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Protein

Structural maintenance of chromosomes protein 1A

Gene

SMC1A

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

Functioni

Involved in chromosome cohesion during cell cycle and in DNA repair. Central component of cohesin complex. The cohesin complex is required for the cohesion of sister chromatids after DNA replication. The cohesin complex apparently forms a large proteinaceous ring within which sister chromatids can be trapped. At anaphase, the complex is cleaved and dissociates from chromatin, allowing sister chromatids to segregate. The cohesin complex may also play a role in spindle pole assembly during mitosis. Involved in DNA repair via its interaction with BRCA1 and its related phosphorylation by ATM, or via its phosphorylation by ATR. Works as a downstream effector both in the ATM/NBS1 branch and in the ATR/MSH2 branch of S-phase checkpoint.1 Publication

Miscellaneous

Mutated Cornelia de Lange cell lines display genomic instability and sensitivity to ionizing radiation and interstrand cross-linking agents.

Regions

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Nucleotide bindingi32 – 39ATPSequence analysis8

GO - Molecular functioni

  • ATP binding Source: UniProtKB-KW
  • chromatin binding Source: UniProtKB
  • mediator complex binding Source: Ensembl
  • protein heterodimerization activity Source: UniProtKB
  • RNA binding Source: UniProtKB

GO - Biological processi

  • cell division Source: UniProtKB-KW
  • DNA repair Source: UniProtKB
  • meiotic cell cycle Source: UniProtKB
  • mitotic sister chromatid cohesion Source: UniProtKB
  • mitotic sister chromatid segregation Source: UniProtKB
  • mitotic spindle organization Source: UniProtKB
  • negative regulation of DNA endoreduplication Source: BHF-UCL
  • regulation of mitotic spindle assembly Source: UniProtKB
  • response to DNA damage checkpoint signaling Source: UniProtKB
  • response to radiation Source: UniProtKB
  • sister chromatid cohesion Source: BHF-UCL
  • stem cell population maintenance Source: Ensembl

Keywordsi

Biological processCell cycle, Cell division, DNA damage, DNA repair, Meiosis, Mitosis
LigandATP-binding, Nucleotide-binding

Enzyme and pathway databases

ReactomeiR-HSA-1221632. Meiotic synapsis.
R-HSA-2467813. Separation of Sister Chromatids.
R-HSA-2468052. Establishment of Sister Chromatid Cohesion.
R-HSA-2470946. Cohesin Loading onto Chromatin.
R-HSA-2500257. Resolution of Sister Chromatid Cohesion.
R-HSA-3108214. SUMOylation of DNA damage response and repair proteins.
SignaLinkiQ14683.
SIGNORiQ14683.

Names & Taxonomyi

Protein namesi
Recommended name:
Structural maintenance of chromosomes protein 1A
Short name:
SMC protein 1A
Short name:
SMC-1-alpha
Short name:
SMC-1A
Alternative name(s):
Sb1.8
Gene namesi
Name:SMC1A
Synonyms:DXS423E, KIAA0178, SB1.8, SMC1, SMC1L1
OrganismiHomo sapiens (Human)
Taxonomic identifieri9606 [NCBI]
Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresPrimatesHaplorrhiniCatarrhiniHominidaeHomo
Proteomesi
  • UP000005640 Componenti: Chromosome X

Organism-specific databases

EuPathDBiHostDB:ENSG00000072501.17.
HGNCiHGNC:11111. SMC1A.

