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Protein

SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily A containing DEAD/H box 1

Gene

SMARCAD1

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

Functioni

DNA helicase that possesses intrinsic ATP-dependent nucleosome-remodeling activity and is both required for DNA repair and heterochromatin organization. Promotes DNA end resection of double-strand breaks (DSBs) following DNA damage: probably acts by weakening histone DNA interactions in nucleosomes flanking DSBs. Required for the restoration of heterochromatin organization after replication. Acts at replication sites to facilitate the maintenance of heterochromatin by directing H3 and H4 histones deacetylation, H3 'Lys-9' trimethylation (H3K9me3) and restoration of silencing.2 Publications

Catalytic activityi

ATP + H2O = ADP + phosphate.

Regions

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Nucleotide bindingi521 – 529ATPPROSITE-ProRule annotation9
Nucleotide bindingi897 – 904ATPPROSITE-ProRule annotation8

GO - Molecular functioni

  • ATP binding Source: UniProtKB-KW
  • DNA binding Source: UniProtKB
  • helicase activity Source: UniProtKB-KW
  • nucleic acid binding Source: UniProtKB

GO - Biological processi

  • ATP-dependent chromatin remodeling Source: UniProtKB
  • chromatin organization Source: UniProtKB
  • chromatin remodeling Source: UniProtKB
  • chromosome separation Source: UniProtKB
  • DNA double-strand break processing Source: UniProtKB
  • histone H3 deacetylation Source: UniProtKB
  • histone H4 deacetylation Source: UniProtKB
  • nucleotide metabolic process Source: UniProtKB
  • positive regulation of transcription, DNA-templated Source: UniProtKB
  • protein homooligomerization Source: UniProtKB
  • regulation of DNA recombination Source: UniProtKB
Complete GO annotation...

Keywords - Molecular functioni

Chromatin regulator, Helicase, Hydrolase

Keywords - Biological processi

DNA damage, DNA repair

Keywords - Ligandi

ATP-binding, DNA-binding, Nucleotide-binding

Enzyme and pathway databases

SIGNORiQ9H4L7.

Names & Taxonomyi

Protein namesi
Recommended name:
SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily A containing DEAD/H box 1 (EC:3.6.4.12)
Alternative name(s):
ATP-dependent helicase 1
Short name:
hHEL1
Gene namesi
Name:SMARCAD1
Synonyms:KIAA1122
OrganismiHomo sapiens (Human)
Taxonomic identifieri9606 [NCBI]
Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresPrimatesHaplorrhiniCatarrhiniHominidaeHomo
Proteomesi
  • UP000005640 Componenti: Chromosome 4

Organism-specific databases

HGNCiHGNC:18398. SMARCAD1.

Subcellular locationi

  • Nucleus
  • Chromosome

  • Note: Colocalizes with PCNA at replication forks during S phase. Recruited to double-strand breaks (DSBs) sites of DNA damage.

GO - Cellular componenti

  • heterochromatin Source: UniProtKB
  • nuclear matrix Source: UniProtKB
  • nuclear replication fork Source: UniProtKB
  • nucleoplasm Source: HPA
  • site of double-strand break Source: UniProtKB
Complete GO annotation...

Keywords - Cellular componenti

Chromosome, Nucleus

Pathology & Biotechi

Involvement in diseasei

Adermatoglyphia (ADERM)1 Publication
The disease is caused by mutations affecting the gene represented in this entry. A splice site mutation causing aberrant splicing of isoform 3 is likely to exert a loss-of-function effect and is associated with ADERM.
Disease descriptionAn autosomal dominant condition characterized by the lack of epidermal ridges on the palms and soles, which results in the absence of fingerprints, and is associated with a reduced number of sweat gland openings and reduced sweating of palms and soles.
See also OMIM:136000

Mutagenesis

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Mutagenesisi528K → R: No effect on subcellular localization and on histone deacetylation. 1 Publication1

Organism-specific databases

DisGeNETi56916.
MalaCardsiSMARCAD1.
MIMi136000. phenotype.
OpenTargetsiENSG00000163104.
Orphaneti289465. Isolated adermatoglyphia.
PharmGKBiPA134954731.

Polymorphism and mutation databases

BioMutaiSMARCAD1.
DMDMi306526240.

