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Protein

Protein lin-54 homolog

Gene

LIN54

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

Functioni

Component of the DREAM complex, a multiprotein complex that can both act as a transcription activator or repressor depending on the context (PubMed:17671431, PubMed:17531812). In G0 phase, the complex binds to more than 800 promoters and is required for repression of E2F target genes (PubMed:17671431, PubMed:17531812). In S phase, the complex selectively binds to the promoters of G2/M genes whose products are required for mitosis and participates in their cell cycle dependent activation (PubMed:17671431, PubMed:17531812). In the complex, acts as a DNA-binding protein that binds the promoter of CDK1 in a sequence-specific manner (PubMed:19725879). Specifically recognizes the consensus motif 5'-TTYRAA-3' in target DNA (PubMed:27465258).4 Publications

Sites

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Metal bindingi525Zinc 1Combined sources1
Metal bindingi525Zinc 2Combined sources1
Metal bindingi527Zinc 1Combined sources1
Metal bindingi532Zinc 1Combined sources1
Metal bindingi532Zinc 3Combined sources1
Sitei536Critical for interaction with target DNA1 Publication1
Metal bindingi537Zinc 1Combined sources1
Metal bindingi539Zinc 2Combined sources1
Metal bindingi546Zinc 2Combined sources1
Metal bindingi546Zinc 3Combined sources1
Metal bindingi549Zinc 2Combined sources1
Metal bindingi551Zinc 3Combined sources1
Metal bindingi554Zinc 3Combined sources1
Metal bindingi599Zinc 4Combined sources1
Metal bindingi599Zinc 5Combined sources1
Metal bindingi601Zinc 4Combined sources1
Metal bindingi606Zinc 4Combined sources1
Metal bindingi606Zinc 6Combined sources1
Sitei610Critical for interaction with target DNA1 Publication1
Metal bindingi611Zinc 4Combined sources1
Metal bindingi613Zinc 5Combined sources1
Metal bindingi620Zinc 5Combined sources1
Metal bindingi620Zinc 6Combined sources1
Metal bindingi624Zinc 5Combined sources1
Metal bindingi626Zinc 6Combined sources1
Metal bindingi629Zinc 6Combined sources1

GO - Molecular functioni

GO - Biological processi

Keywordsi

Molecular functionActivator, DNA-binding, Repressor
Biological processCell cycle, Transcription, Transcription regulation
LigandMetal-binding, Zinc

Enzyme and pathway databases

ReactomeiR-HSA-1362277 Transcription of E2F targets under negative control by DREAM complex
R-HSA-1362300 Transcription of E2F targets under negative control by p107 (RBL1) and p130 (RBL2) in complex with HDAC1
R-HSA-1538133 G0 and Early G1
R-HSA-156711 Polo-like kinase mediated events
R-HSA-539107 Activation of E2F1 target genes at G1/S
R-HSA-69202 Cyclin E associated events during G1/S transition
R-HSA-69656 Cyclin A:Cdk2-associated events at S phase entry

Names & Taxonomyi

Protein namesi
Recommended name:
Protein lin-54 homolog
Alternative name(s):
CXC domain-containing protein 1
Gene namesi
Name:LIN54
Synonyms:CXCDC1, KIAA2037
OrganismiHomo sapiens (Human)
Taxonomic identifieri9606 [NCBI]
Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresPrimatesHaplorrhiniCatarrhiniHominidaeHomo
Proteomesi
  • UP000005640 Componenti: Chromosome 4

Organism-specific databases

EuPathDBiHostDB:ENSG00000189308.10
HGNCiHGNC:25397 LIN54
MIMi613367 gene
neXtProtiNX_Q6MZP7

Subcellular locationi

Extracellular region or secreted Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi apparatus Nucleus Mitochondrion Manual annotation Automatic computational assertionGraphics by Christian Stolte; Source: COMPARTMENTS

Keywords - Cellular componenti

Nucleus

Pathology & Biotechi

Mutagenesis

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Mutagenesisi525C → Y: Abolishes DNA-binding to the CDK1 promoter; when associated with Y-527. 1 Publication1
Mutagenesisi527C → Y: Abolishes DNA-binding to the CDK1 promoter; when associated with Y-525. 1 Publication1
Mutagenesisi536Y → A, F or R: Loss of DNA-binding. 1 Publication1
Mutagenesisi610Y → A, F or R: Loss of DNA-binding. 1 Publication1

