Q04692 (SMRCD_MOUSE) Reviewed, UniProtKB/Swiss-Prot

Names and origin

Protein names

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 SMARCAD1
Enhancer trap locus homolog 1
Short name=Etl-1

Gene names

Name:	Smarcad1
Synonyms:	Etl1, Kiaa1122

Organism

Mus musculus (Mouse) [Reference proteome]

Taxonomic identifier

10090 [NCBI]

Taxonomic lineage

cellular organisms › Eukaryota › Opisthokonta › Metazoa › Eumetazoa › Bilateria › Deuterostomia › Chordata › Craniata › Vertebrata › Gnathostomata › Teleostomi › Euteleostomi › Sarcopterygii › Tetrapoda › Amniota › Mammalia › Theria › Eutheria › Euarchontoglires › Glires › Rodentia › Sciurognathi › Muroidea › Muridae › Murinae › Mus › Mus

Protein attributes

Sequence length	1021 AA.
Sequence status	Complete.
Protein existence	Evidence at protein level

General annotation (Comments)

Function	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.
Catalytic activity	ATP + H2O = ADP + phosphate.
Subunit structure	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.
Subcellular location	Nucleus. 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. Ref.5 Ref.10 Ref.12
Developmental stage	Detected at low levels in fertilized and unfertilized eggs. Levels increased in two-cell embryos, decreased up to morula stage and were highest in blastocysts. Highly expressed in the inner cell mass of 3.5 day old blastocysts. Highly expressed in ectoderm and visceral endoderm at day 5.5. Detected throughout the brain and spinal cord at day 10 to 15. Detected in the basal layer of the epidermis after day 12.5, in particular on snout and distal on fore- and hindlimbs. Ref.5
Disruption phenotype	Deficient mice have reduced viability and show growth retardation, skeletal dysplasia and impaired fertility. Ref.6
Sequence similarities	Belongs to the SNF2/RAD54 helicase family. Contains 2 CUE domains. Contains 1 helicase ATP-binding domain. Contains 1 helicase C-terminal domain.
Sequence caution	The sequence BAC65736.1 differs from that shown. Reason: Erroneous initiation. Translation N-terminally shortened. The sequence CAA49560.1 differs from that shown. Reason: Erroneous initiation. Translation N-terminally shortened.

Ontologies

Keywords
Biological process	DNA damage DNA repair
Cellular component	Chromosome Nucleus
Coding sequence diversity	Alternative splicing
Domain	Repeat
Ligand	ATP-binding DNA-binding Nucleotide-binding
Molecular function	Chromatin regulator Helicase Hydrolase
PTM	Phosphoprotein
Technical term	Complete proteome Reference proteome
Gene Ontology (GO)
Biological_process	ATP-dependent chromatin remodeling Inferred from sequence or structural similarity. Source: UniProtKB DNA double-strand break processing Inferred from sequence or structural similarity. Source: UniProtKB chromosome separation Inferred from sequence or structural similarity. Source: UniProtKB histone H3 deacetylation Inferred from sequence or structural similarity. Source: UniProtKB histone H4 deacetylation Inferred from sequence or structural similarity. Source: UniProtKB regulation of DNA recombination Inferred from sequence or structural similarity PubMed 11031099. Source: UniProtKB
Cellular_component	heterochromatin Inferred from direct assay Ref.12. Source: UniProtKB nuclear replication fork Inferred from electronic annotation. Source: Compara nucleus Inferred from direct assay Ref.12. Source: UniProtKB site of double-strand break Inferred from sequence or structural similarity. Source: UniProtKB
Molecular_function	ATP binding Inferred from electronic annotation. Source: UniProtKB-KW DNA binding Inferred from electronic annotation. Source: UniProtKB-KW helicase activity Inferred from electronic annotation. Source: UniProtKB-KW
Complete GO annotation...

Alternative products

This entry describes 2 isoforms produced by alternative splicing. [Align] [Select]

Isoform 1 (identifier: Q04692-1)

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.

Isoform 2 (identifier: Q04692-2)

The sequence of this isoform differs from the canonical sequence as follows:
     1-185: Missing.

Note: No experimental confirmation available.

