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Reviewed, UniProtKB/Swiss-Prot Q9UIS9 (MBD1_HUMAN)

Last modified June 16, 2009. Version 80. Feed History...

Clusters with 100%, 90%, 50% identity | Documents (6) | Third-party data | Customize display text xml rdf/xml gff fasta
Names and origin · Protein attributes · General annotation (Comments) · Ontologies · Binary interactions · Alternative products · Sequence annotation (Features) · Sequences · References · Cross-references · Entry information · Relevant documents

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Names and origin

Protein namesRecommended name:
    Methyl-CpG-binding domain protein 1
Alternative name(s):
    Methyl-CpG-binding protein MBD1
    Protein containing methyl-CpG-binding domain 1
    CXXC-type zinc finger protein 3
Gene names
Name: MBD1
Synonyms: CXXC3, PCM1
OrganismHomo sapiens (Human)
Taxonomic identifier9606 [NCBI]
Taxonomic lineageEukaryota › Metazoa › Chordata › Craniata › Vertebrata › Euteleostomi › Mammalia › Eutheria › Euarchontoglires › Primates › Haplorrhini › Catarrhini › Hominidae › Homo

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Protein attributes

Sequence length605 AA.
Sequence statusComplete.
Sequence processingThe displayed sequence is not processed.
Protein existenceEvidence at protein level.

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General annotation (Comments)

Function

Transcriptional repressor that binds CpG islands in promoters where the DNA is methylated at position 5 of cytosine within CpG dinucleotides. Binding is abolished by the presence of 7-mG that is produced by DNA damage by methylmethanesulfonate (MMS). Acts as transcriptional repressor and plays a role in gene silencing by recruiting AFT7IP, which in turn recruits factors such as the histone methyltransferase SETDB1. Probably forms a complex with SETDB1 and ATF7IP that represses transcription and couples DNA methylation and histone 'Lys-9' trimethylation. Isoform 1 and isoform 2 can also repress transcription from unmethylated promoters. Ref.1 Ref.3 Ref.7 Ref.8 Ref.9 Ref.10 Ref.11 Ref.12 Ref.13 Ref.21

Subunit structure

Binds OASL, AFT7IP and AFT7IP2. Binds CHAF1A and the SUV39H1-CBX5 complex via the MBD domain. Binds MGP via the TRD domain. May be part of the MeCP1 complex. During DNA replication, it recruits SETDB1 to form a S phase-specific complex that facilitates methylation of H3 'Lys-9' during replication-coupled chromatin assembly and is at least composed of the CAF-1 subunit CHAF1A, MBD1 and SETDB1.

Subcellular location

Nucleus speckle. Note: Nuclear, in a punctate pattern. Associated with euchromatic regions of the chromosomes, with pericentromeric regions on chromosome 1 and with telomeric regions from several chromosomes. Ref.1 Ref.3 Ref.8 Ref.9 Ref.12 Ref.21

Tissue specificity

Widely expressed. Ref.1

Induction

Up-regulated by interferon. Ref.4

Domain

The methyl-CpG-binding domain (MBD) functions both in binding to methylated DNA and in protein interactions.

The third CXXC-type zinc finger mediates binding to non-methylated CpG dinucleotides.

The transcriptional repression domain (TRD) is involved in transcription repression and in protein interactions.

Post-translational modification

Sumoylated with SUMO1 by PIAS1 and PIAS3. Sumoylation affects transcriptional silencing by preventing the interaction with SETDB1. In contrast, sumoylation may increase interaction with AFT7IP. Ref.16 Ref.17

Phosphorylated upon DNA damage, probably by ATM or ATR. Ref.16 Ref.15 Ref.18 Ref.19

Sequence similarities

Contains 3 CXXC-type zinc fingers.

Contains 1 MBD (methyl-CpG-binding) domain.

