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P28068 (DMB_HUMAN) Reviewed, UniProtKB/Swiss-Prot

Last modified April 16, 2014. Version 143. Feed History...

Clusters with 100%, 90%, 50% identity | Documents (6) | Third-party data text xml rdf/xml gff fasta
to top of pageNames·Attributes·General annotation·Ontologies·Sequence annotation·Sequences·References·Cross-refs·Entry info·DocumentsCustomize order

Names and origin

Protein namesRecommended name:
HLA class II histocompatibility antigen, DM beta chain
Alternative name(s):
MHC class II antigen DMB
Really interesting new gene 7 protein
Gene names
Name:HLA-DMB
Synonyms:DMB, RING7
OrganismHomo sapiens (Human) [Reference proteome]
Taxonomic identifier9606 [NCBI]
Taxonomic lineageEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresPrimatesHaplorrhiniCatarrhiniHominidaeHomo

Protein attributes

Sequence length263 AA.
Sequence statusComplete.
Sequence processingThe displayed sequence is further processed into a mature form.
Protein existenceEvidence at protein level

General annotation (Comments)

Function

Plays a critical role in catalyzing the release of class II-associated invariant chain peptide (CLIP) from newly synthesized MHC class II molecules and freeing the peptide binding site for acquisition of antigenic peptides. In B-cells, the interaction between HLA-DM and MHC class II molecules is regulated by HLA-DO. Ref.12 Ref.15 Ref.16

Subunit structure

Heterodimer of an alpha chain (DMA) and a beta chain (DMB). Ref.15 Ref.16

Subcellular location

Late endosome membrane; Single-pass type I membrane protein. Lysosome membrane; Single-pass type I membrane protein. Note: Localizes to late endocytic compartment. Associates with lysosome membranes. Ref.13

Domain

The YXXZ (Tyr-Xaa-Xaa-Zaa, where Zaa is a hydrophobic residue) motif mediates the targeting to the lysosomal compartments.

Polymorphism

The following alleles of DMB are known: DMB*01:01, DMB*01:02, DMB*01:03, DMB*01:04 (DMB3.4), DMB*01:05, DMB*01:06, and DMB*01:07. The sequence shown is that of DMB*01:01.

Sequence similarities

Belongs to the MHC class II family.

Contains 1 Ig-like C1-type (immunoglobulin-like) domain.

Sequence annotation (Features)

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifier

Molecule processing

Signal peptide1 – 1818 Potential
Chain19 – 263245HLA class II histocompatibility antigen, DM beta chain
PRO_0000018960

Regions

Topological domain19 – 218200Lumenal Potential
Transmembrane219 – 23921Helical; Potential
Topological domain240 – 26324Cytoplasmic Potential
Domain114 – 20895Ig-like C1-type
Region19 – 11294Beta-1
Region113 – 20795Beta-2
Region208 – 21811Connecting peptide Potential
Motif248 – 2514YXXZ motif

Amino acid modifications

Glycosylation1101N-linked (GlcNAc...) Ref.14
Disulfide bond29 ↔ 97 Ref.15 Ref.16
Disulfide bond135 ↔ 192 Ref.15 Ref.16

Natural variations

Natural variant281T → A in allele DMB*01:07.
Corresponds to variant rs17583782 [ dbSNP | Ensembl ].
VAR_050360
Natural variant451S → F in allele DMB*01:06.
Corresponds to variant rs41560814 [ dbSNP | Ensembl ].
VAR_016752
Natural variant491D → V in allele DMB*01:07.
Corresponds to variant rs17617333 [ dbSNP | Ensembl ].
VAR_050361
Natural variant711S → N in allele DMB*01:07.
Corresponds to variant rs17617321 [ dbSNP | Ensembl ].
VAR_050362
Natural variant1621A → E in allele DMB*01:02 and allele DMB*01:06.
VAR_016753
Natural variant1621A → V in allele DMB*01:04 and allele DMB*01:05.
VAR_016754
Natural variant1971I → T in allele DMB*01:03, allele DMB*01:04 and allele DMB*01:06. Ref.5
Corresponds to variant rs1042337 [ dbSNP | Ensembl ].
VAR_016755

Experimental info

Mutagenesis2481Y → A: Abolishes targeting to endosomes and results in relocalization to the cell membrane. Ref.13
Mutagenesis2511L → A: Abolishes targeting to endosomes and results in relocalization to the cell membrane. Ref.13

Secondary structure

................................... 263
Helix Strand Turn

Details...