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_00000743561 – 1026SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily A containing DEAD/H box 1Add BLAST1026

Amino acid modifications

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Modified residuei1N-acetylmethionineCombined sources1
Modified residuei54PhosphothreonineCombined sources1
Modified residuei57PhosphoserineCombined sources1
Modified residuei71PhosphothreonineCombined sources1
Cross-linki77Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in SUMO2)Combined sources
Modified residuei79PhosphoserineCombined sources1
Modified residuei124PhosphoserineCombined sources1
Modified residuei127PhosphoserineCombined sources1
Modified residuei132PhosphoserineCombined sources1
Modified residuei146PhosphoserineCombined sources1
Modified residuei152PhosphoserineCombined sources1
Modified residuei211PhosphoserineCombined sources1
Modified residuei214PhosphoserineCombined sources1
Modified residuei217PhosphotyrosineCombined sources1
Modified residuei239PhosphoserineCombined sources1
Modified residuei242PhosphoserineCombined sources1
Modified residuei302PhosphoserineCombined sources1

Keywords - PTMi

Acetylation, Isopeptide bond, Phosphoprotein, Ubl conjugation

Proteomic databases

EPDiQ9H4L7.
MaxQBiQ9H4L7.
PaxDbiQ9H4L7.
PeptideAtlasiQ9H4L7.
PRIDEiQ9H4L7.

PTM databases

iPTMnetiQ9H4L7.
PhosphoSitePlusiQ9H4L7.

Expressioni

Tissue specificityi

Isoform 1 is expressed ubiquitously. Isoform 3 is expressed mainly in skin, fibroblasts, keratinocytes and esophagus.2 Publications

Gene expression databases

BgeeiENSG00000163104.
CleanExiHS_SMARCAD1.
ExpressionAtlasiQ9H4L7. baseline and differential.
GenevisibleiQ9H4L7. HS.

Organism-specific databases

HPAiHPA016737.

Interactioni

Subunit structurei

Binds to DNA preferentially in the vicinity of transcriptional start sites. Interacts with MSH2 and TRIM28. Part of a complex composed of TRIM28, HDAC1, HDAC2 and EHMT2. Interacts with PCNA.2 Publications

Protein-protein interaction databases

BioGridi121244. 137 interactors.
IntActiQ9H4L7. 6 interactors.
STRINGi9606.ENSP00000351947.

Structurei

3D structure databases

ProteinModelPortaliQ9H4L7.
SMRiQ9H4L7.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Domaini157 – 199CUE 1PROSITE-ProRule annotationAdd BLAST43
Domaini251 – 294CUE 2PROSITE-ProRule annotationAdd BLAST44
Domaini509 – 677Helicase ATP-bindingPROSITE-ProRule annotationAdd BLAST169
Domaini858 – 1010Helicase C-terminalPROSITE-ProRule annotationAdd BLAST153

Motif

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Motifi628 – 631DEGH box4
Motifi721 – 738Nuclear localization signalSequence analysisAdd BLAST18
Motifi1005 – 1008DEGD box4

Sequence similaritiesi

Belongs to the SNF2/RAD54 helicase family.Curated
Contains 2 CUE domains.PROSITE-ProRule annotation
Contains 1 helicase ATP-binding domain.PROSITE-ProRule annotation
Contains 1 helicase C-terminal domain.PROSITE-ProRule annotation

Keywords - Domaini

Repeat

Phylogenomic databases

eggNOGiKOG0389. Eukaryota.
ENOG410XNUT. LUCA.
GeneTreeiENSGT00860000133865.
HOGENOMiHOG000172362.
HOVERGENiHBG055804.
InParanoidiQ9H4L7.
KOiK14439.
OMAiRSQNYPK.
OrthoDBiEOG091G0307.
PhylomeDBiQ9H4L7.
TreeFamiTF105768.

Family and domain databases

Gene3Di3.40.50.300. 2 hits.
InterProiIPR003892. CUE.
IPR014001. Helicase_ATP-bd.
IPR001650. Helicase_C.
IPR027417. P-loop_NTPase.
IPR000330. SNF2_N.
[Graphical view]
PfamiPF00271. Helicase_C. 1 hit.
PF00176. SNF2_N. 1 hit.
[Graphical view]
SMARTiSM00487. DEXDc. 1 hit.
SM00490. HELICc. 1 hit.
[Graphical view]
SUPFAMiSSF52540. SSF52540. 2 hits.
PROSITEiPS51140. CUE. 2 hits.
PS51192. HELICASE_ATP_BIND_1. 1 hit.
PS51194. HELICASE_CTER. 1 hit.
[Graphical view]

Sequences (3)i

Sequence statusi: Complete.

