HLA class II histocompatibility antigen, DM beta chain precursor

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Reviewed, UniProtKB/Swiss-Prot P28068 (2DMB_HUMAN)

Last modified July 7, 2009. Version 93. History...

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

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Names and origin

Protein names

Recommended name:
HLA class II histocompatibility antigen, DM beta chain
Alternative name(s):
MHC class II antigen DMB

Gene names

Name:	HLA-DMB
Synonyms:	DMB, RING7

Organism

Homo sapiens (Human) [Complete proteome]

Taxonomic identifier

9606 [NCBI]

Taxonomic lineage

Eukaryota › Metazoa › Chordata › Craniata › Vertebrata › Euteleostomi › Mammalia › Eutheria › Euarchontoglires › Primates › Haplorrhini › Catarrhini › Hominidae › Homo

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Protein attributes

Sequence length	263 AA.
Sequence status	Complete.
Sequence processing	The displayed sequence is further processed into a mature form.
Protein existence	Evidence at protein level.

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General annotation (Comments)

Function	Plays a critical role in catalyzing the release of class II HLA-associated invariant chain-derived peptides (CLIP) from newly synthesized class II HLA molecules and freeing the peptide binding site for acquisition of antigenic peptides. Ref.10
Subunit structure	Heterodimer of an alpha chain (DMA) and a beta chain (DMB).
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.11
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: DMB0101, DMB0102, DMB0103, DMB0104 (DMB3.4), DMB0105, DMB0106, and DMB0107. The sequence shown is that of DMB0101.
Sequence similarities	Belongs to the MHC class II family. Contains 1 Ig-like C1-type (immunoglobulin-like) domain.

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Ontologies

Keywords
Biological process	Immune response
Cellular component	Endosome Lysosome MHC II Membrane
Coding sequence diversity	Polymorphism
Domain	Signal Transmembrane
PTM	Glycoprotein
Technical term	3D-structure Complete proteome
Gene Ontology (GO)
Biological process	antigen processing and presentation of peptide or polysaccharide antigen via MHC class II Inferred from electronic annotation. Source: UniProtKB-KW immune response Inferred from electronic annotation. Source: UniProtKB-KW
Cellular component	MHC class II protein complex Inferred from electronic annotation. Source: UniProtKB-KW integral to membrane Inferred from electronic annotation. Source: UniProtKB-KW late endosome membrane Inferred from electronic annotation. Source: UniProtKB-SubCell lysosomal membrane Inferred from electronic annotation. Source: UniProtKB-SubCell
Complete GO annotation...

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Sequence annotation (Features)

Feature key

Position(s)

Length

Description

Graphical view

Feature identifier

Molecule processing

Signal peptide

1 – 18

Potential

Chain

19 – 263

245

HLA class II histocompatibility antigen, DM beta chain

PRO_0000018960

Regions

Topological domain

19 – 218

200

Lumenal Potential

Transmembrane

219 – 239

Potential

Topological domain

240 – 263

Cytoplasmic Potential

Domain

114 – 208

Ig-like C1-type

Region

19 – 112

Beta-1

Region

113 – 207

Beta-2

Region

208 – 218

Connecting peptide Potential

Motif

248 – 251

YXXZ motif

Amino acid modifications

Glycosylation

110

N-linked (GlcNAc...) Ref.12

Natural variations

Natural variant

T → A in allele DMB*0107. dbSNP rs17583782.

VAR_050360

Natural variant

S → F in allele DMB*0106. dbSNP rs41560814.

VAR_016752

Natural variant

D → V in allele DMB*0107. dbSNP rs17617333.

VAR_050361

Natural variant

S → N in allele DMB*0107. dbSNP rs17617321.

VAR_050362

Natural variant

162

A → E in allele DMB*0102 and allele DMB*0106.

VAR_016753

Natural variant

162

A → V in allele DMB*0104 and allele DMB*0105.

VAR_016754

Natural variant

197

I → T in allele DMB*0103, allele DMB*0104 and allele DMB*0106. dbSNP rs1042337.

VAR_016755

Experimental info

Mutagenesis

248

Y → A: Abolishes targeting to endosomes and results in relocalization to the cell membrane. Ref.11

Mutagenesis

251

L → A: Abolishes targeting to endosomes and results in relocalization to the cell membrane. Ref.11

Secondary structure

263

Helix Strand Turn

Details...

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Sequences

Sequence

Length

Mass (Da)

Tools

P28068-1 [UniParc].