Organism-specific databases

DisGeNETi132660
OpenTargetsiENSG00000189308
PharmGKBiPA162394056

Polymorphism and mutation databases

DMDMi313104222

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_00003413891 – 749Protein lin-54 homologAdd BLAST749

Amino acid modifications

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Cross-linki139Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in SUMO2)Combined sources
Modified residuei244N6-acetyllysineCombined sources1
Modified residuei249N6-acetyllysineCombined sources1
Modified residuei264PhosphoserineCombined sources1
Modified residuei282PhosphoserineCombined sources1
Modified residuei310PhosphoserineCombined sources1
Modified residuei314PhosphoserineCombined sources1
Cross-linki357Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in SUMO2)Combined sources
Modified residuei635PhosphoserineCombined sources1
Cross-linki639Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in SUMO2)Combined sources
Cross-linki659Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in SUMO2)Combined sources
Cross-linki661Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in SUMO2)Combined sources

Keywords - PTMi

Acetylation, Isopeptide bond, Phosphoprotein, Ubl conjugation

Proteomic databases

EPDiQ6MZP7
MaxQBiQ6MZP7
PaxDbiQ6MZP7
PeptideAtlasiQ6MZP7
PRIDEiQ6MZP7
ProteomicsDBi66576
66577 [Q6MZP7-2]
66578 [Q6MZP7-3]
66579 [Q6MZP7-4]
66580 [Q6MZP7-5]

PTM databases

iPTMnetiQ6MZP7
PhosphoSitePlusiQ6MZP7

Expressioni

Gene expression databases

BgeeiENSG00000189308 Expressed in 105 organ(s), highest expression level in corpus callosum
CleanExiHS_LIN54
ExpressionAtlasiQ6MZP7 baseline and differential
GenevisibleiQ6MZP7 HS

Organism-specific databases

HPAiHPA056606

Interactioni

Subunit structurei

Component of the DREAM complex (also named LINC complex) at least composed of E2F4, E2F5, LIN9, LIN37, LIN52, LIN54, MYBL1, MYBL2, RBL1, RBL2, RBBP4, TFDP1 and TFDP2. The complex exists in quiescent cells where it represses cell cycle-dependent genes. It dissociates in S phase when LIN9, LIN37, LIN52 and LIN54 form a subcomplex that binds to MYBL2.2 Publications

Sites

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Sitei574Interaction with DNA1 Publication1

Binary interactionsi

Protein-protein interaction databases

BioGridi126328, 27 interactors
CORUMiQ6MZP7
IntActiQ6MZP7, 42 interactors
MINTiQ6MZP7
STRINGi9606.ENSP00000341947

Structurei

Secondary structure

1749
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details

3D structure databases

ProteinModelPortaliQ6MZP7
SMRiQ6MZP7
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Domaini521 – 634CRCPROSITE-ProRule annotationAdd BLAST114

Region

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Regioni523 – 536DNA-binding1 PublicationAdd BLAST14
Regioni583 – 596Linker1 PublicationAdd BLAST14
Regioni599 – 612DNA-binding1 PublicationAdd BLAST14

Domaini

The CRC domain mediates DNA-binding (PubMed:19725879, PubMed:27465258). It contains two CXC subdomains (joined by a flexible linker) which are both required for efficient association with target DNA (PubMed:27465258). Each CXC subdomain coordinates three Zn2+ ions (PubMed:27465258).2 Publications

Sequence similaritiesi

Belongs to the lin-54 family.Curated

Phylogenomic databases

eggNOGiKOG1171 Eukaryota
ENOG4110UR5 LUCA
GeneTreeiENSGT00390000013974
HOGENOMiHOG000082518
HOVERGENiHBG108088
InParanoidiQ6MZP7
KOiK21776
OMAiTPGIQTQ
OrthoDBiEOG091G09E2
PhylomeDBiQ6MZP7
TreeFamiTF313189

Family and domain databases

InterProiView protein in InterPro
IPR005172 CRC
IPR028307 Lin-54_fam
IPR033467 Tesmin/TSO1-like_CXC
PANTHERiPTHR12446 PTHR12446, 1 hit
PfamiView protein in Pfam
PF03638 TCR, 2 hits
SMARTiView protein in SMART
SM01114 CXC, 2 hits
PROSITEiView protein in PROSITE
PS51634 CRC, 1 hit

Sequences (5+)i

Sequence statusi: Complete.

