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Protein

Structural maintenance of chromosomes flexible hinge domain-containing protein 1

Gene

Smchd1

Organism
Mus musculus (Mouse)
Status
Reviewed-Annotation score: Annotation score: 4 out of 5-Experimental evidence at protein leveli

Functioni

Required for maintenance of X inactivation in females and hypermethylation of CpG islands associated with inactive X. Involved in a pathway that mediates the methylation of a subset of CpG islands slowly and requires the de novo methyltransferase DNMT3B. May be required for DUX4 silencing in somatic cells.2 Publications

GO - Molecular functioni

GO - Biological processi

  • chromosome organization Source: InterPro
  • dosage compensation by inactivation of X chromosome Source: MGI
  • inactivation of X chromosome by DNA methylation Source: MGI
Complete GO annotation...

Names & Taxonomyi

Protein namesi
Recommended name:
Structural maintenance of chromosomes flexible hinge domain-containing protein 1
Gene namesi
Name:Smchd1
Synonyms:Kiaa0650
OrganismiMus musculus (Mouse)
Taxonomic identifieri10090 [NCBI]
Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresGliresRodentiaSciurognathiMuroideaMuridaeMurinaeMusMus
Proteomesi
  • UP000000589 Componenti: Chromosome 17

Organism-specific databases

MGIiMGI:1921605. Smchd1.

Subcellular locationi

GO - Cellular componenti

  • Barr body Source: MGI
  • chromosome, telomeric region Source: Ensembl
Complete GO annotation...

Keywords - Cellular componenti

Chromosome

Pathology & Biotechi

Disruption phenotypei

Defects in Smchd1 are the cause of the MommeD1 (modifier of murine metastable epialleles) phenotype, a semi-dominant suppressor of variegation. Mice display female-specific mid-gestation lethality and hypomethylation of the X-linked gene Hprt1, due to defects in X inactivation. Mice do not show defects on telomeres length.2 Publications

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Initiator methionineiRemovedBy similarity
Chaini2 – 20072006Structural maintenance of chromosomes flexible hinge domain-containing protein 1PRO_0000332145Add
BLAST

Amino acid modifications

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Modified residuei2 – 21N-acetylalanineBy similarity
Modified residuei833 – 8331PhosphoserineCombined sources
Modified residuei1350 – 13501N6-acetyllysineBy similarity
Cross-linki1375 – 1375Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in SUMO2)By similarity
Modified residuei1803 – 18031N6-succinyllysineCombined sources

Post-translational modificationi

Sumoylated with SUMO1.1 Publication

Keywords - PTMi

Acetylation, Isopeptide bond, Phosphoprotein, Ubl conjugation

Proteomic databases

EPDiQ6P5D8.
MaxQBiQ6P5D8.
PaxDbiQ6P5D8.
PRIDEiQ6P5D8.

PTM databases

iPTMnetiQ6P5D8.
PhosphoSiteiQ6P5D8.

Expressioni

Gene expression databases

BgeeiQ6P5D8.
GenevisibleiQ6P5D8. MM.

Interactioni

Protein-protein interaction databases

BioGridi216686. 20 interactions.
IntActiQ6P5D8. 20 interactions.
MINTiMINT-4127034.
STRINGi10090.ENSMUSP00000121835.

Family & Domainsi

Phylogenomic databases

eggNOGiENOG410IISP. Eukaryota.
ENOG410XRY2. LUCA.
GeneTreeiENSGT00390000006950.
HOVERGENiHBG108493.
InParanoidiQ6P5D8.
OMAiTQQVPHI.
OrthoDBiEOG72JWF8.
PhylomeDBiQ6P5D8.
TreeFamiTF329426.

Family and domain databases

Gene3Di3.30.565.10. 2 hits.
InterProiIPR003594. HATPase_C.
IPR010935. SMC_hinge.
[Graphical view]
PfamiPF06470. SMC_hinge. 1 hit.
[Graphical view]
SMARTiSM00968. SMC_hinge. 1 hit.
[Graphical view]
SUPFAMiSSF55874. SSF55874. 1 hit.
SSF75553. SSF75553. 1 hit.

Sequencei

Sequence statusi: Complete.

Sequence processingi: The displayed sequence is further processed into a mature form.