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

263

28,943

        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

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References

	« Hide 'large scale' referencesShow '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: 1922365] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [MRNA] (ALLELE DMB*0101).
[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: 8034636] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA] (ALLELE DMB*0101).
[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: 8568858] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA] (ALLELE DMB*0101).
[4]	*"Identification of a novel HLA-DMB allele (DMB0107) 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: 15787724] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [MRNA] (ALLELE DMB*0107).
[5]	"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] (ALLELE DMB*0101). Tissue: Lymph.
[6]	"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: 8225438] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA] OF 114-207 (ALLELES DMB0102 AND DMB0103).
[7]	"Characterization of HLA-DMB polymorphism." Carrington M., Yeager M., Mann D. Immunogenetics 38:446-449(1993) [PubMed: 8406617] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA] OF 121-200 (ALLELE DMB*0104).
[8]	"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: 9157091] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA] OF 113-207 (ALLELE DMB*0105). Tissue: Blood.
[9]	*"The nucleotide sequence of a new DMB allele, DMB0106."** McTernan C.L., Mijovic C.H., Cockram C.S., Barnett A.H. Tissue Antigens 55:470-472(2000) [PubMed: 10885572] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA] OF 19-112 AND 152-207 (ALLELE DMB*0106).
[10]	"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: 8849454] [Abstract] Cited for: FUNCTION.
[11]	"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: 8757605] [Abstract] Cited for: SUBCELLULAR LOCATION, MUTAGENESIS OF TYR-248 AND LEU-251.
[12]	"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: 16335952] [Abstract] Cited for: GLYCOSYLATION [LARGE SCALE ANALYSIS] AT ASN-110, MASS SPECTROMETRY. Tissue: Plasma.
[13]	"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: 9768757] [Abstract] Cited for: X-RAY CRYSTALLOGRAPHY (2.5 ANGSTROMS) OF 19-218.
+	Additional computationally mapped references.

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Cross-references

Sequence databases

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.
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.

IPI

IPI00000793.

PIR

I37533.

RefSeq

NP_002109.1.

UniGene

Hs.654428

3D structure databases

Entry	Method	Resolution (Å)	Chain	Positions	PDBsum
1HDM	X-ray	2.50	B	19-218	[»]
2BC4	X-ray	2.27	B/D	19-218	[»]

ModBase

Search...

Protein-protein interaction databases

DIP

DIP:6185N.

Proteomic databases

PRIDE

P28068.

Genome annotation databases

Ensembl

ENSG00000206294. Homo sapiens. [Contig view]

GeneID

3109.

KEGG

hsa:3109.

UCSC

uc003ocl.1. human.

Organism-specific databases

GeneCards

GC06Mf32973.

H-InvDB

HIX0005762.
HIX0057755.
HIX0057992.

HGNC

HGNC:4935. HLA-DMB.

HPA

HPA012298.

MIM

142856. gene.

PharmGKB

PA35059.

GenAtlas

Search...

Phylogenomic databases

HOGENOM

P28068.

HOVERGEN

P28068.

Enzyme and pathway databases

Reactome

REACT_6900. Signaling in Immune system.

Gene expression databases

CleanEx

HS_HLA-DMB.

Family and domain databases

InterPro

IPR007110. Ig-like.
IPR013783. Ig-like_fold.
IPR003006. Ig/MHC_CS.
IPR003597. Ig_C1-set.
IPR014745. MHC_II_a/b_N.
IPR000353. MHC_II_b_N.
[Graphical view]

Gene3D

G3DSA:2.60.40.10. Ig-like_fold. 1 hit.
G3DSA:3.10.320.10. MHC_II_alpha_N. 1 hit.

Pfam

PF07654. C1-set. 1 hit.
PF00969. MHC_II_beta. 1 hit.
[Graphical view]

SMART

SM00407. IGc1. 1 hit.
[Graphical view]

PROSITE

PS50835. IG_LIKE. 1 hit.
PS00290. IG_MHC. 1 hit.
[Graphical view]

ProtoNet

Search...

Other Resources

NextBio

12337.

SOURCE

Search...

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Entry information

Entry name

2DMB_HUMAN

Accession

Primary (citable) accession number: P28068
Secondary accession number(s): O77936

Q9XRX2

Entry history

Integrated into UniProtKB/Swiss-Prot:	August 1, 1992
Last sequence update:	August 1, 1992
Last modified:	July 7, 2009
This is version 93 of the entry and version 1 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation project

HPI (Human Proteome Initiative)

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