This entry describes 5 isoformsi produced by alternative splicing. AlignAdd to basket

This entry has 5 described isoforms and 1 potential isoform that is computationally mapped.iShow all

Isoform 1 (identifier: Q6MZP7-1) [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
MEVVPAEVNS LLPEEIMDTG ITLVDDDSIE AVIVSSPIPM ETELEEIVNI
60 70 80 90 100
NSTGDSTATP ISTEPITVYS NHTNQVAVNT TITKADSNTT VKPAFPSGLQ
110 120 130 140 150
KLGAQTPVTI SANQIILNKV SQTSDLKLGN QTLKPDGQKL ILTTLGKSGS
160 170 180 190 200
PIVLALPHSQ LPQAQKVTTQ AQSGDAKLPP QQIKVVTIGG RPEVKPVIGV
210 220 230 240 250
SALTPGSQLI NTTTQPSVLQ TQQLKTVQIA KKPRTPTSGP VITKLIFAKP
260 270 280 290 300
INSKAVTGQT TQVSPPVIAG RVLSQSTPGT PSKTITISES GVIGSTLNST
310 320 330 340 350
TQTPNKIAIS PLKSPNKAVK STVQTITVGG VSTSQFKTII PLATAPNVQQ
360 370 380 390 400
IQVPGSKFHY VRLVTATSAS SSTQPVSQNP STNTQPLQQA KPVVVNTTPV
410 420 430 440 450
RMSVPIVSAQ AVKQVVPKPI NPTSQIVTTS QPQQRLIMPA TPLPQIQPNL
460 470 480 490 500
TNLPPGTVLA PAPGTGNVGY AVLPAQYVTQ LQQSSYVSIA SNSTFTGTSG
510 520 530 540 550
IQTQARLPFN GIIPSESASR PRKPCNCTKS LCLKLYCDCF ANGEFCNNCN
560 570 580 590 600
CTNCYNNLEH ENERQKAIKA CLDRNPEAFK PKIGKGKEGE SDRRHSKGCN
610 620 630 640 650
CKRSGCLKNY CECYEAKIMC SSICKCIGCK NFEESPERKT LMHLADAAEV
660 670 680 690 700
RVQQQTAAKT KLSSQISDLL TRPTPALNSG GGKLPFTFVT KEVAEATCNC
710 720 730 740
LLAQAEQADK KGKSKAAAER MILEEFGRCL MSVINSAGKA KSDPCAMNC
Length:749
Mass (Da):79,494
Last modified:November 30, 2010 - v3
Checksum:iA3E4513CB0118B78
GO
Isoform 2 (identifier: Q6MZP7-2) [UniParc]FASTAAdd to basket

The sequence of this isoform differs from the canonical sequence as follows:
     229-317: Missing.

Note: No experimental confirmation available.
Show »
Length:660
Mass (Da):70,378
Checksum:iF34917B51B87B370
GO
Isoform 3 (identifier: Q6MZP7-3) [UniParc]FASTAAdd to basket

The sequence of this isoform differs from the canonical sequence as follows:
     8-228: Missing.

Show »
Length:528
Mass (Da):56,284
Checksum:i7EEAFDD538973450
GO
Isoform 4 (identifier: Q6MZP7-4) [UniParc]FASTAAdd to basket

The sequence of this isoform differs from the canonical sequence as follows:
     1-401: Missing.

Note: No experimental confirmation available.
Show »
Length:348
Mass (Da):37,613
Checksum:iB65DCCA3258768FB
GO
Isoform 5 (identifier: Q6MZP7-5) [UniParc]FASTAAdd to basket

The sequence of this isoform differs from the canonical sequence as follows:
     229-243: IAKKPRTPTSGPVIT → VGFFHSLLPELHQRP
     244-749: Missing.

Note: No experimental confirmation available.
Show »
Length:243
Mass (Da):25,743
Checksum:i6ECC642FE3E55419
GO

Computationally mapped potential isoform sequencesi

There is 1 potential isoform mapped to this entry.BLASTAlignShow allAdd to basket
EntryEntry nameProtein names
Gene namesLengthAnnotation
D6REW4D6REW4_HUMAN
Protein lin-54 homolog
LIN54
62Annotation score:

Sequence cautioni

The sequence BAC98377 differs from that shown. Reason: Erroneous initiation. Translation N-terminally shortened.Curated

Experimental Info

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Sequence conflicti9N → S in CAE45981 (PubMed:17974005).Curated1
Sequence conflicti743D → A in CAE45981 (PubMed:17974005).Curated1