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

Centromere, Chromosome, Kinetochore, Nucleus

Pathology & Biotechi

Involvement in diseasei

Cornelia de Lange syndrome 2 (CDLS2)8 Publications
The disease is caused by mutations affecting the gene represented in this entry.
Disease descriptionA form of Cornelia de Lange syndrome, a clinically heterogeneous developmental disorder associated with malformations affecting multiple systems. Characterized by facial dysmorphisms, abnormal hands and feet, growth delay, cognitive retardation, hirsutism, gastroesophageal dysfunction and cardiac, ophthalmologic and genitourinary anomalies.
See also OMIM:300590
Feature keyPosition(s)DescriptionActionsGraphical viewLength
Natural variantiVAR_06278558 – 62Missing in CDLS2. 3 Publications5
Natural variantiVAR_062786133F → V in CDLS2. 2 Publications1
Natural variantiVAR_062787141E → K in CDLS2. 1 PublicationCorresponds to variant dbSNP:rs587784420Ensembl.1
Natural variantiVAR_062788196R → H in CDLS2. 4 Publications1
Natural variantiVAR_062789268Missing in CDLS2. 2 Publications1
Natural variantiVAR_062790306Missing in CDLS2. 1 Publication1
Natural variantiVAR_078274398R → G in CDLS2. 1 Publication1
Natural variantiVAR_062791398R → Q in CDLS2. 1 PublicationCorresponds to variant dbSNP:rs587784403Ensembl.1
Natural variantiVAR_026529493E → A in CDLS2; affects the affinity of SMC hinge dimers for DNA; mutated hinge dimers bind DNA with higher affinity than wild-type proteins. 2 PublicationsCorresponds to variant dbSNP:rs122454122Ensembl.1
Natural variantiVAR_062792496R → C in CDLS2; affects the affinity of SMC hinge dimers for DNA; mutated hinge dimers bind DNA with higher affinity than wild-type proteins. 3 Publications1
Natural variantiVAR_062793496R → H in CDLS2; affects the affinity of SMC hinge dimers for DNA; mutated hinge dimers bind DNA with higher affinity than wild-type proteins. 3 PublicationsCorresponds to variant dbSNP:rs122454123Ensembl.1
Natural variantiVAR_078275651V → M in CDLS2; unknown pathological significance. 1 Publication1
Natural variantiVAR_062794683Missing in CDLS2. 1 Publication1
Natural variantiVAR_062795693R → G in CDLS2. 1 Publication1
Natural variantiVAR_078276693R → Q in CDLS2. 1 PublicationCorresponds to variant dbSNP:rs587784408Ensembl.1
Natural variantiVAR_064542711R → Q in CDLS2. 1 PublicationCorresponds to variant dbSNP:rs782176647Ensembl.1
Natural variantiVAR_062796711R → W in CDLS2. 2 PublicationsCorresponds to variant dbSNP:rs587784409Ensembl.1
Natural variantiVAR_062797781C → F in CDLS2. 1 Publication1
Natural variantiVAR_064543784I → T in CDLS2. 2 PublicationsCorresponds to variant dbSNP:rs387906702Ensembl.1
Natural variantiVAR_062798790R → Q in CDLS2. 3 PublicationsCorresponds to variant dbSNP:rs797045993Ensembl.1
Natural variantiVAR_062799816R → G in CDLS2. 1 Publication1
Natural variantiVAR_026530832Missing in CDLS2. 1 Publication1
Natural variantiVAR_0628001049R → Q in CDLS2. 1 PublicationCorresponds to variant dbSNP:rs587784416Ensembl.1
Natural variantiVAR_0628011085Y → C in CDLS2. 1 PublicationCorresponds to variant dbSNP:rs587784418Ensembl.1
Natural variantiVAR_0628021122F → L in CDLS2. 2 Publications1
Natural variantiVAR_0628031123R → W in CDLS2. 1 Publication1
Natural variantiVAR_0782771166N → T in CDLS2; unknown pathological significance. 1 Publication1
Natural variantiVAR_0782781189L → F in CDLS2; unknown pathological significance. 1 Publication1

Mutagenesis

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Mutagenesisi957S → A: Reduces phosphorylation and the S-phase checkpoint activation. Abolishes S-phase activation; when associated with A-966. 1 Publication1
Mutagenesisi966S → A: Reduces phosphorylation and the S-phase checkpoint activation. Increases sensitivity to DNA methylation. Abolishes S-phase activation; when associated with A-957. 2 Publications1

Keywords - Diseasei

Disease mutation, Mental retardation

Organism-specific databases

DisGeNETi8243.
GeneReviewsiSMC1A.
MalaCardsiSMC1A.
MIMi300590. phenotype.
OpenTargetsiENSG00000072501.
Orphaneti199. Cornelia de Lange syndrome.
PharmGKBiPA35961.

Polymorphism and mutation databases

DMDMi29336622.