Sequences

Sequence LengthMass (Da)Tools
P28068 [UniParc].

Last modified August 1, 1992. Version 1.
Checksum: 9B50F6CC22B3A4BA

FASTA26328,943
        10         20         30         40         50         60 
MITFLPLLLG LSLGCTGAGG FVAHVESTCL LDDAGTPKDF TYCISFNKDL LTCWDPEENK 

        70         80         90        100        110        120 
MAPCEFGVLN SLANVLSQHL NQKDTLMQRL RNGLQNCATH TQPFWGSLTN RTRPPSVQVA 

       130        140        150        160        170        180 
KTTPFNTREP VMLACYVWGF YPAEVTITWR KNGKLVMPHS SAHKTAQPNG DWTYQTLSHL 

       190        200        210        220        230        240 
ALTPSYGDTY TCVVEHIGAP EPILRDWTPG LSPMQTLKVS VSAVTLGLGL IIFSLGVISW 

       250        260 
RRAGHSSYTP LPGSNYSEGW HIS 

« Hide

References

« Hide 'large scale' references
[1]"A new human HLA class II-related locus, DM."
Kelly A.P., Monaco J.J., Cho S., Trowsdale J.
Nature 353:571-573(1991) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [MRNA] (ALLELE DMB*01:01).
[2]"Genomic organization of HLA-DMA and HLA-DMB. Comparison of the gene organization of all six class II families in the human major histocompatibility complex."
Radley E., Alderton R.P., Kelly A., Trowsdale J., Beck S.
J. Biol. Chem. 269:18834-18838(1994) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA] (ALLELE DMB*01:01).
[3]"Evolutionary dynamics of non-coding sequences within the class II region of the human MHC."
Beck S., Abdulla S., Alderton R.P., Glynne R.J., Gut I.G., Hosking L.K., Jackson A., Kelly A., Newell W.R., Sanseau P., Radley E., Thorpe K.L., Trowsdale J.
J. Mol. Biol. 255:1-13(1996) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA] (ALLELE DMB*01:01).
[4]"Identification of a novel HLA-DMB allele (DMB*0107) in the Korean population."
Gu H., Moon S.-M., Kim J.-J., Ryu H.-J., Kwack K., Kimm K., Lee J.-K., Oh B.
Tissue Antigens 65:393-394(2005) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [MRNA] (ALLELE DMB*01:07).
[5]"The DNA sequence and analysis of human chromosome 6."
Mungall A.J., Palmer S.A., Sims S.K., Edwards C.A., Ashurst J.L., Wilming L., Jones M.C., Horton R., Hunt S.E., Scott C.E., Gilbert J.G.R., Clamp M.E., Bethel G., Milne S., Ainscough R., Almeida J.P., Ambrose K.D., Andrews T.D. expand/collapse author list , Ashwell R.I.S., Babbage A.K., Bagguley C.L., Bailey J., Banerjee R., Barker D.J., Barlow K.F., Bates K., Beare D.M., Beasley H., Beasley O., Bird C.P., Blakey S.E., Bray-Allen S., Brook J., Brown A.J., Brown J.Y., Burford D.C., Burrill W., Burton J., Carder C., Carter N.P., Chapman J.C., Clark S.Y., Clark G., Clee C.M., Clegg S., Cobley V., Collier R.E., Collins J.E., Colman L.K., Corby N.R., Coville G.J., Culley K.M., Dhami P., Davies J., Dunn M., Earthrowl M.E., Ellington A.E., Evans K.A., Faulkner L., Francis M.D., Frankish A., Frankland J., French L., Garner P., Garnett J., Ghori M.J., Gilby L.M., Gillson