Q6P5D8-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MAAEGASDPA GLSEGSGRDG AVDGCRTVYL FDRRGKDSEL GDRALQVSEH
60 70 80 90 100
ADYAGFRASV CQTIGISSEE KFVITTTSRK EITCNNFDHT VKDGVTLYLL
110 120 130 140 150
QSVDQSLLTA TKERIDFLPH YDTLVKSGMY EYYASEGQNP LPFALAELID
160 170 180 190 200
NSLSATSRNN GVRRIQIKLL FDETQGKPAV AVVDNGRGMT SKQLNNWAVY
210 220 230 240 250
RLSKFTRQGD FESDHSGYVR PLPVPRSLNS DISYFGVGGK QAVFFVGQSA
260 270 280 290 300
RMISKPIDSK DVHELVLSKE DFEKKEKNKE AIYSGYIRNR KPADSAHITN
310 320 330 340 350
DDERFLHNLI EEEKEKDSFT AVVITGVQPE HIQYLKNYLH LWTRQLTHIY
360 370 380 390 400
HYYIHGPKGN EISTAKAIGP FNNIDIEISL FEKGKTPKII NLREIQDDMQ
410 420 430 440 450
TLYINTASDS FEFKAHVEGD GVVEGVIRYH PFLYDRETFP DDPCFPSKLK
460 470 480 490 500
DEDDDDDCFI SEKAARGKRP IFECFWNGRL IPYTSVGDFD WCAPPKKRGL
510 520 530 540 550
VPIECFNRIS GALFTNDKFQ VSTNKLTFMD LELKLKDKNT LFTRILNGQE
560 570 580 590 600
QRMKIDREFA LWLKDCHEKH DKQIKFTLFK GIITRPDLPT KKQGPWATFS
610 620 630 640 650
AIEWDGKIYK AGQLVKTIKT LPLCYGSIVR FFLHGDHDGE VYATGGEVQI
660 670 680 690 700
AMEPQALYDE IKTVPIAKLD RTVAEKTIRK YVEDEMARLP DRLSVTWPEG
710 720 730 740 750
DELLPNEVRP AGTPIGALRI EILNKKGEAM QKLPGTSHGG SKKLLVELKV
760 770 780 790 800
ILHTSSGNKE IISHISQHGG KWPYWFKKME NIQKLGNYTL KLQVVLNESN
810 820 830 840 850
ADTYAGRSLP SKVIKFSVKE GKPEKFSFGL LDSPFRVGVP FNIPLELQDE
860 870 880 890 900
FGHTTQLLSD IEPVLEASGL SLHYEGITKG PNCVIQGVVA KGPVNSCQGK
910 920 930 940 950
NFNLKVILPG LKEDSQILKI RLLPGPPHQL KVKPDSEVLV IENGTAFPFQ
960 970 980 990 1000
VEVVDESDNI TAQPKLIVHC KFLGAPNLPV YTVDCSSSGT SILTGSPIQV
1010 1020 1030 1040 1050
QNIKKDQKTL TARIEIPSCK DVSPVEKTIK LLPSSHAACL QIFSVEEQKA
1060 1070 1080 1090 1100
IQIKHQDEVT WVAGDVIRNL IFQMYDEGER EINITPSLAE KIKVNWTPEV
1110 1120 1130 1140 1150
NKEHLVQGLL PDVQVPTSVK DVRYCHVSFQ DDHVCLESAF TVRPLPDDPK
1160 1170 1180 1190 1200
HLKCELKGGK TVQMGQELQG EIVVIIADQY GNQISSFSPD SLSTLSITGD
1210 1220 1230 1240 1250
GLDSSNLKIT LEANSQSVSV QGIRFTPGPP GPKDLCFTWR EFSDFLRVQL
1260 1270 1280 1290 1300
VSGPPTKLLL MDWPELKESI PVINGRQLEN PLIVQLCDQW DNPALVPNVK
1310 1320 1330 1340 1350
ICLIKASSLR LLPSNQQHKT DDKGRANLGV FTVCAPRGEH TVQVKGVYNK
1360 1370 1380 1390 1400
STIEGPTIKL TILPDPEKPI RLNVKYDQDA SFIAGDIFTD FMVSVISESG
1410 1420 1430 1440 1450
SVIKNINPTR ISMKMWKLSS GMSRPPANAE TFSCNKIKGN DKEDGCFYFR
1460 1470 1480 1490 1500
EKTIPNKVGA YCIQFDFMID KTNILSSQQV IVDVLPNQPM KLVPDSQPAT
1510 1520 1530 1540 1550
PAVSNVRSIA SRTLVKDLRL SITDNYGNHT GMDLVGTVVA TIKGFNEEDT
1560 1570 1580 1590 1600
DTPLFIGKVR TLEFPFVKGS AEITTLVLAE NSPGRDSTEY FIIFEPRLST
1610 1620 1630 1640 1650
VSGTLESYSL PFMFYNDVKK QQQMAALTKE KDELSKSITM YRSLFDANKQ
1660 1670 1680 1690 1700
LVDEMKCQAE EAKLKETQLR NELKAYNIDI PATQQTTHIE ALLEKKITEQ
1710 1720 1730 1740 1750
NELKKRPRRL CTLPNYTKRS GDILGKIAHL AQIEDDRAAM VISWHLASDM
1760 1770 1780 1790 1800
DCVVTLTTDA ARAIYDETQG RQQVLPLDSI YRKTLPDWKR PLPHFRNGKL
1810 1820 1830 1840 1850
HFKPFGNPVF ARDLLTFPDN IEHCETVFGM LLGDTIILDN LDAANHYRKE
1860 1870 1880 1890 1900
VVKITHCPTL LTRDGDRIRS NGKFGGLQNK APPMDKLRGM VFGAPVPKQC
1910 1920 1930 1940 1950
VVLGKQIDLI QQYRTALYRL SSVNEDLDNQ LQYLHTPDMK KKKQELDEQE
1960 1970 1980 1990 2000
KSLKRIEQKL GMTPVRRCNE SLCHSPKIEV TECPIPTKRM RRESTRQNRR