Sequence annotation (Features)

	Feature key	Position(s)	Length	Description	Graphical view	Feature identifier
Molecule processing
	Chain	1 – 1021	1021	SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily A containing DEAD/H box 1		PRO_0000074357
Regions
	Domain	156 – 198	43	CUE 1
	Domain	247 – 290	44	CUE 2
	Domain	504 – 672	169	Helicase ATP-binding
	Domain	853 – 1005	153	Helicase C-terminal
	Nucleotide binding	516 – 524	9	ATP By similarity
	Nucleotide binding	892 – 899	8	ATP By similarity
	Motif	623 – 626	4	DEGH box
	Motif	716 – 733	18	Nuclear localization signal Potential
	Motif	1000 – 1003	4	DEAD box
Amino acid modifications
	Modified residue	54	1	Phosphothreonine By similarity
	Modified residue	57	1	Phosphoserine By similarity
	Modified residue	79	1	Phosphoserine By similarity
	Modified residue	124	1	Phosphoserine Ref.8 Ref.11
	Modified residue	127	1	Phosphoserine By similarity
	Modified residue	132	1	Phosphoserine Ref.8
	Modified residue	137	1	Phosphoserine Ref.9
	Modified residue	144	1	Phosphoserine Ref.9
	Modified residue	145	1	Phosphoserine Ref.9
	Modified residue	151	1	Phosphoserine By similarity
	Modified residue	210	1	Phosphoserine Ref.8
	Modified residue	211	1	Phosphoserine Ref.8
	Modified residue	212	1	Phosphoserine Ref.8
	Modified residue	213	1	Phosphoserine Ref.8
	Modified residue	235	1	Phosphoserine By similarity
	Modified residue	238	1	Phosphoserine By similarity
	Modified residue	298	1	Phosphoserine By similarity
	Modified residue	403	1	Phosphoserine Ref.7
Natural variations
	Alternative sequence	1 – 185	185	Missing in isoform 2.		VSP_007080
Experimental info
	Sequence conflict	857	1	I → S in CAA49560. Ref.1

Sequences

	Sequence		Length	Mass (Da)
	Isoform 1 [UniParc]. Last modified March 28, 2003. Version 2. Checksum: E3237AA2B135538A	FASTA	1,021	116,451
	10 20 30 40 50 60 MNLFNLDRFR FEKRSKIEEA PEAAPQPSQA RPSSPISLSA EEENAEGEGS RANTPDSDVT 70 80 90 100 110 120 EKTEDSSVPE PPDNERKASL SCFQNQRAIQ EYIDLSSDTE DVSPNCSSTV QEKKFSKDTV 130 140 150 160 170 180 IIVSEPSEDE ESHDLPSVTR RNDSSELEDL SELEDLKDAK LQTLKELFPQ RSDSDLLKLI 190 200 210 220 230 240 ESTSTMDGAI AAALLMFGDA GGGPRKRKLS SSSEEDDVND DQSVKQPRGD RGEESNESAE 250 260 270 280 290 300 ASSNWEKQES IVLKLQKEFP NFDKQELREV LKEHEWMYTE ALESLKVFAE DQDVQCASQS 310 320 330 340 350 360 EVTNGKEVAR NQNYSKNATK IKMKQKISVK PQNGFNKKRK KNVFNPKKAV EDSEYDSGSD 370 380 390 400 410 420 AGSSLDEDYS SCEEVMEDGY KGKILHFLQV SSIAELTLIP KCSQKKAQKI TELRPFNNWE 430 440 450 460 470 480 ALFTKMSKIN GLSEDLIWNC KTVIQERDVV IRLMNKCEDI SNKLTKQVTM LTGNGGGWNR 490 500 510 520 530 540 EQPSLLNQSL SLKPYQKVGL NWLALVHKHG LNGILADEMG LGKTIQAIAF LAYLFQEGNK 550 560 570 580 590 600 GPHLIVVPAS TIDNWLREVN LWCPSLNVLC YYGSQEERKQ IRFNIHNKYE DYNVIVTTYN 610 620 630 640 650 660 CAISSSDDRS LFRRLKLNYA IFDEGHMLKN MGSIRYQHLM TINARNRLLL TGTPVQNNLL 670 680 690 700 710 720 ELMSLLNFVM PHMFSSSTSE IRRMFSSKTK PADEQSIYEK ERIAHAKQII KPFILRRVKE 730 740 750 760 770 780 EVLKLLPPKK DRIELCAMSE KQEQLYSGLF NRLKKSINNL EKNTEMCNVM MQLRKMANHP 790 800 810 820 830 840 LLHRQYYTPE KLKEMSQLML KEPTHCEANP DLIFEDMEVM TDFELHVLCK QYQHINSYQL 850 860 870 880 890 900 DMDLILDSGK FRALGCILSE LKQKGDRVVL FSQFTMMLDI LEVLLKHHQH RYLRLDGKTQ 910 920 930 940 950 960 ISERIHLIDE FNTDMDIFVF LLSTKAGGLG INLTSANVVI LHDIDCNPYN DKQAEDRCHR 970 980 990 1000 1010 1020 VGQTKEVLVI KLISQGTIEE SMLKINQQKL KLEQDMTTVD EADEGSMPAD IATLLKTSMG L
	Isoform 2 [UniParc]. Checksum: DD7B56518C73242B	FASTA	836	95,787
	10 20 30 40 50 60 MDGAIAAALL MFGDAGGGPR KRKLSSSSEE DDVNDDQSVK QPRGDRGEES NESAEASSNW 70 80 90 100 110 120 EKQESIVLKL QKEFPNFDKQ ELREVLKEHE WMYTEALESL KVFAEDQDVQ CASQSEVTNG 130 140 150 160 170 180 KEVARNQNYS KNATKIKMKQ KISVKPQNGF NKKRKKNVFN PKKAVEDSEY DSGSDAGSSL 190 200 210 220 230 240 DEDYSSCEEV MEDGYKGKIL HFLQVSSIAE LTLIPKCSQK KAQKITELRP FNNWEALFTK 250 260 270 280 290 300 MSKINGLSED LIWNCKTVIQ ERDVVIRLMN KCEDISNKLT KQVTMLTGNG GGWNREQPSL 310 320 330 340 350 360 LNQSLSLKPY QKVGLNWLAL VHKHGLNGIL ADEMGLGKTI QAIAFLAYLF QEGNKGPHLI 370 380 390 400 410 420 VVPASTIDNW LREVNLWCPS LNVLCYYGSQ EERKQIRFNI HNKYEDYNVI VTTYNCAISS 430 440 450 460 470 480 SDDRSLFRRL KLNYAIFDEG HMLKNMGSIR YQHLMTINAR NRLLLTGTPV QNNLLELMSL 490 500 510 520 530 540 LNFVMPHMFS SSTSEIRRMF SSKTKPADEQ SIYEKERIAH AKQIIKPFIL RRVKEEVLKL 550 560 570 580 590 600 LPPKKDRIEL CAMSEKQEQL YSGLFNRLKK SINNLEKNTE MCNVMMQLRK MANHPLLHRQ 610 620 630 640 650 660 YYTPEKLKEM SQLMLKEPTH CEANPDLIFE DMEVMTDFEL HVLCKQYQHI NSYQLDMDLI 670 680 690 700 710 720 LDSGKFRALG CILSELKQKG DRVVLFSQFT MMLDILEVLL KHHQHRYLRL DGKTQISERI 730 740 750 760 770 780 HLIDEFNTDM DIFVFLLSTK AGGLGINLTS ANVVILHDID CNPYNDKQAE DRCHRVGQTK 790 800 810 820 830 EVLVIKLISQ GTIEESMLKI NQQKLKLEQD MTTVDEADEG SMPADIATLL KTSMGL