C.J., Glithero R.J., Grafham D.V., Grant M., Gribble S., Griffiths C., Griffiths M.N.D., Hall R., Halls K.S., Hammond S., Harley J.L., Hart E.A., Heath P.D., Heathcott R., Holmes S.J., Howden P.J., Howe K.L., Howell G.R., Huckle E., Humphray S.J., Humphries M.D., Hunt A.R., Johnson C.M., Joy A.A., Kay M., Keenan S.J., Kimberley A.M., King A., Laird G.K., Langford C., Lawlor S., Leongamornlert D.A., Leversha M., Lloyd C.R., Lloyd D.M., Loveland J.E., Lovell J., Martin S., Mashreghi-Mohammadi M., Maslen G.L., Matthews L., McCann O.T., McLaren S.J., McLay K., McMurray A., Moore M.J.F., Mullikin J.C., Niblett D., Nickerson T., Novik K.L., Oliver K., Overton-Larty E.K., Parker A., Patel R., Pearce A.V., Peck A.I., Phillimore B.J.C.T., Phillips S., Plumb R.W., Porter K.M., Ramsey Y., Ranby S.A., Rice C.M., Ross M.T., Searle S.M., Sehra H.K., Sheridan E., Skuce C.D., Smith S., Smith M., Spraggon L., Squares S.L., Steward C.A., Sycamore N., Tamlyn-Hall G., Tester J., Theaker A.J., Thomas D.W., Thorpe A., Tracey A., Tromans A., Tubby B., Wall M., Wallis J.M., West A.P., White S.S., Whitehead S.L., Whittaker H., Wild A., Willey D.J., Wilmer T.E., Wood J.M., Wray P.W., Wyatt J.C., Young L., Younger R.M., Bentley D.R., Coulson A., Durbin R.M., Hubbard T., Sulston J.E., Dunham I., Rogers J., Beck S.
Nature 425:805-811(2003) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA], VARIANT THR-197.
[6]Mural R.J., Istrail S., Sutton G.G., Florea L., Halpern A.L., Mobarry C.M., Lippert R., Walenz B., Shatkay H., Dew I., Miller J.R., Flanigan M.J., Edwards N.J., Bolanos R., Fasulo D., Halldorsson B.V., Hannenhalli S., Turner R. expand/collapse author list , Yooseph S., Lu F., Nusskern D.R., Shue B.C., Zheng X.H., Zhong F., Delcher A.L., Huson D.H., Kravitz S.A., Mouchard L., Reinert K., Remington K.A., Clark A.G., Waterman M.S., Eichler E.E., Adams M.D., Hunkapiller M.W., Myers E.W., Venter J.C.
Submitted (JUL-2005) to the EMBL/GenBank/DDBJ databases
Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
[7]"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] (ALLELE DMB*01:01).
Tissue: Lymph.
[8]"Limited polymorphism in HLA-DM does not involve the peptide binding groove."
Sanderson F., Powis S.H., Kelly A.P., Trowsdale J.
Immunogenetics 39:56-58(1994) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA] OF 114-207 (ALLELES DMB*01:02 AND DMB*01:03).
[9]"Characterization of HLA-DMB polymorphism."
Carrington M., Yeager M., Mann D.
Immunogenetics 38:446-449(1993) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA] OF 121-200 (ALLELE DMB*01:04).
[10]"Three HLA-DMB variants in Korean patients with autoimmune diseases."
Kim T.-G., Carrington M., Choi H.B., Kim H.Y., Han H.
Hum. Immunol. 46:58-60(1996) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA] OF 113-207 (ALLELE DMB*01:05).
Tissue: Blood.
[11]"The nucleotide sequence of a new DMB allele, DMB*0106."
