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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
Rattus norvegicus (Rat)
Status
Reviewed-Annotation score: Annotation score: 4 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 (By similarity).By similarity

Catalytic activityi

ATP + H2O = ADP + phosphate.

Regions

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Nucleotide bindingi519 – 5279ATPPROSITE-ProRule annotation
Nucleotide bindingi895 – 9028ATPPROSITE-ProRule annotation

GO - Molecular functioni

GO - Biological processi

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

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)
Gene namesi
Name:Smarcad1
OrganismiRattus norvegicus (Rat)
Taxonomic identifieri10116 [NCBI]
Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresGliresRodentiaSciurognathiMuroideaMuridaeMurinaeRattus
Proteomesi
  • UP000002494 Componenti: Chromosome 4

Organism-specific databases

RGDi1309640. Smarcad1.

Subcellular locationi

  • Nucleus By similarity
  • Chromosome By similarity

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

GO - Cellular componenti

Complete GO annotation...

Keywords - Cellular componenti

Chromosome, Nucleus

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 10241024SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily A containing DEAD/H box 1PRO_0000416934Add
BLAST

Amino acid modifications

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Modified residuei1 – 11N-acetylmethionineBy similarity
Modified residuei54 – 541PhosphothreonineBy similarity
Modified residuei57 – 571PhosphoserineBy similarity
Cross-linki77 – 77Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in SUMO2)By similarity
Modified residuei79 – 791PhosphoserineBy similarity
Modified residuei124 – 1241PhosphoserineCombined sources
Modified residuei127 – 1271PhosphoserineCombined sources
Modified residuei132 – 1321PhosphoserineBy similarity
Modified residuei145 – 1451PhosphoserineBy similarity
Modified residuei151 – 1511PhosphoserineCombined sources
Modified residuei210 – 2101PhosphoserineBy similarity
Modified residuei213 – 2131PhosphoserineBy similarity
Modified residuei216 – 2161PhosphotyrosineBy similarity
Modified residuei238 – 2381PhosphoserineBy similarity
Modified residuei241 – 2411PhosphoserineBy similarity
Modified residuei301 – 3011PhosphoserineBy similarity

Keywords - PTMi

Acetylation, Isopeptide bond, Phosphoprotein, Ubl conjugation

Proteomic databases

PaxDbiD3Z9Z9.
PRIDEiD3Z9Z9.

PTM databases

iPTMnetiD3Z9Z9.

Expressioni

Gene expression databases

GenevisibleiD3Z9Z9. RN.

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 (By similarity).By similarity

Protein-protein interaction databases

STRINGi10116.ENSRNOP00000008585.

Structurei

3D structure databases

ProteinModelPortaliD3Z9Z9.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Domaini156 – 19843CUE 1PROSITE-ProRule annotationAdd
BLAST
Domaini250 – 29344CUE 2PROSITE-ProRule annotationAdd
BLAST
Domaini507 – 675169Helicase ATP-bindingPROSITE-ProRule annotationAdd
BLAST
Domaini856 – 1008153Helicase C-terminalPROSITE-ProRule annotationAdd
BLAST

Motif

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Motifi626 – 6294DEGH boxBy similarity
Motifi719 – 73618Nuclear localization signalSequence analysisAdd
BLAST
Motifi1003 – 10064DEAD boxPROSITE-ProRule annotation

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.
GeneTreeiENSGT00630000089890.
InParanoidiD3Z9Z9.
KOiK14439.
OMAiRSQNYPK.
OrthoDBiEOG7QNVKC.
PhylomeDBiD3Z9Z9.
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]

Sequencei

Sequence statusi: Complete.