This entry describes 3 isoformsi produced by alternative splicing. AlignAdd to basket

Isoform 1 (identifier: Q9H4L7-1) [UniParc]FASTAAdd to basket
Also known as: Long

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
MNLFNLDRFR FEKRNKIEEA PEATPQPSQP GPSSPISLSA EEENAEGEVS
60 70 80 90 100
RANTPDSDIT EKTEDSSVPE TPDNERKASI SYFKNQRGIQ YIDLSSDSED
110 120 130 140 150
VVSPNCSNTV QEKTFNKDTV IIVSEPSEDE ESQGLPTMAR RNDDISELED
160 170 180 190 200
LSELEDLKDA KLQTLKELFP QRSDNDLLKL IESTSTMDGA IAAALLMFGD
210 220 230 240 250
AGGGPRKRKL SSSSEPYEED EFNDDQSIKK TRLDHGEESN ESAESSSNWE
260 270 280 290 300
KQESIVLKLQ KEFPNFDKQE LREVLKEHEW MYTEALESLK VFAEDQDMQY
310 320 330 340 350
VSQSEVPNGK EVSSRSQNYP KNATKTKLKQ KFSMKAQNGF NKKRKKNVFN
360 370 380 390 400
PKRVVEDSEY DSGSDVGSSL DEDYSSGEEV MEDGYKGKIL HFLQDASIGE
410 420 430 440 450
LTLIPQCSQK KAQKITELRP FNSWEALFTK MSKTNGLSED LIWHCKTLIQ
460 470 480 490 500
ERDVVIRLMN KCEDISNKLT KQVTMLTGNG GGWNIEQPSI LNQSLSLKPY
510 520 530 540 550
QKVGLNWLAL VHKHGLNGIL ADEMGLGKTI QAIAFLAYLY QEGNNGPHLI
560 570 580 590 600
VVPASTIDNW LREVNLWCPT LKVLCYYGSQ EERKQIRFNI HSRYEDYNVI
610 620 630 640 650
VTTYNCAISS SDDRSLFRRL KLNYAIFDEG HMLKNMGSIR YQHLMTINAN
660 670 680 690 700
NRLLLTGTPV QNNLLELMSL LNFVMPHMFS SSTSEIRRMF SSKTKSADEQ
710 720 730 740 750
SIYEKERIAH AKQIIKPFIL RRVKEEVLKQ LPPKKDRIEL CAMSEKQEQL
760 770 780 790 800
YLGLFNRLKK SINNLEKNTE MCNVMMQLRK MANHPLLHRQ YYTAEKLKEM
810 820 830 840 850
SQLMLKEPTH CEANPDLIFE DMEVMTDFEL HVLCKQYRHI NNFQLDMDLI
860 870 880 890 900
LDSGKFRVLG CILSELKQKG DRVVLFSQFT MMLDILEVLL KHHQHRYLRL
910 920 930 940 950
DGKTQISERI HLIDEFNTDM DIFVFLLSTK AGGLGINLTS ANVVILHDID
960 970 980 990 1000
CNPYNDKQAE DRCHRVGQTK EVLVIKLISQ GTIEESMLKI NQQKLKLEQD
1010 1020
MTTVDEGDEG SMPADIATLL KTSMGL
Length:1,026
Mass (Da):117,402
Last modified:October 5, 2010 - v2
Checksum:i0A5DB5653F478413
GO
Isoform 2 (identifier: Q9H4L7-2) [UniParc]FASTAAdd to basket

The sequence of this isoform differs from the canonical sequence as follows:
     765-765: L → LVT

Show »
Length:1,028
Mass (Da):117,603
Checksum:i0F1C3F3AB7224F23
GO
Isoform 3 (identifier: Q9H4L7-3) [UniParc]FASTAAdd to basket
Also known as: Short

The sequence of this isoform differs from the canonical sequence as follows:
     1-430: Missing.