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_00001189891 – 1233Structural maintenance of chromosomes protein 1AAdd BLAST1233

Amino acid modifications

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Modified residuei358PhosphoserineCombined sources1
Modified residuei360PhosphoserineCombined sources1
Modified residuei648N6-acetyllysineCombined sources1
Modified residuei713N6-acetyllysineCombined sources1
Modified residuei957Phosphoserine; by ATMCombined sources1 Publication1
Modified residuei962PhosphoserineCombined sources1
Modified residuei966Phosphoserine; by ATM and ATRCombined sources3 Publications1
Modified residuei970PhosphoserineCombined sources1
Modified residuei1037N6-acetyllysineBy similarity1

Post-translational modificationi

Phosphorylated by ATM upon ionizing radiation in a NBS1-dependent manner. Phosphorylated by ATR upon DNA methylation in a MSH2/MSH6-dependent manner. Phosphorylation of Ser-957 and Ser-966 activates it and is required for S-phase checkpoint activation.2 Publications

Keywords - PTMi

Acetylation, Phosphoprotein

Proteomic databases

EPDiQ14683.
MaxQBiQ14683.
PaxDbiQ14683.
PeptideAtlasiQ14683.
PRIDEiQ14683.

PTM databases

iPTMnetiQ14683.
PhosphoSitePlusiQ14683.
SwissPalmiQ14683.

Expressioni

Gene expression databases

BgeeiENSG00000072501.
CleanExiHS_SMC1A.
ExpressionAtlasiQ14683. baseline and differential.
GenevisibleiQ14683. HS.

Organism-specific databases

HPAiCAB025404.
HPA005499.

Interactioni

Subunit structurei

Interacts with POLE. Interacts with SYCP2. Interacts with BRCA1. Found in a complex with CDCA5, SMC3 and RAD21, PDS5A/SCC-112 and PDS5B/APRIN (By similarity). Forms a heterodimer with SMC3 in cohesin complexes. Cohesin complexes are composed of the SMC1 (SMC1A or SMC1B) and SMC3 heterodimer attached via their hinge domain, RAD21 which link them, and one STAG protein (STAG1, STAG2 or STAG3), which interacts with RAD21. In germ cell cohesin complexes, SMC1A is mutually exclusive with SMC1B. Interacts with BRCA1. Interacts with NDC80. Interacts with RPGR. Interacts with BRAT1.By similarity6 Publications

Binary interactionsi

Show more details

GO - Molecular functioni

  • mediator complex binding Source: Ensembl
  • protein heterodimerization activity Source: UniProtKB

Protein-protein interaction databases

BioGridi113871. 138 interactors.
CORUMiQ14683.
DIPiDIP-30911N.
IntActiQ14683. 98 interactors.
MINTiMINT-233274.
STRINGi9606.ENSP00000323421.

Structurei

3D structure databases

ProteinModelPortaliQ14683.
SMRiQ14683.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Region

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Regioni504 – 659Flexible hingeAdd BLAST156

Coiled coil

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Coiled coili104 – 124Sequence analysisAdd BLAST21
Coiled coili163 – 503Sequence analysisAdd BLAST341
Coiled coili660 – 935Sequence analysisAdd BLAST276
Coiled coili991 – 1068Sequence analysisAdd BLAST78

Compositional bias

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Compositional biasi1128 – 1163Ala/Asp-rich (DA-box)Add BLAST36

Domaini

The flexible hinge domain, which separates the large intramolecular coiled coil regions, allows the heterotypic interaction with the corresponding domain of SMC3, forming a V-shaped heterodimer. The two heads of the heterodimer are then connected by different ends of the cleavable RAD21 protein, forming a ring structure (By similarity).By similarity

Sequence similaritiesi

Belongs to the SMC family. SMC1 subfamily.Curated

Keywords - Domaini

Coiled coil

Phylogenomic databases

eggNOGiKOG0018. Eukaryota.
COG1196. LUCA.
GeneTreeiENSGT00580000081569.
HOGENOMiHOG000195481.
HOVERGENiHBG039593.
InParanoidiQ14683.
KOiK06636.
OMAiTATQYRS.
OrthoDBiEOG091G00R5.
PhylomeDBiQ14683.
TreeFamiTF101156.

Family and domain databases

InterProiView protein in InterPro
IPR027417. P-loop_NTPase.
IPR003395. RecF/RecN/SMC_N.
IPR024704. SMC.
IPR029683. SMC1A_metazoan.
IPR010935. SMC_hinge.
PANTHERiPTHR18937:SF292. PTHR18937:SF292. 1 hit.
PfamiView protein in Pfam
PF06470. SMC_hinge. 1 hit.
PF02463. SMC_N. 1 hit.
PIRSFiPIRSF005719. SMC. 1 hit.
SMARTiView protein in SMART
SM00968. SMC_hinge. 1 hit.
SUPFAMiSSF52540. SSF52540. 2 hits.
SSF75553. SSF75553. 1 hit.