PKGDVPN
Length:2,007
Mass (Da):225,648
Last modified:April 29, 2008 - v2
Checksum:i1A41FC47C54B5415
GO

Sequence cautioni

The sequence AAH44905.1 differs from that shown. Reason: Erroneous initiation. Curated
The sequence BAB30222.1 differs from that shown. Reason: Frameshift at position 1122. Curated

Experimental Info

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Sequence conflicti1120 – 11201K → E in BAB30222 (PubMed:19468303).Curated
Sequence conflicti1611 – 16111P → S in BAC97991 (PubMed:14621295).Curated

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AC107664 Genomic DNA. No translation available.
AC126942 Genomic DNA. No translation available.
AK016419 mRNA. Translation: BAB30222.1. Frameshift.
AK078494 mRNA. Translation: BAC37307.1.
BC044905 mRNA. Translation: AAH44905.1. Different initiation.
BC058205 mRNA. Translation: AAH58205.1.
BC058618 mRNA. Translation: AAH58618.1.
BC062946 mRNA. Translation: AAH62946.1.
AK129181 mRNA. Translation: BAC97991.1.
CCDSiCCDS28958.2.
RefSeqiNP_083163.3. NM_028887.3.
UniGeneiMm.194450.

Genome annotation databases

EnsembliENSMUST00000127430; ENSMUSP00000121835; ENSMUSG00000024054.
GeneIDi74355.
KEGGimmu:74355.
UCSCiuc008dmh.2. mouse.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AC107664 Genomic DNA. No translation available.
AC126942 Genomic DNA. No translation available.
AK016419 mRNA. Translation: BAB30222.1. Frameshift.
AK078494 mRNA. Translation: BAC37307.1.
BC044905 mRNA. Translation: AAH44905.1. Different initiation.
BC058205 mRNA. Translation: AAH58205.1.
BC058618 mRNA. Translation: AAH58618.1.
BC062946 mRNA. Translation: AAH62946.1.
AK129181 mRNA. Translation: BAC97991.1.
CCDSiCCDS28958.2.
RefSeqiNP_083163.3. NM_028887.3.
UniGeneiMm.194450.

3D structure databases

ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi216686. 20 interactions.
IntActiQ6P5D8. 20 interactions.
MINTiMINT-4127034.
STRINGi10090.ENSMUSP00000121835.

PTM databases

iPTMnetiQ6P5D8.
PhosphoSiteiQ6P5D8.

Proteomic databases

EPDiQ6P5D8.
MaxQBiQ6P5D8.
PaxDbiQ6P5D8.
PRIDEiQ6P5D8.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsembliENSMUST00000127430; ENSMUSP00000121835; ENSMUSG00000024054.
GeneIDi74355.
KEGGimmu:74355.
UCSCiuc008dmh.2. mouse.

Organism-specific databases

CTDi23347.
MGIiMGI:1921605. Smchd1.
RougeiSearch...

Phylogenomic databases

eggNOGiENOG410IISP. Eukaryota.
ENOG410XRY2. LUCA.
GeneTreeiENSGT00390000006950.
HOVERGENiHBG108493.
InParanoidiQ6P5D8.
OMAiTQQVPHI.
OrthoDBiEOG72JWF8.
PhylomeDBiQ6P5D8.
TreeFamiTF329426.