Note: Skin-specific.
Show »
Length:596
Mass (Da):68,774
Checksum:i6BBB9C2EB02E2A97
GO

Sequence cautioni

The sequence AAH17953 differs from that shown. Contaminating sequence. Potential poly-A sequence.Curated
The sequence BAA86436 differs from that shown. Reason: Erroneous initiation. Translation N-terminally shortened.Curated
The sequence BAB14759 differs from that shown. Reason: Erroneous initiation. Translation N-terminally extended.Curated

Experimental Info

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Sequence conflicti215E → D in AAH17953 (PubMed:15489334).Curated1
Sequence conflicti937N → D in BAB14759 (PubMed:14702039).Curated1

Natural variant

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Natural variantiVAR_02803766S → F.Corresponds to variant rs11723410dbSNPEnsembl.1
Natural variantiVAR_028038135L → F.Corresponds to variant rs2664891dbSNPEnsembl.1
Natural variantiVAR_028039140R → C.Corresponds to variant rs2632398dbSNPEnsembl.1
Natural variantiVAR_028040245S → Y.Corresponds to variant rs3103117dbSNPEnsembl.1
Natural variantiVAR_028041247S → N.Combined sources1 PublicationCorresponds to variant rs11722476dbSNPEnsembl.1
Natural variantiVAR_028042301V → A.Combined sources2 PublicationsCorresponds to variant rs7439869dbSNPEnsembl.1
Natural variantiVAR_028043351P → Q.1 PublicationCorresponds to variant rs17854344dbSNPEnsembl.1
Natural variantiVAR_028044972V → A.1 PublicationCorresponds to variant rs17857297dbSNPEnsembl.1

Alternative sequence

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Alternative sequenceiVSP_0431101 – 430Missing in isoform 3. 1 PublicationAdd BLAST430
Alternative sequenceiVSP_007104765L → LVT in isoform 2. 3 Publications1

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AY008271 mRNA. Translation: AAG16639.1.
AB032948 mRNA. Translation: BAA86436.2. Different initiation.
AK023990 mRNA. Translation: BAB14759.1. Different initiation.
AK027490 mRNA. Translation: BAB55150.1.
AK301668 mRNA. Translation: BAH13535.1.
AC096746 Genomic DNA. No translation available.
BC017953 mRNA. Translation: AAH17953.1. Sequence problems.
BC045534 mRNA. Translation: AAH45534.1.
AL359929 mRNA. Translation: CAB95769.1.
AL512768 mRNA. Translation: CAC21685.1.
CCDSiCCDS3639.1. [Q9H4L7-1]
CCDS47101.1. [Q9H4L7-2]
CCDS58914.1. [Q9H4L7-3]
RefSeqiNP_001121901.1. NM_001128429.2. [Q9H4L7-2]
NP_001121902.1. NM_001128430.1. [Q9H4L7-2]
NP_001241878.1. NM_001254949.1. [Q9H4L7-3]
NP_064544.2. NM_020159.4. [Q9H4L7-1]
XP_016863952.1. XM_017008463.1. [Q9H4L7-1]
UniGeneiHs.410406.

Genome annotation databases

EnsembliENST00000354268; ENSP00000346217; ENSG00000163104. [Q9H4L7-1]
ENST00000359052; ENSP00000351947; ENSG00000163104. [Q9H4L7-2]
ENST00000457823; ENSP00000415576; ENSG00000163104. [Q9H4L7-2]
ENST00000509418; ENSP00000423286; ENSG00000163104. [Q9H4L7-3]
GeneIDi56916.
KEGGihsa:56916.
UCSCiuc003htb.5. human. [Q9H4L7-1]

Keywords - Coding sequence diversityi

Alternative splicing, Polymorphism

Cross-referencesi

Web resourcesi

Protein Spotlight

The ends of our fingers - Issue 136 of March 2012

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AY008271 mRNA. Translation: AAG16639.1.
AB032948 mRNA. Translation: BAA86436.2. Different initiation.
AK023990 mRNA. Translation: BAB14759.1. Different initiation.
AK027490 mRNA. Translation: BAB55150.1.
AK301668 mRNA. Translation: BAH13535.1.
AC096746 Genomic DNA. No translation available.
BC017953 mRNA. Translation: AAH17953.1. Sequence problems.
BC045534 mRNA. Translation: AAH45534.1.
AL359929 mRNA. Translation: CAB95769.1.
AL512768 mRNA. Translation: CAC21685.1.
CCDSiCCDS3639.1. [Q9H4L7-1]
CCDS47101.1. [Q9H4L7-2]
CCDS58914.1. [Q9H4L7-3]
RefSeqiNP_001121901.1. NM_001128429.2. [Q9H4L7-2]
NP_001121902.1. NM_001128430.1. [Q9H4L7-2]
NP_001241878.1. NM_001254949.1. [Q9H4L7-3]
NP_064544.2. NM_020159.4. [Q9H4L7-1]
XP_016863952.1. XM_017008463.1. [Q9H4L7-1]
UniGeneiHs.410406.