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Alternative products

This entry describes 8 isoforms produced by alternative splicing. [Align] [Select]
Isoform 1 (identifier: Q9UIS9-1)

Also known as: MBD1v1;

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: Q9UIS9-2)

Also known as: MBD1v2;

The sequence of this isoform differs from the canonical sequence as follows:
     304-326: Missing.
     483-528: Missing.
     593-605: RSKDLKKPGARKQ → SLQGRHSGRE...RRSWCPSSQS
Isoform 3 (identifier: Q9UIS9-3)

Also known as: MBD1v3;

The sequence of this isoform differs from the canonical sequence as follows:
     328-383: Missing.
Isoform 4 (identifier: Q9UIS9-4)

Also known as: MBD1v3;

The sequence of this isoform differs from the canonical sequence as follows:
     327-382: Missing.
     483-528: Missing.
Isoform 5 (identifier: Q9UIS9-5)

Also known as: PCM1;

The sequence of this isoform differs from the canonical sequence as follows:
     173-221: Missing.
Isoform 6 (identifier: Q9UIS9-6)

Also known as: MBD1v6;

The sequence of this isoform differs from the canonical sequence as follows:
     483-528: Missing.
     573-596: ITEIFSLGGTRFRDTAVWLPRSKD → EPTTQPQYSGNFDNDLYEIYLIDI
     597-605: Missing.
Isoform 7 (identifier: Q9UIS9-7)

The sequence of this isoform differs from the canonical sequence as follows:
     327-382: Missing.
Isoform 8 (identifier: Q9UIS9-8)

The sequence of this isoform differs from the canonical sequence as follows:
     304-326: Missing.
     483-528: Missing.

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Sequence annotation (Features)

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifier

Molecule processing

Chain1 – 605605Methyl-CpG-binding domain protein 1
PRO_0000096258

Regions

Domain1 – 6969MBD
Zinc finger169 – 21648CXXC-type 1
Zinc finger217 – 26347CXXC-type 2
Zinc finger330 – 37849CXXC-type 3
Region529 – 59264TRD
Motif84 – 885Nuclear localization signal Potential
Compositional bias284 – 31330Pro-rich

Amino acid modifications

Modified residue521Phosphotyrosine Ref.15
Modified residue2951Phosphoserine Ref.18
Modified residue3011Phosphothreonine Ref.18
Modified residue3911Phosphoserine Ref.19
Modified residue3991Phosphoserine Ref.19
Cross-link499Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in SUMO) Ref.16
Cross-link538Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in SUMO) Ref.16

Natural variations

Alternative sequence173 – 22149Missing in isoform 5.
VSP_011064
Alternative sequence304 – 32623Missing in isoform 2 and isoform 8.
VSP_011065
Alternative sequence327 – 38256Missing in isoform 4 and isoform 7.
VSP_011066
Alternative sequence328 – 38356Missing in isoform 3.
VSP_011067
Alternative sequence483 – 52846Missing in isoform 2, isoform 4, isoform 6 and isoform 8.
VSP_011068
Alternative sequence573 – 59624ITEIF…PRSKD → EPTTQPQYSGNFDNDLYEIY LIDI in isoform 6.
VSP_011069
Alternative sequence593 – 60513RSKDL…GARKQ → SLQGRHSGREDGCKVWETED TVEPTSTSWNPRGWPGTHVS LSPPPASMMWVSCRRSWCPS SQS in isoform 2.
VSP_011070
Alternative sequence597 – 6059Missing in isoform 6.
VSP_011071
Natural variant4011P → A: dbSNP rs125555. Ref.2
VAR_019513