References

	« Hide 'large scale' referencesShow 'large scale' references »
[1]	"The mouse Enhancer trap locus 1 (Etl-1): a novel mammalian gene related to Drosophila and yeast transcriptional regulator genes." Soininen R., Schoor M., Henseling U., Tepe C., Kisters-Woike B., Rossant J., Gossler A. Mech. Dev. 39:111-123(1992) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [MRNA] (ISOFORM 1). Strain: C57BL/6. Tissue: Embryo.
[2]	"Prediction of the coding sequences of mouse homologues of KIAA gene: II. The complete nucleotide sequences of 400 mouse KIAA-homologous cDNAs identified by screening of terminal sequences of cDNA clones randomly sampled from size-fractionated libraries." Okazaki N., Kikuno R., Ohara R., Inamoto S., Aizawa H., Yuasa S., Nakajima D., Nagase T., Ohara O., Koga H. DNA Res. 10:35-48(2003) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] (ISOFORM 1). Tissue: Brain.
[3]	"The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC)." The MGC Project Team Genome Res. 14:2121-2127(2004) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] (ISOFORM 2). Strain: FVB/N.
[4]	"The transcriptional landscape of the mammalian genome." Carninci P., Kasukawa T., Katayama S., Gough J., Frith M.C., Maeda N., Oyama R., Ravasi T., Lenhard B., Wells C., Kodzius R., Shimokawa K., Bajic V.B., Brenner S.E., Batalov S., Forrest A.R., Zavolan M., Davis M.J. , Wilming L.G., Aidinis V., Allen J.E., Ambesi-Impiombato A., Apweiler R., Aturaliya R.N., Bailey T.L., Bansal M., Baxter L., Beisel K.W., Bersano T., Bono H., Chalk A.M., Chiu K.P., Choudhary V., Christoffels A., Clutterbuck D.R., Crowe M.L., Dalla E., Dalrymple B.P., de Bono B., Della Gatta G., di Bernardo D., Down T., Engstrom P., Fagiolini M., Faulkner G., Fletcher C.F., Fukushima T., Furuno M., Futaki S., Gariboldi M., Georgii-Hemming P., Gingeras T.R., Gojobori T., Green R.E., Gustincich S., Harbers M., Hayashi Y., Hensch T.K., Hirokawa N., Hill D., Huminiecki L., Iacono M., Ikeo K., Iwama A., Ishikawa T., Jakt M., Kanapin A., Katoh M., Kawasawa Y., Kelso J., Kitamura H., Kitano H., Kollias G., Krishnan S.P., Kruger A., Kummerfeld S.K., Kurochkin I.V., Lareau L.F., Lazarevic D., Lipovich L., Liu J., Liuni S., McWilliam S., Madan Babu M., Madera M., Marchionni L., Matsuda H., Matsuzawa S., Miki H., Mignone F., Miyake S., Morris K., Mottagui-Tabar S., Mulder N., Nakano N., Nakauchi H., Ng P., Nilsson R., Nishiguchi S., Nishikawa S., Nori F., Ohara O., Okazaki Y., Orlando V., Pang K.C., Pavan W.J., Pavesi G., Pesole G., Petrovsky N., Piazza S., Reed J., Reid J.F., Ring B.Z., Ringwald M., Rost B., Ruan Y., Salzberg S.L., Sandelin A., Schneider C., Schoenbach C., Sekiguchi K., Semple C.A., Seno S., Sessa L., Sheng Y., Shibata Y., Shimada H., Shimada K., Silva D., Sinclair B., Sperling S., Stupka E., Sugiura K., Sultana R., Takenaka Y., Taki K., Tammoja K., Tan S.L., Tang S., Taylor M.S., Tegner J., Teichmann S.A., Ueda H.R., van Nimwegen E., Verardo R., Wei C.L., Yagi K., Yamanishi H., Zabarovsky E., Zhu S., Zimmer A., Hide W., Bult C., Grimmond S.M., Teasdale R.D., Liu E.T., Brusic V., Quackenbush J., Wahlestedt C., Mattick J.S., Hume D.A., Kai C., Sasaki