3D structure databases

ProteinModelPortaliQ9H4L7.
SMRiQ9H4L7.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi121244. 137 interactors.
IntActiQ9H4L7. 6 interactors.
STRINGi9606.ENSP00000351947.

PTM databases

iPTMnetiQ9H4L7.
PhosphoSitePlusiQ9H4L7.

Polymorphism and mutation databases

BioMutaiSMARCAD1.
DMDMi306526240.

Proteomic databases

EPDiQ9H4L7.
MaxQBiQ9H4L7.
PaxDbiQ9H4L7.
PeptideAtlasiQ9H4L7.
PRIDEiQ9H4L7.

Protocols and materials databases

DNASUi56916.
Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsembliENST00000354268; ENSP00000346217; ENSG00000163104. [Q9H4L7-1]
ENST00000359052; ENSP00000351947; ENSG00000163104. [Q9H4L7-2]
ENST00000457823; ENSP00000415576; ENSG00000163104. [Q9H4L7-2]
ENST00000509418; ENSP00000423286; ENSG00000163104. [Q9H4L7-3]
GeneIDi56916.
KEGGihsa:56916.
UCSCiuc003htb.5. human. [Q9H4L7-1]

Organism-specific databases

CTDi56916.
DisGeNETi56916.
GeneCardsiSMARCAD1.
H-InvDBHIX0004380.
HGNCiHGNC:18398. SMARCAD1.
HPAiHPA016737.
MalaCardsiSMARCAD1.
MIMi136000. phenotype.
612761. gene.
neXtProtiNX_Q9H4L7.
OpenTargetsiENSG00000163104.
Orphaneti289465. Isolated adermatoglyphia.
PharmGKBiPA134954731.
HUGEiSearch...
GenAtlasiSearch...

Phylogenomic databases

eggNOGiKOG0389. Eukaryota.
ENOG410XNUT. LUCA.
GeneTreeiENSGT00860000133865.
HOGENOMiHOG000172362.
HOVERGENiHBG055804.
InParanoidiQ9H4L7.
KOiK14439.
OMAiRSQNYPK.
OrthoDBiEOG091G0307.
PhylomeDBiQ9H4L7.
TreeFamiTF105768.

Enzyme and pathway databases

SIGNORiQ9H4L7.

Miscellaneous databases

ChiTaRSiSMARCAD1. human.
GeneWikiiSMARCAD1.
GenomeRNAii56916.
PROiQ9H4L7.
SOURCEiSearch...

Gene expression databases

BgeeiENSG00000163104.
CleanExiHS_SMARCAD1.
ExpressionAtlasiQ9H4L7. baseline and differential.
GenevisibleiQ9H4L7. HS.

Family and domain databases

Gene3Di3.40.50.300. 2 hits.
InterProiIPR003892. CUE.
IPR014001. Helicase_ATP-bd.
IPR001650. Helicase_C.
IPR027417. P-loop_NTPase.
IPR000330. SNF2_N.
[Graphical view]
PfamiPF00271. Helicase_C. 1 hit.
PF00176. SNF2_N. 1 hit.
[Graphical view]
SMARTiSM00487. DEXDc. 1 hit.
SM00490. HELICc. 1 hit.
[Graphical view]
SUPFAMiSSF52540. SSF52540. 2 hits.
PROSITEiPS51140. CUE. 2 hits.
PS51192. HELICASE_ATP_BIND_1. 1 hit.
PS51194. HELICASE_CTER. 1 hit.
[Graphical view]
ProtoNetiSearch...

Entry informationi

Entry nameiSMRCD_HUMAN
AccessioniPrimary (citable) accession number: Q9H4L7
Secondary accession number(s): B7Z799
, Q05D56, Q96SX1, Q9H017, Q9H860, Q9NPU9, Q9ULU7
Entry historyi
Integrated into UniProtKB/Swiss-Prot: March 28, 2003
Last sequence update: October 5, 2010
Last modified: November 30, 2016
This is version 151 of the entry and version 2 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 4
    Human chromosome 4: entries, gene names and cross-references to MIM
  2. Human entries with polymorphisms or disease mutations
    List of human entries with polymorphisms or disease mutations
  3. Human polymorphisms and disease mutations
    Index of human polymorphisms and disease mutations
  4. MIM cross-references
    Online Mendelian Inheritance in Man (MIM) cross-references in UniProtKB/Swiss-Prot
  5. Protein Spotlight
    Protein Spotlight articles and cited UniProtKB/Swiss-Prot entries
  6. 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.