McTernan C.L., Mijovic C.H., Cockram C.S., Barnett A.H.
Tissue Antigens 55:470-472(2000) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA] OF 19-112 AND 152-207 (ALLELE DMB*01:06).
[12]"Enhanced dissociation of HLA-DR-bound peptides in the presence of HLA-DM."
Weber D.A., Evavold B.D., Jensen P.E.
Science 274:618-620(1996) [PubMed] [Europe PMC] [Abstract]
Cited for: FUNCTION.
[13]"Targeting signal and subcellular compartments involved in the intracellular trafficking of HLA-DMB."
Copier J., Kleijmeer M.J., Ponnambalam S., Oorschot V., Potter P., Trowsdale J., Kelly A.
J. Immunol. 157:1017-1027(1996) [PubMed] [Europe PMC] [Abstract]
Cited for: SUBCELLULAR LOCATION, MUTAGENESIS OF TYR-248 AND LEU-251.
[14]"Human plasma N-glycoproteome analysis by immunoaffinity subtraction, hydrazide chemistry, and mass spectrometry."
Liu T., Qian W.-J., Gritsenko M.A., Camp D.G. II, Monroe M.E., Moore R.J., Smith R.D.
J. Proteome Res. 4:2070-2080(2005) [PubMed] [Europe PMC] [Abstract]
Cited for: GLYCOSYLATION [LARGE SCALE ANALYSIS] AT ASN-110.
Tissue: Plasma.
[15]"The structure of HLA-DM, the peptide exchange catalyst that loads antigen onto class II MHC molecules during antigen presentation."
Mosyak L., Zaller D.M., Wiley D.C.
Immunity 9:377-383(1998) [PubMed] [Europe PMC] [Abstract]
Cited for: X-RAY CRYSTALLOGRAPHY (2.5 ANGSTROMS) OF 19-218 IN COMPLEX WITH DMA, FUNCTION, SUBUNIT, DISULFIDE BONDS.
[16]"Small molecules that enhance the catalytic efficiency of HLA-DM."
Nicholson M.J., Moradi B., Seth N.P., Xing X., Cuny G.D., Stein R.L., Wucherpfennig K.W.
J. Immunol. 176:4208-4220(2006) [PubMed] [Europe PMC] [Abstract]
Cited for: X-RAY CRYSTALLOGRAPHY (2.27 ANGSTROMS) OF 19-218 IN COMPLEX WITH DMA, FUNCTION, SUBUNIT, DISULFIDE BONDS.
+Additional computationally mapped references.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ
Z23139 mRNA. Translation: CAA80670.1.
U15085 mRNA. Translation: AAB60387.1.
X76776 Genomic DNA. Translation: CAA54171.1.
X87344 Genomic DNA. Translation: CAA60782.1.
AY645722 mRNA. Translation: AAV97947.1.
AL662845 Genomic DNA. Translation: CAI17490.1.
AL645941 Genomic DNA. Translation: CAI18108.1.
AL935042 Genomic DNA. Translation: CAI18685.1.
BX088556 Genomic DNA. Translation: CAM26271.1.
BX927138 Genomic DNA. Translation: CAQ08457.1.
CR936913 Genomic DNA. Translation: CAQ08780.1.
CR759798 Genomic DNA. Translation: CAQ09462.1.
CR752645 Genomic DNA. Translation: CAQ09834.1.
CH471081 Genomic DNA. Translation: EAX03657.1.
BC027175 mRNA. Translation: AAH27175.1.
Z24750 Genomic DNA. No translation available.
Z24751 Genomic DNA. No translation available.
U00700 Genomic DNA. Translation: AAA03296.1.
U16762 Genomic DNA. Translation: AAC50514.1.
AF134890 Genomic DNA. Translation: AAD30279.1.
AF072680 Genomic DNA. Translation: AAC26112.1.
PIRI37533.
RefSeqNP_002109.2. NM_002118.4.
UniGeneHs.351279.