D., Tomaru Y., Fukuda S., Kanamori-Katayama M., Suzuki M., Aoki J., Arakawa T., Iida J., Imamura K., Itoh M., Kato T., Kawaji H., Kawagashira N., Kawashima T., Kojima M., Kondo S., Konno H., Nakano K., Ninomiya N., Nishio T., Okada M., Plessy C., Shibata K., Shiraki T., Suzuki S., Tagami M., Waki K., Watahiki A., Okamura-Oho Y., Suzuki H., Kawai J., Hayashizaki Y. Science 309:1559-1563(2005) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] OF 1-760. Strain: C57BL/6J. Tissue: Testis.
[5]	"The Etl-1 gene encodes a nuclear protein differentially expressed during early mouse development." Schoor M., Schuster-Gossler K., Gossler A. Dev. Dyn. 197:227-237(1993) [PubMed] [Europe PMC] [Abstract] Cited for: SUBCELLULAR LOCATION, DEVELOPMENTAL STAGE.
[6]	"Skeletal dysplasias, growth retardation, reduced postnatal survival, and impaired fertility in mice lacking the SNF2/SWI2 family member ETL1." Schoor M., Schuster-Gossler K., Roopenian D., Gossler A. Mech. Dev. 85:73-83(1999) [PubMed] [Europe PMC] [Abstract] Cited for: DISRUPTION PHENOTYPE.
[7]	"Protein phosphorylation and expression profiling by Yin-yang multidimensional liquid chromatography (Yin-yang MDLC) mass spectrometry." Dai J., Jin W.-H., Sheng Q.-H., Shieh C.-H., Wu J.-R., Zeng R. J. Proteome Res. 6:250-262(2007) [PubMed] [Europe PMC] [Abstract] Cited for: PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-403, MASS SPECTROMETRY. Tissue: Liver.
[8]	"A differential phosphoproteomic analysis of retinoic acid-treated P19 cells." Smith J.C., Duchesne M.A., Tozzi P., Ethier M., Figeys D. J. Proteome Res. 6:3174-3186(2007) [PubMed] [Europe PMC] [Abstract] Cited for: PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-124; SER-132; SER-210; SER-211; SER-212 AND SER-213, MASS SPECTROMETRY. Tissue: Teratocarcinoma.
[9]	"Large-scale phosphorylation analysis of mouse liver." Villen J., Beausoleil S.A., Gerber S.A., Gygi S.P. Proc. Natl. Acad. Sci. U.S.A. 104:1488-1493(2007) [PubMed] [Europe PMC] [Abstract] Cited for: PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-137; SER-144 AND SER-145, MASS SPECTROMETRY. Tissue: Liver.
[10]	"The novel protein complex with SMARCAD1/KIAA1122 binds to the vicinity of TSS." Okazaki N., Ikeda S., Ohara R., Shimada K., Yanagawa T., Nagase T., Ohara O., Koga H. J. Mol. Biol. 382:257-265(2008) [PubMed] [Europe PMC] [Abstract] Cited for: SUBCELLULAR LOCATION.
[11]	"Solid tumor proteome and phosphoproteome analysis by high resolution mass spectrometry." Zanivan S., Gnad F., Wickstroem S.A., Geiger T., Macek B., Cox J., Faessler R., Mann M. J. Proteome Res. 7:5314-5326(2008) [PubMed] [Europe PMC] [Abstract] Cited for: PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-124, MASS SPECTROMETRY. Tissue: Melanoma.
[12]	"Maintenance of silent chromatin through replication requires SWI/SNF-like chromatin remodeler SMARCAD1." Rowbotham S.P., Barki L., Neves-Costa A., Santos F., Dean W., Hawkes N., Choudhary P., Will W.R., Webster J., Oxley D., Green C.M., Varga-Weisz P., Mermoud J.E. Mol. Cell 42:285-296(2011) [PubMed] [Europe PMC] [Abstract] Cited for: SUBCELLULAR LOCATION.
+	Additional computationally mapped references.

