Length:292
Mass (Da):32,882
Checksum:iD19CF028814D51FD
GO

Alternative sequence

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Alternative sequenceiVSP_0538951 – 73Missing in isoform 2. 1 PublicationAdd BLAST73

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AF169284 mRNA. Translation: AAF34411.1.
AF216709 mRNA. Translation: AAG36778.1.
AK022176 mRNA. Translation: BAB13976.1.
AK294455 mRNA. Translation: BAG57691.1.
AC087859 Genomic DNA. No translation available.
BC000646 mRNA. Translation: AAH00646.1.
CCDSiCCDS33688.1. [Q9NZU5-1]
CCDS63534.1. [Q9NZU5-2]
RefSeqiNP_001265162.1. NM_001278233.1. [Q9NZU5-2]
NP_001265163.1. NM_001278234.1.
NP_001265164.1. NM_001278235.1.
NP_055398.1. NM_014583.3. [Q9NZU5-1]
UniGeneiHs.475353.
Hs.732705.

Genome annotation databases

EnsembliENST00000157600; ENSP00000157600; ENSG00000071282. [Q9NZU5-1]
ENST00000454244; ENSP00000396515; ENSG00000071282. [Q9NZU5-2]
GeneIDi29995.
KEGGihsa:29995.
UCSCiuc010hci.4. human. [Q9NZU5-1]

Keywords - Coding sequence diversityi

Alternative splicing

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AF169284 mRNA. Translation: AAF34411.1.
AF216709 mRNA. Translation: AAG36778.1.
AK022176 mRNA. Translation: BAB13976.1.
AK294455 mRNA. Translation: BAG57691.1.
AC087859 Genomic DNA. No translation available.
BC000646 mRNA. Translation: AAH00646.1.
CCDSiCCDS33688.1. [Q9NZU5-1]
CCDS63534.1. [Q9NZU5-2]
RefSeqiNP_001265162.1. NM_001278233.1. [Q9NZU5-2]
NP_001265163.1. NM_001278234.1.
NP_001265164.1. NM_001278235.1.
NP_055398.1. NM_014583.3. [Q9NZU5-1]
UniGeneiHs.475353.
Hs.732705.

3D structure databases

ProteinModelPortaliQ9NZU5.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi119020. 8 interactors.
IntActiQ9NZU5. 5 interactors.
MINTiMINT-6492974.
STRINGi9606.ENSP00000157600.

PTM databases

iPTMnetiQ9NZU5.
PhosphoSitePlusiQ9NZU5.

Polymorphism and mutation databases

DMDMi20978521.

Proteomic databases

EPDiQ9NZU5.
MaxQBiQ9NZU5.
PaxDbiQ9NZU5.
PeptideAtlasiQ9NZU5.
PRIDEiQ9NZU5.

Protocols and materials databases

DNASUi29995.
Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsembliENST00000157600; ENSP00000157600; ENSG00000071282. [Q9NZU5-1]
ENST00000454244; ENSP00000396515; ENSG00000071282. [Q9NZU5-2]
GeneIDi29995.
KEGGihsa:29995.
UCSCiuc010hci.4. human. [Q9NZU5-1]

Organism-specific databases

CTDi29995.
DisGeNETi29995.
GeneCardsiLMCD1.
HGNCiHGNC:6633. LMCD1.
HPAiHPA024059.
MIMi604859. gene.
neXtProtiNX_Q9NZU5.
OpenTargetsiENSG00000071282.
PharmGKBiPA30401.
GenAtlasiSearch...

Phylogenomic databases

eggNOGiENOG410INGI. Eukaryota.
ENOG410ZPX3. LUCA.
GeneTreeiENSGT00550000074438.
HOGENOMiHOG000231628.
HOVERGENiHBG001038.
InParanoidiQ9NZU5.
OMAiAGYSKQW.
OrthoDBiEOG091G07C5.
PhylomeDBiQ9NZU5.
TreeFamiTF313265.

Enzyme and pathway databases

BioCyciZFISH:ENSG00000071282-MONOMER.
ReactomeiR-HSA-5683826. Surfactant metabolism.

Miscellaneous databases

ChiTaRSiLMCD1. human.
GenomeRNAii29995.
PROiQ9NZU5.
SOURCEiSearch...

Gene expression databases

BgeeiENSG00000071282.
CleanExiHS_LMCD1.
ExpressionAtlasiQ9NZU5. baseline and differential.
GenevisibleiQ9NZU5. HS.

Family and domain databases

CDDicd09829. PET_testin. 1 hit.
Gene3Di2.10.110.10. 2 hits.
InterProiIPR010442. PET_domain.
IPR033724. PET_testin.
IPR001781. Znf_LIM.
[Graphical view]
PfamiPF00412. LIM. 2 hits.
PF06297. PET. 1 hit.
[Graphical view]
SMARTiSM00132. LIM. 2 hits.
[Graphical view]
PROSITEiPS00478. LIM_DOMAIN_1. 2 hits.
PS50023. LIM_DOMAIN_2. 2 hits.
PS51303. PET. 1 hit.
[Graphical view]
ProtoNetiSearch...

Entry informationi

Entry nameiLMCD1_HUMAN
AccessioniPrimary (citable) accession number: Q9NZU5
Secondary accession number(s): B4DG80
Entry historyi
Integrated into UniProtKB/Swiss-Prot: May 15, 2002
Last sequence update: October 1, 2000
Last modified: November 30, 2016
This is version 128 of the entry and version 1 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, Reference proteome

Documents

  1. Human chromosome 3
    Human chromosome 3: entries, gene names and cross-references to MIM
  2. MIM cross-references
    Online Mendelian Inheritance in Man (MIM) cross-references in UniProtKB/Swiss-Prot
  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.