Miscellaneous databases

ChiTaRSiSmchd1. mouse.
NextBioi340527.
PROiQ6P5D8.
SOURCEiSearch...

Gene expression databases

BgeeiQ6P5D8.
GenevisibleiQ6P5D8. MM.

Family and domain databases

Gene3Di3.30.565.10. 2 hits.
InterProiIPR003594. HATPase_C.
IPR010935. SMC_hinge.
[Graphical view]
PfamiPF06470. SMC_hinge. 1 hit.
[Graphical view]
SMARTiSM00968. SMC_hinge. 1 hit.
[Graphical view]
SUPFAMiSSF55874. SSF55874. 1 hit.
SSF75553. SSF75553. 1 hit.
ProtoNetiSearch...

Publicationsi

« Hide 'large scale' publications
  1. Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: C57BL/6J.
  2. "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 1-272 AND 1116-2007.
    Strain: C57BL/6J.
    Tissue: Muellerian duct.
  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] OF 660-2007.
    Strain: C57BL/6J and Czech II.
    Tissue: Brain, Eye and Mammary tumor.
  4. "Prediction of the coding sequences of mouse homologues of KIAA gene: III. The complete nucleotide sequences of 500 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., Koseki H., Hiraoka S., Saga Y., Nagase T., Ohara O., Koga H.
    DNA Res. 10:167-180(2003) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] OF 942-2007.
    Tissue: Embryonic tail.
  5. "SmcHD1, containing a structural-maintenance-of-chromosomes hinge domain, has a critical role in X inactivation."
    Blewitt M.E., Gendrel A.V., Pang Z., Sparrow D.B., Whitelaw N., Craig J.M., Apedaile A., Hilton D.J., Dunwoodie S.L., Brockdorff N., Kay G.F., Whitelaw E.
    Nat. Genet. 40:663-669(2008) [PubMed] [Europe PMC] [Abstract]
    Cited for: FUNCTION, DISRUPTION PHENOTYPE, SUBCELLULAR LOCATION.
  6. Cited for: PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-833, IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
    Tissue: Kidney, Lung, Pancreas, Spleen and Testis.
  7. "Reduced dosage of the modifiers of epigenetic reprogramming Dnmt1, Dnmt3L, SmcHD1 and Foxo3a has no detectable effect on mouse telomere length in vivo."
    Roberts A.R., Blewitt M.E., Youngson N.A., Whitelaw E., Chong S.
    Chromosoma 120:377-385(2011) [PubMed] [Europe PMC] [Abstract]
    Cited for: DISRUPTION PHENOTYPE.
  8. "Smchd1-dependent and -independent pathways determine developmental dynamics of CpG island methylation on the inactive X chromosome."
    Gendrel A.V., Apedaile A., Coker H., Termanis A., Zvetkova I., Godwin J., Tang Y.A., Huntley D., Montana G., Taylor S., Giannoulatou E., Heard E., Stancheva I., Brockdorff N.
    Dev. Cell 23:265-279(2012) [PubMed] [Europe PMC] [Abstract]
    Cited for: FUNCTION.
  9. "In vivo localization and identification of SUMOylated proteins in the brain of His6-HA-SUMO1 knock-in mice."
    Tirard M., Hsiao H.H., Nikolov M., Urlaub H., Melchior F., Brose N.
    Proc. Natl. Acad. Sci. U.S.A. 109:21122-21127(2012) [PubMed] [Europe PMC] [Abstract]
    Cited for: SUMOYLATION WITH SUMO1.
  10. "SIRT5-mediated lysine desuccinylation impacts diverse metabolic pathways."
    Park J., Chen Y., Tishkoff D.X., Peng C., Tan M., Dai L., Xie Z., Zhang Y., Zwaans B.M., Skinner M.E., Lombard D.B., Zhao Y.
    Mol. Cell 50:919-930(2013) [PubMed] [Europe PMC] [Abstract]
    Cited for: SUCCINYLATION [LARGE SCALE ANALYSIS] AT LYS-1803, IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
    Tissue: Embryonic fibroblast.

Entry informationi

Entry nameiSMHD1_MOUSE
AccessioniPrimary (citable) accession number: Q6P5D8
Secondary accession number(s): Q6PDM8
, Q6PE93, Q6ZQ78, Q811H3, Q8BP09, Q9D4M7
Entry historyi
Integrated into UniProtKB/Swiss-Prot: April 29, 2008
Last sequence update: April 29, 2008
Last modified: May 11, 2016
This is version 91 of the entry and version 2 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. MGD cross-references
    Mouse Genome Database (MGD) cross-references in UniProtKB/Swiss-Prot

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.