D3Z9Z9-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MNLFNLDRFR FEKRSKIEEA PEAAPQPSQP GPSSPISLSA EEENAEGEVS
60 70 80 90 100
RANTPDSDVT EKTEDSSVPE PPDNESKASL SCFQNQRTIQ EYIDLSSDSE
110 120 130 140 150
DVSPNCSSTV QEKKFSKDTV IIVSEPSEDE ESHDLPSATR RNDISELEDL
160 170 180 190 200
SELEDLKDAK LQTLKELFPQ RSDSDLLKLI DSTSTMDGAI AAALLKFGDA
210 220 230 240 250
GGGPRKRKLS SSSEAYEEDE ANDDQSLKKP RGDRREESNE SAEASSNWEK
260 270 280 290 300
QESIVLKLQK EFPNFDKQEL REVLKEHEWM YTEALESLKV FAEDQDVQCA
310 320 330 340 350
SQSEVTNGKE VARNQNYSKN AAKIKMKQKI SMKPQNGFNK KRKKNVFNPK
360 370 380 390 400
KAVEDSEYDS GSDAGSSLDE DYSSCEEVME DGYKGKILHF LQDASIGELT
410 420 430 440 450
LIPKCSQKKA QKIIELRPFN NWETLFTKMS KINGLSEDLI WNCKTVIQER
460 470 480 490 500
DVVIRLMNKC EDISNKLTKQ VTMLTGNGGG WNIEQPSLLN QSLSLKPYQK
510 520 530 540 550
VGLNWLALVH KHGLNGILAD EMGLGKTIQA IAFLAYLFQE GNKGPHLIVV
560 570 580 590 600
PASTIDNWLR EVNLWCPTLN VLCYYGSQEE RKQIRFNIHN KYEDYNVIVT
610 620 630 640 650
TYNCAISSSD DRSLFRRLKL NYAIFDEGHM LKNMGSIRYQ HLMTINARNR
660 670 680 690 700
LLLTGTPVQN NLLELMSLLN FVMPHMFSSS TSEIRRMFSS KTKPADEQSI
710 720 730 740 750
YEKERIAHAK QIIKPFILRR VKEEVLKLLP PKKDQIELCA MSEKQEQLYS
760 770 780 790 800
GLFNRLKKSI NNLEKNTEMC NVMMQLRKMA NHPLLHRQYY TAEKLKEMSQ
810 820 830 840 850
LMLKEPTHCE ANPDLIFEDM EVMTDFELHV LCKQYQHINS YQLDMDLILD
860 870 880 890 900
SGKFRTLGCI LSELKQKGDR VVLFSQFTMM LDILEVLLKH HQHRYLRLDG
910 920 930 940 950
KTQISERIHL IDEFNTDMDI FVFLLSTKAG GLGINLTSAN VVILHDIDCN
960 970 980 990 1000
PYNDKQAEDR CHRVGQTKEV LVIKLISQGT IEESMLKINQ QKLKLEQDMT
1010 1020
TVDEADEGSM PADIATLLKT SMGL
Length:1,024
Mass (Da):116,788
Last modified:April 20, 2010 - v1
Checksum:i0378D83371B66539
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AABR03032021 Genomic DNA. No translation available.
RefSeqiNP_001101334.2. NM_001107864.2.
XP_006236661.1. XM_006236599.1.
XP_006236662.1. XM_006236600.2.
UniGeneiRn.7758.

Genome annotation databases

EnsembliENSRNOT00000008585; ENSRNOP00000008585; ENSRNOG00000006391.
GeneIDi312398.
KEGGirno:312398.
UCSCiRGD:1309640. rat.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AABR03032021 Genomic DNA. No translation available.
RefSeqiNP_001101334.2. NM_001107864.2.
XP_006236661.1. XM_006236599.1.
XP_006236662.1. XM_006236600.2.
UniGeneiRn.7758.

3D structure databases

ProteinModelPortaliD3Z9Z9.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

STRINGi10116.ENSRNOP00000008585.

PTM databases

iPTMnetiD3Z9Z9.

Proteomic databases

PaxDbiD3Z9Z9.
PRIDEiD3Z9Z9.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsembliENSRNOT00000008585; ENSRNOP00000008585; ENSRNOG00000006391.
GeneIDi312398.
KEGGirno:312398.
UCSCiRGD:1309640. rat.

Organism-specific databases

CTDi56916.
RGDi1309640. Smarcad1.

Phylogenomic databases

eggNOGiKOG0389. Eukaryota.
ENOG410XNUT. LUCA.
GeneTreeiENSGT00630000089890.
InParanoidiD3Z9Z9.
KOiK14439.
OMAiRSQNYPK.
OrthoDBiEOG7QNVKC.
PhylomeDBiD3Z9Z9.
TreeFamiTF105768.

Miscellaneous databases

PROiD3Z9Z9.

Gene expression databases

GenevisibleiD3Z9Z9. RN.

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...