Experimental info

Mutagenesis221R → A: Abolishes binding to methylated DNA.
Mutagenesis301R → A: Strongly reduces binding to methylated DNA. Ref.20
Mutagenesis321D → A: Strongly reduces binding to methylated DNA. Ref.20
Mutagenesis341Y → A: Reduces binding to methylated DNA. Ref.20
Mutagenesis441R → A: Abolishes binding to methylated DNA. Ref.20
Mutagenesis451S → A: Slightly reduces binding to methylated DNA. Ref.20
Mutagenesis521Y → A: No effect. Ref.20
Mutagenesis641F → A: Disrupts tertiary structure and abolishes DNA binding. Ref.20
Mutagenesis4991K → A: Abolishes sumoylation; when associated with A-538. Ref.16
Mutagenesis5011E → A: Abolishes sumoylation; when associated with A-540. Ref.16
Mutagenesis5381K → A: Abolishes sumoylation; when associated with A-499. Ref.16
Mutagenesis5401E → A: Abolishes sumoylation; when associated with A-501. Ref.16
Mutagenesis5761I → R: Abolishes interaction with AFT7IP and subsequent transcription repression activity. Ref.14
Sequence conflict2391H → R in ABP02056. Ref.5
Sequence conflict3301T → M in ABP02056. Ref.5
Sequence conflict348 – 3492MD → NG Ref.1
Sequence conflict348 – 3492MD → NG Ref.3
Sequence conflict348 – 3492MD → NG Ref.4
Sequence conflict4891L → M in CAA71735. Ref.1

Secondary structure

1 ............... 605
Helix Strand Turn

Details...

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Sequences

Sequence LengthMass (Da)Tools
Isoform 1 (MBD1v1) [UniParc].

Last modified July 19, 2004. Version 2.
Checksum: 665732782CC6A32A

FASTA60566,607
        10         20         30         40         50         60 
MAEDWLDCPA LGPGWKRREV FRKSGATCGR SDTYYQSPTG DRIRSKVELT RYLGPACDLT 

        70         80         90        100        110        120 
LFDFKQGILC YPAPKAHPVA VASKKRKKPS RPAKTRKRQV GPQSGEVRKE APRDETKADT 

       130        140        150        160        170        180 
DTAPASFPAP GCCENCGISF SGDGTQRQRL KTLCKDCRAQ RIAFNREQRM FKRVGCGECA 

       190        200        210        220        230        240 
ACQVTEDCGA CSTCLLQLPH DVASGLFCKC ERRRCLRIVE RSRGCGVCRG CQTQEDCGHC 

       250        260        270        280        290        300 
PICLRPPRPG LRRQWKCVQR RCLRGKHARR KGGCDSKMAA RRRPGAQPLP PPPPSQSPEP 

       310        320        330        340        350        360 
TEPHPRALAP SPPAEFIYYC VDEDELQPYT NRRQNRKCGA CAACLRRMDC GRCDFCCDKP 

       370        380        390        400        410        420 
KFGGSNQKRQ KCRWRQCLQF AMKRLLPSVW SESEDGAGSP PPYRRRKRPS SARRHHLGPT 

       430        440        450        460        470        480 
LKPTLATRTA QPDHTQAPTK QEAGGGFVLP PPGTDLVFLR EGASSPVQVP GPVAASTEAL 

       490        500        510        520        530        540 
LQEAQCSGLS WVVALPQVKQ EKADTQDEWT PGTAVLTSPV LVPGCPSKAV DPGLPSVKQE 

       550        560        570        580        590        600 
PPDPEEDKEE NKDDSASKLA PEEEAGGAGT PVITEIFSLG GTRFRDTAVW LPRSKDLKKP 


GARKQ

« Hide

Isoform 2 (MBD1v2).

Checksum: B77C386F65EA8718
Show »

FASTA58664,677
Isoform 3 (MBD1v3).

Checksum: B9A2031843757B12
Show »

FASTA54960,001
Isoform 4 (MBD1v3).

Checksum: C5D0267B1D464ACD
Show »

FASTA50355,167
Isoform 5 (PCM1).

Checksum: 2426F8B3EFD49E3B
Show »

FASTA55661,265
Isoform 6 (MBD1v6).

Checksum: 34194D340ED94FAB
Show »

FASTA55060,848
Isoform 7.

Checksum: 45456E4E96182B5C
Show »

FASTA54960,001
Isoform 8.