3D structure databases

PDBe
RCSB PDB
PDBj
EntryMethodResolution (Å)ChainPositionsPDBsum
1HDMX-ray2.50B19-218[»]
2BC4X-ray2.27B/D19-218[»]
4FQXX-ray2.60D19-211[»]
4GBXX-ray3.00D19-211[»]
4I0PX-ray3.20B/F21-211[»]
ProteinModelPortalP28068.
SMRP28068. Positions 21-217.
ModBaseSearch...
MobiDBSearch...

Protein-protein interaction databases

BioGrid109354. 6 interactions.
DIPDIP-6185N.
IntActP28068. 7 interactions.
MINTMINT-1539801.
STRING9606.ENSP00000393646.

PTM databases

PhosphoSiteP28068.

Polymorphism databases

DMDM133160.

Proteomic databases

PaxDbP28068.
PRIDEP28068.

Protocols and materials databases

DNASU3109.
StructuralBiologyKnowledgebaseSearch...

Genome annotation databases

EnsemblENST00000383231; ENSP00000372718; ENSG00000241674.
ENST00000395312; ENSP00000378723; ENSG00000242092.
ENST00000412948; ENSP00000413471; ENSG00000241296.
ENST00000418107; ENSP00000398890; ENSG00000242574.
ENST00000424822; ENSP00000414817; ENSG00000234154.
ENST00000428420; ENSP00000393646; ENSG00000239329.
ENST00000440078; ENSP00000411321; ENSG00000226264.
ENST00000450897; ENSP00000408453; ENSG00000242386.
GeneID3109.
KEGGhsa:3109.

Organism-specific databases

CTD3109.
GeneCardsGC06M032903.
GC06Mi32885.
GC06Mj32824.
GC06Mk32880.
GC06Ml33056.
GC06Mm32935.
GC06Mn32831.
GC06Mo32992.
H-InvDBHIX0166396.
HIX0207613.
HIX0207705.
HIX0207762.
HGNCHGNC:4935. HLA-DMB.
HPAHPA012298.
MIM142856. gene.
neXtProtNX_P28068.
PharmGKBPA35059.
GenAtlasSearch...

Phylogenomic databases

eggNOGNOG40558.
HOVERGENHBG007327.
InParanoidP28068.
KOK06752.
OMADCATHTQ.
PhylomeDBP28068.
TreeFamTF335727.

Enzyme and pathway databases

ReactomeREACT_6900. Immune System.

Gene expression databases

ArrayExpressP28068.
BgeeP28068.
CleanExHS_HLA-DMB.
GenevestigatorP28068.

Family and domain databases

Gene3D2.60.40.10. 1 hit.
3.10.320.10. 1 hit.
InterProIPR007110. Ig-like_dom.
IPR013783. Ig-like_fold.
IPR003006. Ig/MHC_CS.
IPR003597. Ig_C1-set.
IPR011162. MHC_I/II-like_Ag-recog.
IPR014745. MHC_II_a/b_N.
IPR000353. MHC_II_b_N.
[Graphical view]
PfamPF07654. C1-set. 1 hit.
PF00969. MHC_II_beta. 1 hit.
[Graphical view]
SMARTSM00407. IGc1. 1 hit.
SM00921. MHC_II_beta. 1 hit.
[Graphical view]
SUPFAMSSF54452. SSF54452. 1 hit.
PROSITEPS50835. IG_LIKE. 1 hit.
PS00290. IG_MHC. 1 hit.
[Graphical view]
ProtoNetSearch...

Other

EvolutionaryTraceP28068.
GeneWikiHLA-DMB.
GenomeRNAi3109.
NextBio12337.
PROP28068.
SOURCESearch...

Entry information

Entry nameDMB_HUMAN
AccessionPrimary (citable) accession number: P28068
Secondary accession number(s): O77936 expand/collapse secondary AC list , Q13012, Q29751, Q58ZE2, Q5SNZ8, Q5STC4, Q9XRX2
Entry history
Integrated into UniProtKB/Swiss-Prot: August 1, 1992
Last sequence update: August 1, 1992
Last modified: April 16, 2014
This is version 143 of the entry and version 1 of the sequence. [Complete history]
Entry statusReviewed (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.

Relevant documents

SIMILARITY comments

Index of protein domains and families

PDB cross-references

Index of Protein Data Bank (PDB) cross-references

MIM cross-references

Online Mendelian Inheritance in Man (MIM) cross-references in UniProtKB/Swiss-Prot

Human polymorphisms and disease mutations

Index of human polymorphisms and disease mutations

Human entries with polymorphisms or disease mutations

List of human entries with polymorphisms or disease mutations

Human chromosome 6

Human chromosome 6: entries, gene names and cross-references to MIM