Alternative sequence

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Alternative sequenceiVSP_0342721 – 401Missing in isoform 4. 1 PublicationAdd BLAST401
Alternative sequenceiVSP_0342738 – 228Missing in isoform 3. 2 PublicationsAdd BLAST221
Alternative sequenceiVSP_034274229 – 317Missing in isoform 2. 1 PublicationAdd BLAST89
Alternative sequenceiVSP_034275229 – 243IAKKP…GPVIT → VGFFHSLLPELHQRP in isoform 5. 1 PublicationAdd BLAST15
Alternative sequenceiVSP_034276244 – 749Missing in isoform 5. 1 PublicationAdd BLAST506

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AB111889 mRNA Translation: BAC98377.1 Different initiation.
AK292769 mRNA Translation: BAF85458.1
BX640657 mRNA Translation: CAE45799.1
BX640966 mRNA Translation: CAE45981.1
AC021105 Genomic DNA No translation available.
BC109277 mRNA Translation: AAI09278.1
BC109278 mRNA Translation: AAI09279.1
CCDSiCCDS3599.1 [Q6MZP7-1]
CCDS47089.1 [Q6MZP7-3]
CCDS75157.1 [Q6MZP7-2]
RefSeqiNP_001108479.1, NM_001115007.2 [Q6MZP7-3]
NP_001108480.1, NM_001115008.2 [Q6MZP7-3]
NP_001275925.1, NM_001288996.1 [Q6MZP7-2]
NP_001275926.1, NM_001288997.1 [Q6MZP7-3]
NP_919258.2, NM_194282.3 [Q6MZP7-1]
XP_005262807.1, XM_005262750.4 [Q6MZP7-1]
XP_006714144.1, XM_006714081.3 [Q6MZP7-1]
XP_016863217.1, XM_017007728.1 [Q6MZP7-2]
XP_016863218.1, XM_017007729.1 [Q6MZP7-4]
XP_016863219.1, XM_017007730.1 [Q6MZP7-4]
UniGeneiHs.96952

Genome annotation databases

EnsembliENST00000340417; ENSP00000341947; ENSG00000189308 [Q6MZP7-1]
ENST00000442461; ENSP00000398265; ENSG00000189308 [Q6MZP7-3]
ENST00000446851; ENSP00000407139; ENSG00000189308 [Q6MZP7-3]
ENST00000505397; ENSP00000425844; ENSG00000189308 [Q6MZP7-1]
ENST00000506560; ENSP00000423475; ENSG00000189308 [Q6MZP7-2]
ENST00000508171; ENSP00000427413; ENSG00000189308 [Q6MZP7-5]
ENST00000510557; ENSP00000421045; ENSG00000189308 [Q6MZP7-3]
GeneIDi132660
KEGGihsa:132660
UCSCiuc003hnx.5 human [Q6MZP7-1]

Keywords - Coding sequence diversityi

Alternative splicing

Similar proteinsi

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AB111889 mRNA Translation: BAC98377.1 Different initiation.
AK292769 mRNA Translation: BAF85458.1
BX640657 mRNA Translation: CAE45799.1
BX640966 mRNA Translation: CAE45981.1
AC021105 Genomic DNA No translation available.
BC109277 mRNA Translation: AAI09278.1
BC109278 mRNA Translation: AAI09279.1
CCDSiCCDS3599.1 [Q6MZP7-1]
CCDS47089.1 [Q6MZP7-3]
CCDS75157.1 [Q6MZP7-2]
RefSeqiNP_001108479.1, NM_001115007.2 [Q6MZP7-3]
NP_001108480.1, NM_001115008.2 [Q6MZP7-3]
NP_001275925.1, NM_001288996.1 [Q6MZP7-2]
NP_001275926.1, NM_001288997.1 [Q6MZP7-3]
NP_919258.2, NM_194282.3 [Q6MZP7-1]
XP_005262807.1, XM_005262750.4 [Q6MZP7-1]
XP_006714144.1, XM_006714081.3 [Q6MZP7-1]
XP_016863217.1, XM_017007728.1 [Q6MZP7-2]
XP_016863218.1, XM_017007729.1 [Q6MZP7-4]
XP_016863219.1, XM_017007730.1 [Q6MZP7-4]
UniGeneiHs.96952