Checksum: 9ED6B5AEF1FF8BD9
Show »

FASTA53659,158

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References

« Hide 'large scale' references
[1]"A component of the transcriptional repressor MeCP1 shares a motif with DNA methyltransferase and HRX proteins."
Cross S.H., Meehan R.R., Nan X., Bird A.
Nat. Genet. 16:256-259(1997) [PubMed: 9207790] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [MRNA] (ISOFORM 5), FUNCTION, INTERACTION WITH THE MECP1 COMPLEX, SUBCELLULAR LOCATION, TISSUE SPECIFICITY.
[2]"Genomic structure and chromosomal mapping of the murine and human mbd1, mbd2, mbd3, and mbd4 genes."
Hendrich B., Abbott C., McQueen H., Chambers D., Cross S.H., Bird A.
Mamm. Genome 10:906-912(1999) [PubMed: 10441743] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA], VARIANT ALA-401.
[3]"Methylation-mediated transcriptional silencing in euchromatin by methyl-CpG binding protein MBD1 isoforms."
Fujita N., Takebayashi S., Okumura K., Kudo S., Chiba T., Saya H., Nakao M.
Mol. Cell. Biol. 19:6415-6426(1999) [PubMed: 10454587] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [MRNA] (ISOFORMS 1; 2; 3 AND 4), FUNCTION, SUBCELLULAR LOCATION.
Tissue: Fibroblast.
[4]"Interaction between the 2'-5' oligoadenylate synthetase-like protein p59 OASL and the transcriptional repressor methyl CpG-binding protein 1."
Andersen J.B., Strandbygaard D.J., Hartmann R., Justesen J.
Eur. J. Biochem. 271:628-636(2004) [PubMed: 14728690] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE (ISOFORM 6), INDUCTION BY INTERFERON, INTERACTION WITH OASL.
Tissue: Leukocyte.
[5]"New splice variant of the methyl-CpG binding protein 1 (MBD1)."
Laget S.M., Xu S.-Y.
Submitted (MAR-2007) to the EMBL/GenBank/DDBJ databases
Cited for: NUCLEOTIDE SEQUENCE [MRNA] (ISOFORM 8).
Tissue: Cervix carcinoma.
[6]"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: 15489334] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] (ISOFORM 7).
Tissue: Prostate.
[7]"Identification and characterization of a family of mammalian methyl-CpG binding proteins."
Hendrich B., Bird A.
Mol. Cell. Biol. 18:6538-6547(1998) [PubMed: 9774669] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [MRNA] OF 169-220, FUNCTION.
[8]"Active repression of methylated genes by the chromosomal protein MBD1."
Ng H.-H., Jeppesen P., Bird A.
Mol. Cell. Biol. 20:1394-1406(2000) [PubMed: 10648624] [Abstract]
Cited for: FUNCTION, SUBCELLULAR LOCATION.
[9]"Methyl-CpG binding domain 1 (MBD1) interacts with the Suv39h1-HP1 heterochromatic complex for DNA methylation-based transcriptional repression."
Fujita N., Watanabe S., Ichimura T., Tsuruzoe S., Shinkai Y., Tachibana M., Chiba T., Nakao M.
J. Biol. Chem. 278:24132-24138(2003) [PubMed: 12711603] [Abstract]
Cited for: FUNCTION, SUBCELLULAR LOCATION, INTERACTION WITH THE SUV39H1-CBX5 COMPLEX.
[10]"MCAF mediates MBD1-dependent transcriptional repression."
Fujita N., Watanabe S., Ichimura T., Ohkuma Y., Chiba T., Saya H., Nakao M.
Mol. Cell. Biol. 23:2834-2843(2003) [PubMed: 12665582] [Abstract]
Cited for: FUNCTION, INTERACTION WITH AFT7IP.
[11]"The methyl-CpG binding protein MBD1 interacts with the p150 subunit of chromatin assembly factor 1."
Reese B.E., Bachman K.E., Baylin S.B., Rountree M.R.
Mol. Cell. Biol. 23:3226-3236(2003) [PubMed: 12697822] [Abstract]
Cited for: FUNCTION, INTERACTION WITH CHAF1A.
[12]"Role of human ribosomal RNA (rRNA) promoter methylation and of methyl-CpG-binding protein MBD2 in the suppression of rRNA gene expression."