Sequencei

Sequence statusi: Complete.

Q14683-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MGFLKLIEIE NFKSYKGRQI IGPFQRFTAI IGPNGSGKSN LMDAISFVLG
60 70 80 90 100
EKTSNLRVKT LRDLIHGAPV GKPAANRAFV SMVYSEEGAE DRTFARVIVG
110 120 130 140 150
GSSEYKINNK VVQLHEYSEE LEKLGILIKA RNFLVFQGAV ESIAMKNPKE
160 170 180 190 200
RTALFEEISR SGELAQEYDK RKKEMVKAEE DTQFNYHRKK NIAAERKEAK
210 220 230 240 250
QEKEEADRYQ RLKDEVVRAQ VQLQLFKLYH NEVEIEKLNK ELASKNKEIE
260 270 280 290 300
KDKKRMDKVE DELKEKKKEL GKMMREQQQI EKEIKEKDSE LNQKRPQYIK
310 320 330 340 350
AKENTSHKIK KLEAAKKSLQ NAQKHYKKRK GDMDELEKEM LSVEKARQEF
360 370 380 390 400
EERMEEESQS QGRDLTLEEN QVKKYHRLKE EASKRAATLA QELEKFNRDQ
410 420 430 440 450
KADQDRLDLE ERKKVETEAK IKQKLREIEE NQKRIEKLEE YITTSKQSLE
460 470 480 490 500
EQKKLEGELT EEVEMAKRRI DEINKELNQV MEQLGDARID RQESSRQQRK
510 520 530 540 550
AEIMESIKRL YPGSVYGRLI DLCQPTQKKY QIAVTKVLGK NMDAIIVDSE
560 570 580 590 600
KTGRDCIQYI KEQRGEPETF LPLDYLEVKP TDEKLRELKG AKLVIDVIRY
610 620 630 640 650
EPPHIKKALQ YACGNALVCD NVEDARRIAF GGHQRHKTVA LDGTLFQKSG
660 670 680 690 700
VISGGASDLK AKARRWDEKA VDKLKEKKER LTEELKEQMK AKRKEAELRQ
710 720 730 740 750
VQSQAHGLQM RLKYSQSDLE QTKTRHLALN LQEKSKLESE LANFGPRIND
760 770 780 790 800
IKRIIQSRER EMKDLKEKMN QVEDEVFEEF CREIGVRNIR EFEEEKVKRQ
810 820 830 840 850
NEIAKKRLEF ENQKTRLGIQ LDFEKNQLKE DQDKVHMWEQ TVKKDENEIE
860 870 880 890 900
KLKKEEQRHM KIIDETMAQL QDLKNQHLAK KSEVNDKNHE MEEIRKKLGG
910 920 930 940 950
ANKEMTHLQK EVTAIETKLE QKRSDRHNLL QACKMQDIKL PLSKGTMDDI
960 970 980 990 1000
SQEEGSSQGE DSVSGSQRIS SIYAREALIE IDYGDLCEDL KDAQAEEEIK
1010 1020 1030 1040 1050
QEMNTLQQKL NEQQSVLQRI AAPNMKAMEK LESVRDKFQE TSDEFEAARK
1060 1070 1080 1090 1100
RAKKAKQAFE QIKKERFDRF NACFESVATN IDEIYKALSR NSSAQAFLGP
1110 1120 1130 1140 1150
ENPEEPYLDG INYNCVAPGK RFRPMDNLSG GEKTVAALAL LFAIHSYKPA
1160 1170 1180 1190 1200
PFFVLDEIDA ALDNTNIGKV ANYIKEQSTC NFQAIVISLK EEFYTKAESL
1210 1220 1230
IGVYPEQGDC VISKVLTFDL TKYPDANPNP NEQ
Length:1,233
Mass (Da):143,233
Last modified:October 1, 2002 - v2
Checksum:iE0A44CA7476C88A6
GO

Experimental Info

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Sequence conflicti163 – 164EL → DV in AAB34405 (PubMed:7757074).Curated2