Publicationsi

  1. "Genome sequence of the Brown Norway rat yields insights into mammalian evolution."
    Gibbs R.A., Weinstock G.M., Metzker M.L., Muzny D.M., Sodergren E.J., Scherer S., Scott G., Steffen D., Worley K.C., Burch P.E., Okwuonu G., Hines S., Lewis L., Deramo C., Delgado O., Dugan-Rocha S., Miner G., Morgan M.
    , Hawes A., Gill R., Holt R.A., Adams M.D., Amanatides P.G., Baden-Tillson H., Barnstead M., Chin S., Evans C.A., Ferriera S., Fosler C., Glodek A., Gu Z., Jennings D., Kraft C.L., Nguyen T., Pfannkoch C.M., Sitter C., Sutton G.G., Venter J.C., Woodage T., Smith D., Lee H.-M., Gustafson E., Cahill P., Kana A., Doucette-Stamm L., Weinstock K., Fechtel K., Weiss R.B., Dunn D.M., Green E.D., Blakesley R.W., Bouffard G.G., De Jong P.J., Osoegawa K., Zhu B., Marra M., Schein J., Bosdet I., Fjell C., Jones S., Krzywinski M., Mathewson C., Siddiqui A., Wye N., McPherson J., Zhao S., Fraser C.M., Shetty J., Shatsman S., Geer K., Chen Y., Abramzon S., Nierman W.C., Havlak P.H., Chen R., Durbin K.J., Egan A., Ren Y., Song X.-Z., Li B., Liu Y., Qin X., Cawley S., Cooney A.J., D'Souza L.M., Martin K., Wu J.Q., Gonzalez-Garay M.L., Jackson A.R., Kalafus K.J., McLeod M.P., Milosavljevic A., Virk D., Volkov A., Wheeler D.A., Zhang Z., Bailey J.A., Eichler E.E., Tuzun E., Birney E., Mongin E., Ureta-Vidal A., Woodwark C., Zdobnov E., Bork P., Suyama M., Torrents D., Alexandersson M., Trask B.J., Young J.M., Huang H., Wang H., Xing H., Daniels S., Gietzen D., Schmidt J., Stevens K., Vitt U., Wingrove J., Camara F., Mar Alba M., Abril J.F., Guigo R., Smit A., Dubchak I., Rubin E.M., Couronne O., Poliakov A., Huebner N., Ganten D., Goesele C., Hummel O., Kreitler T., Lee Y.-A., Monti J., Schulz H., Zimdahl H., Himmelbauer H., Lehrach H., Jacob H.J., Bromberg S., Gullings-Handley J., Jensen-Seaman M.I., Kwitek A.E., Lazar J., Pasko D., Tonellato P.J., Twigger S., Ponting C.P., Duarte J.M., Rice S., Goodstadt L., Beatson S.A., Emes R.D., Winter E.E., Webber C., Brandt P., Nyakatura G., Adetobi M., Chiaromonte F., Elnitski L., Eswara P., Hardison R.C., Hou M., Kolbe D., Makova K., Miller W., Nekrutenko A., Riemer C., Schwartz S., Taylor J., Yang S., Zhang Y., Lindpaintner K., Andrews T.D., Caccamo M., Clamp M., Clarke L., Curwen V., Durbin R.M., Eyras E., Searle S.M., Cooper G.M., Batzoglou S., Brudno M., Sidow A., Stone E.A., Payseur B.A., Bourque G., Lopez-Otin C., Puente X.S., Chakrabarti K., Chatterji S., Dewey C., Pachter L., Bray N., Yap V.B., Caspi A., Tesler G., Pevzner P.A., Haussler D., Roskin K.M., Baertsch R., Clawson H., Furey T.S., Hinrichs A.S., Karolchik D., Kent W.J., Rosenbloom K.R., Trumbower H., Weirauch M., Cooper D.N., Stenson P.D., Ma B., Brent M., Arumugam M., Shteynberg D., Copley R.R., Taylor M.S., Riethman H., Mudunuri U., Peterson J., Guyer M., Felsenfeld A., Old S., Mockrin S., Collins F.S.
    Nature 428:493-521(2004) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: Brown Norway.
  2. "Quantitative maps of protein phosphorylation sites across 14 different rat organs and tissues."
    Lundby A., Secher A., Lage K., Nordsborg N.B., Dmytriyev A., Lundby C., Olsen J.V.
    Nat. Commun. 3:876-876(2012) [PubMed] [Europe PMC] [Abstract]
    Cited for: PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-124; SER-127 AND SER-151, IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].

Entry informationi

Entry nameiSMRCD_RAT
AccessioniPrimary (citable) accession number: D3Z9Z9
Entry historyi
Integrated into UniProtKB/Swiss-Prot: April 18, 2012
Last sequence update: April 20, 2010
Last modified: January 20, 2016
This is version 45 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

Complete proteome, Reference proteome

Documents

  1. 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.