Ghoshal K., Majumder S., Datta J., Motiwala T., Bai S., Sharma S.M., Frankel W., Jacob S.T.
J. Biol. Chem. 279:6783-6793(2004) [PubMed: 14610093] [Abstract]
Cited for: FUNCTION, SUBCELLULAR LOCATION.
[13]"Methyl-CpG binding protein MBD1 couples histone H3 methylation at lysine 9 by SETDB1 to DNA replication and chromatin assembly."
Sarraf S.A., Stancheva I.
Mol. Cell 15:595-605(2004) [PubMed: 15327775] [Abstract]
Cited for: FUNCTION, INTERACTION WITH SETDB1 AND CHAF1A.
[14]"Transcriptional repression and heterochromatin formation by MBD1 and MCAF/AM family proteins."
Ichimura T., Watanabe S., Sakamoto Y., Aoto T., Fujita N., Nakao M.
J. Biol. Chem. 280:13928-13935(2005) [PubMed: 15691849] [Abstract]
Cited for: INTERACTION WITH AFT7IP AND AFT7IP2, MUTAGENESIS OF ILE-576.
[15]"Quantitative phosphoproteome analysis using a dendrimer conjugation chemistry and tandem mass spectrometry."
Tao W.A., Wollscheid B., O'Brien R., Eng J.K., Li X.-J., Bodenmiller B., Watts J.D., Hood L., Aebersold R.
Nat. Methods 2:591-598(2005) [PubMed: 16094384] [Abstract]
Cited for: PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT TYR-52, MASS SPECTROMETRY.
Tissue: T-cell.
[16]"Regulation of MBD1-mediated transcriptional repression by SUMO and PIAS proteins."
Lyst M.J., Nan X., Stancheva I.
EMBO J. 25:5317-5328(2006) [PubMed: 17066076] [Abstract]
Cited for: INTERACTION WITH SETDB1, PHOSPHORYLATION, SUMOYLATION AT LYS-499 AND LYS-538, MUTAGENESIS OF LYS-499; GLU-501; LYS-538 AND GLU-540.
[17]"Involvement of SUMO modification in MBD1- and MCAF1-mediated heterochromatin formation."
Uchimura Y., Ichimura T., Uwada J., Tachibana T., Sugahara S., Nakao M., Saitoh H.
J. Biol. Chem. 281:23180-23190(2006) [PubMed: 16757475] [Abstract]
Cited for: SUMOYLATION, INTERACTION WITH AFT7IP.
[18]"ATM and ATR substrate analysis reveals extensive protein networks responsive to DNA damage."
Matsuoka S., Ballif B.A., Smogorzewska A., McDonald E.R. III, Hurov K.E., Luo J., Bakalarski C.E., Zhao Z., Solimini N., Lerenthal Y., Shiloh Y., Gygi S.P., Elledge S.J.
Science 316:1160-1166(2007) [PubMed: 17525332] [Abstract]
Cited for: PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-295 AND THR-301, MASS SPECTROMETRY.
[19]"A quantitative atlas of mitotic phosphorylation."
Dephoure N., Zhou C., Villen J., Beausoleil S.A., Bakalarski C.E., Elledge S.J., Gygi S.P.
Proc. Natl. Acad. Sci. U.S.A. 105:10762-10767(2008) [PubMed: 18669648] [Abstract]
Cited for: PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-391 AND SER-399, MASS SPECTROMETRY.
[20]"Solution structure of the methyl-CpG-binding domain of the methylation-dependent transcriptional repressor MBD1."
Ohki I., Shimotake N., Fujita N., Nakao M., Shirakawa M.
EMBO J. 18:6653-6661(1999) [PubMed: 10581239] [Abstract]
Cited for: STRUCTURE BY NMR OF 1-75 IN COMPLEX WITH METHYLATED DNA, MUTAGENESIS OF ARG-30; ASP-32; TYR-34; ARG-44; SER-45; TYR-52 AND PHE-64.
[21]"Methylated DNA-binding domain 1 and methylpurine-DNA glycosylase link transcriptional repression and DNA repair in chromatin."
Watanabe S., Ichimura T., Fujita N., Tsuruzoe S., Ohki I., Shirakawa M., Kawasuji M., Nakao M.
Proc. Natl. Acad. Sci. U.S.A. 100:12859-12864(2003) [PubMed: 14555760] [Abstract]
Cited for: STRUCTURE BY NMR OF 1-75 IN COMPLEX WITH METHYLATED DNA, FUNCTION, SUBCELLULAR LOCATION, INTERACTION WITH MPG.
+Additional computationally mapped references.