Natural variant

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Natural variantiVAR_05243828T → P. Corresponds to variant dbSNP:rs34530151Ensembl.1
Natural variantiVAR_06278558 – 62Missing in CDLS2. 3 Publications5
Natural variantiVAR_062786133F → V in CDLS2. 2 Publications1
Natural variantiVAR_062787141E → K in CDLS2. 1 PublicationCorresponds to variant dbSNP:rs587784420Ensembl.1
Natural variantiVAR_062788196R → H in CDLS2. 4 Publications1
Natural variantiVAR_062789268Missing in CDLS2. 2 Publications1
Natural variantiVAR_062790306Missing in CDLS2. 1 Publication1
Natural variantiVAR_078274398R → G in CDLS2. 1 Publication1
Natural variantiVAR_062791398R → Q in CDLS2. 1 PublicationCorresponds to variant dbSNP:rs587784403Ensembl.1
Natural variantiVAR_026529493E → A in CDLS2; affects the affinity of SMC hinge dimers for DNA; mutated hinge dimers bind DNA with higher affinity than wild-type proteins. 2 PublicationsCorresponds to variant dbSNP:rs122454122Ensembl.1
Natural variantiVAR_062792496R → C in CDLS2; affects the affinity of SMC hinge dimers for DNA; mutated hinge dimers bind DNA with higher affinity than wild-type proteins. 3 Publications1
Natural variantiVAR_062793496R → H in CDLS2; affects the affinity of SMC hinge dimers for DNA; mutated hinge dimers bind DNA with higher affinity than wild-type proteins. 3 PublicationsCorresponds to variant dbSNP:rs122454123Ensembl.1
Natural variantiVAR_078275651V → M in CDLS2; unknown pathological significance. 1 Publication1
Natural variantiVAR_062794683Missing in CDLS2. 1 Publication1
Natural variantiVAR_062795693R → G in CDLS2. 1 Publication1
Natural variantiVAR_078276693R → Q in CDLS2. 1 PublicationCorresponds to variant dbSNP:rs587784408Ensembl.1
Natural variantiVAR_064542711R → Q in CDLS2. 1 PublicationCorresponds to variant dbSNP:rs782176647Ensembl.1
Natural variantiVAR_062796711R → W in CDLS2. 2 PublicationsCorresponds to variant dbSNP:rs587784409Ensembl.1
Natural variantiVAR_062797781C → F in CDLS2. 1 Publication1
Natural variantiVAR_064543784I → T in CDLS2. 2 PublicationsCorresponds to variant dbSNP:rs387906702Ensembl.1
Natural variantiVAR_062798790R → Q in CDLS2. 3 PublicationsCorresponds to variant dbSNP:rs797045993Ensembl.1
Natural variantiVAR_062799816R → G in CDLS2. 1 Publication1
Natural variantiVAR_026530832Missing in CDLS2. 1 Publication1
Natural variantiVAR_0628001049R → Q in CDLS2. 1 PublicationCorresponds to variant dbSNP:rs587784416Ensembl.1
Natural variantiVAR_0628011085Y → C in CDLS2. 1 PublicationCorresponds to variant dbSNP:rs587784418Ensembl.1
Natural variantiVAR_0628021122F → L in CDLS2. 2 Publications1
Natural variantiVAR_0628031123R → W in CDLS2. 1 Publication1
Natural variantiVAR_0782771166N → T in CDLS2; unknown pathological significance. 1 Publication1
Natural variantiVAR_0782781189L → F in CDLS2; unknown pathological significance. 1 Publication1

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
S78271 mRNA. Translation: AAB34405.1.
D80000 mRNA. Translation: BAA11495.2.
AL161779, Z97054 Genomic DNA. Translation: CAI42089.1.
Z97054, AL161779 Genomic DNA. Translation: CAI42646.1.
BC112127 mRNA. Translation: AAI12128.1.
CCDSiCCDS14352.1.
PIRiI54383.
RefSeqiNP_006297.2. NM_006306.3.
UniGeneiHs.211602.

Genome annotation databases

EnsembliENST00000322213; ENSP00000323421; ENSG00000072501.
GeneIDi8243.
KEGGihsa:8243.
UCSCiuc004dsg.4. human.

Keywords - Coding sequence diversityi

Polymorphism

Similar proteinsi

Entry informationi

Entry nameiSMC1A_HUMAN
AccessioniPrimary (citable) accession number: Q14683
Secondary accession number(s): O14995, Q16351, Q2M228
Entry historyiIntegrated into UniProtKB/Swiss-Prot: March 25, 2003
Last sequence update: October 1, 2002
Last modified: September 27, 2017
This is version 187 of the entry and version 2 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

Complete proteome, Direct protein sequencing, Reference proteome

Documents

  1. Human chromosome X
    Human chromosome X: 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. SIMILARITY comments
    Index of protein domains and families