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
5FD3X-ray2.42A/B515-646[»]
ProteinModelPortaliQ6MZP7
SMRiQ6MZP7
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi126328, 27 interactors
CORUMiQ6MZP7
IntActiQ6MZP7, 42 interactors
MINTiQ6MZP7
STRINGi9606.ENSP00000341947

PTM databases

iPTMnetiQ6MZP7
PhosphoSitePlusiQ6MZP7

Polymorphism and mutation databases

DMDMi313104222

Proteomic databases

EPDiQ6MZP7
MaxQBiQ6MZP7
PaxDbiQ6MZP7
PeptideAtlasiQ6MZP7
PRIDEiQ6MZP7
ProteomicsDBi66576
66577 [Q6MZP7-2]
66578 [Q6MZP7-3]
66579 [Q6MZP7-4]
66580 [Q6MZP7-5]

Protocols and materials databases

DNASUi132660
Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsembliENST00000340417; ENSP00000341947; ENSG00000189308 [Q6MZP7-1]
ENST00000442461; ENSP00000398265; ENSG00000189308 [Q6MZP7-3]
ENST00000446851; ENSP00000407139; ENSG00000189308 [Q6MZP7-3]
ENST00000505397; ENSP00000425844; ENSG00000189308 [Q6MZP7-1]
ENST00000506560; ENSP00000423475; ENSG00000189308 [Q6MZP7-2]
ENST00000508171; ENSP00000427413; ENSG00000189308 [Q6MZP7-5]
ENST00000510557; ENSP00000421045; ENSG00000189308 [Q6MZP7-3]
GeneIDi132660
KEGGihsa:132660
UCSCiuc003hnx.5 human [Q6MZP7-1]

Organism-specific databases

CTDi132660
DisGeNETi132660
EuPathDBiHostDB:ENSG00000189308.10
GeneCardsiLIN54
H-InvDBiHIX0024607
HGNCiHGNC:25397 LIN54
HPAiHPA056606
MIMi613367 gene
neXtProtiNX_Q6MZP7
OpenTargetsiENSG00000189308
PharmGKBiPA162394056
HUGEiSearch...
GenAtlasiSearch...

Phylogenomic databases

eggNOGiKOG1171 Eukaryota
ENOG4110UR5 LUCA
GeneTreeiENSGT00390000013974
HOGENOMiHOG000082518
HOVERGENiHBG108088
InParanoidiQ6MZP7
KOiK21776
OMAiTPGIQTQ
OrthoDBiEOG091G09E2
PhylomeDBiQ6MZP7
TreeFamiTF313189

Enzyme and pathway databases

ReactomeiR-HSA-1362277 Transcription of E2F targets under negative control by DREAM complex
R-HSA-1362300 Transcription of E2F targets under negative control by p107 (RBL1) and p130 (RBL2) in complex with HDAC1
R-HSA-1538133 G0 and Early G1
R-HSA-156711 Polo-like kinase mediated events
R-HSA-539107 Activation of E2F1 target genes at G1/S
R-HSA-69202 Cyclin E associated events during G1/S transition
R-HSA-69656 Cyclin A:Cdk2-associated events at S phase entry

Miscellaneous databases

ChiTaRSiLIN54 human
GenomeRNAii132660
PROiPR:Q6MZP7
SOURCEiSearch...

Gene expression databases

BgeeiENSG00000189308 Expressed in 105 organ(s), highest expression level in corpus callosum
CleanExiHS_LIN54
ExpressionAtlasiQ6MZP7 baseline and differential
GenevisibleiQ6MZP7 HS

Family and domain databases

InterProiView protein in InterPro
IPR005172 CRC
IPR028307 Lin-54_fam
IPR033467 Tesmin/TSO1-like_CXC
PANTHERiPTHR12446 PTHR12446, 1 hit
PfamiView protein in Pfam
PF03638 TCR, 2 hits
SMARTiView protein in SMART
SM01114 CXC, 2 hits
PROSITEiView protein in PROSITE
PS51634 CRC, 1 hit
ProtoNetiSearch...

Entry informationi

Entry nameiLIN54_HUMAN
AccessioniPrimary (citable) accession number: Q6MZP7
Secondary accession number(s): Q32M68
, Q32M69, Q6N071, Q76B60
Entry historyiIntegrated into UniProtKB/Swiss-Prot: July 22, 2008
Last sequence update: November 30, 2010
Last modified: September 12, 2018
This is version 110 of the entry and version 3 of the sequence. See 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

3D-structure, Complete proteome, Reference proteome
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Main funding by: National Institutes of Health

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