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Cross-references

Sequence databases

Y10746 mRNA. Translation: CAA71735.1.
AF120981, AF120980 Genomic DNA. Translation: AAD50371.1.
AF078830 mRNA. Translation: AAD51442.1.
AF078831 mRNA. Translation: AAD51443.1.
AF078832 mRNA. Translation: AAD51444.1.
AF078833 mRNA. Translation: AAD51445.1.
EF488685 mRNA. Translation: ABP02056.1.
BC033242 mRNA. Translation: AAH33242.1.
AJ564845 mRNA. Translation: CAD92308.1.
AF072241 mRNA. Translation: AAC68870.1.
IPIIPI00438701.
IPI00438702.
IPI00438703.
IPI00438704.
IPI00438705.
IPI00438706.
IPI00438707.
IPI00854577.
RefSeqNP_002375.1.
NP_056669.2.
NP_056670.2.
NP_056671.2.
NP_056723.2.
UniGeneHs.405610

3D structure databases

EntryMethodResolution (Å)ChainPositionsPDBsum
1D9NNMR-A1-75[»]
1IG4NMR-A1-75[»]
ModBaseSearch...

Protein-protein interaction databases

IntActQ9UIS9. 7 interactions.

PTM databases

PhosphoSiteQ9UIS9.

Proteomic databases

PRIDEQ9UIS9.

Genome annotation databases

EnsemblENSG00000141644. Homo sapiens. [Contig view]
GeneID4152.
KEGGhsa:4152.

Organism-specific databases

GeneCardsGC18M046049.
H-InvDBHIX0014448.
HGNCHGNC:6916. MBD1.
HPACAB009017.
MIM156535. gene.
PharmGKBPA30659.
GenAtlasSearch...

Phylogenomic databases

HOVERGENQ9UIS9.
OMAQ9UIS9. LLQEAQC.

Gene expression databases

ArrayExpressQ9UIS9.
BgeeQ9UIS9.
CleanExHS_PCM1.
GermOnlineENSG00000141644. Homo sapiens.

Family and domain databases

InterProIPR001739. Methyl_CpG_DNA-bd.
IPR002857. Znf_CXXC.
[Graphical view]
Gene3DG3DSA:3.30.890.10. Methyl_CpG_DNA-bd. 1 hit.
PfamPF01429. MBD. 1 hit.
PF02008. zf-CXXC. 3 hits.
[Graphical view]
SMARTSM00391. MBD. 1 hit.
[Graphical view]
PROSITEPS50982. MBD. 1 hit.
PS51058. ZF_CXXC. 3 hits.
[Graphical view]
ProtoNetSearch...

Other Resources

NextBio16330.
SOURCESearch...

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Entry information

Entry nameMBD1_HUMAN
AccessionPrimary (citable) accession number: Q9UIS9
Secondary accession number(s): A4UTZ0 expand/collapse secondary AC list , O15248, O95241, Q7Z7B5, Q8N4W4, Q9UNZ6, Q9UNZ7, Q9UNZ8, Q9UNZ9
Entry history
Integrated into UniProtKB/Swiss-Prot: July 19, 2004
Last sequence update: July 19, 2004
Last modified: June 16, 2009
This is version 80 of the entry and version 2 of the sequence. [Complete history]
Entry statusReviewed (UniProtKB/Swiss-Prot)
Annotation projectHPI (Human Proteome Initiative)

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SIMILARITY comments

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Names and origin · Protein attributes · General annotation (Comments) · Ontologies · Binary interactions · Alternative products · Sequence annotation (Features) · Sequences · References · Cross-references · Entry information · Relevant documents