Cross-references

Sequence databases
EMBL GenBank DDBJ	X69942 mRNA. Translation: CAA49560.1. Different initiation. AK122454 mRNA. Translation: BAC65736.1. Different initiation. BC042442 mRNA. Translation: AAH42442.1. AK134442 mRNA. Translation: BAE22146.1. AK147884 mRNA. Translation: BAE28202.1.
IPI	IPI00223926. IPI00556837.
PIR	A56559.
RefSeq	NP_001240321.1. NM_001253392.1. NP_031984.1. NM_007958.1.
UniGene	Mm.99113.
3D structure databases
ProteinModelPortal	Q04692.
SMR	Q04692. Positions 487-782, 848-998.
ModBase	Search...
Protein-protein interaction databases
STRING	10090.ENSMUSP00000031984.
PTM databases
PhosphoSite	Q04692.
Proteomic databases
PaxDb	Q04692.
PRIDE	Q04692.
Protocols and materials databases
StructuralBiologyKnowledgebase	Search...
Genome annotation databases
Ensembl	ENSMUST00000031984; ENSMUSP00000031984; ENSMUSG00000029920.
GeneID	13990.
KEGG	mmu:13990.
UCSC	uc009ced.1. mouse. uc012emw.1. mouse.
Organism-specific databases
CTD	56916.
MGI	MGI:95453. Smarcad1.
Rouge	Search...
Phylogenomic databases
eggNOG	COG0553.
GeneTree	ENSGT00630000089890.
HOGENOM	HOG000172362.
HOVERGEN	HBG055804.
InParanoid	Q04692.
KO	K14439.
OMA	KNQRGIQ.
OrthoDB	EOG4RV2QW.
Gene expression databases
ArrayExpress	Q04692.
Bgee	Q04692.
Genevestigator	Q04692.
GermOnline	ENSMUSG00000029920. Mus musculus.
Family and domain databases
InterPro	IPR003892. CUE. IPR014001. Helicase_ATP-bd. IPR001650. Helicase_C. IPR000330. SNF2_N. [Graphical view]
Pfam	PF00271. Helicase_C. 1 hit. PF00176. SNF2_N. 1 hit. [Graphical view]
SMART	SM00487. DEXDc. 1 hit. SM00490. HELICc. 1 hit. [Graphical view]
PROSITE	PS51140. CUE. 2 hits. PS51192. HELICASE_ATP_BIND_1. 1 hit. PS51194. HELICASE_CTER. 1 hit. [Graphical view]
ProtoNet	Search...
Other
NextBio	284868.
SOURCE	Search...

Entry information

Entry name

SMRCD_MOUSE

Accession

Primary (citable) accession number: Q04692
Secondary accession number(s): Q3UGK6, Q3UYR6

Entry history

Integrated into UniProtKB/Swiss-Prot:	March 28, 2003
Last sequence update:	March 28, 2003
Last modified:	May 1, 2013
This is version 115 of the entry and version 2 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation program

Chordata Protein Annotation Program