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P28067

- DMA_HUMAN

UniProt

P28067 - DMA_HUMAN

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Protein

HLA class II histocompatibility antigen, DM alpha chain

Gene

HLA-DMA

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

Functioni

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.3 Publications

GO - Molecular functioni

  1. MHC class II protein complex binding Source: UniProt

GO - Biological processi

  1. antigen processing and presentation of exogenous peptide antigen via MHC class II Source: Reactome
  2. chaperone mediated protein folding requiring cofactor Source: Ensembl
  3. immunoglobulin mediated immune response Source: Ensembl
  4. inner ear development Source: Ensembl
  5. peptide antigen assembly with MHC class II protein complex Source: UniProt
  6. positive regulation of immune response Source: Ensembl
  7. positive regulation of T cell differentiation Source: Ensembl
  8. positive thymic T cell selection Source: Ensembl
  9. protein transport Source: Ensembl
Complete GO annotation...

Keywords - Biological processi

Immunity

Enzyme and pathway databases

ReactomeiREACT_121399. MHC class II antigen presentation.

Names & Taxonomyi

Protein namesi
Recommended name:
HLA class II histocompatibility antigen, DM alpha chain
Alternative name(s):
MHC class II antigen DMA
Really interesting new gene 6 protein
Gene namesi
Name:HLA-DMA
Synonyms:DMA, RING6
OrganismiHomo sapiens (Human)
Taxonomic identifieri9606 [NCBI]
Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresPrimatesHaplorrhiniCatarrhiniHominidaeHomo
ProteomesiUP000005640: Chromosome 6, UP000005640: Unplaced

Organism-specific databases

HGNCiHGNC:4934. HLA-DMA.

Subcellular locationi

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.

Topology

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Topological domaini27 – 233207LumenalSequence AnalysisAdd
BLAST
Transmembranei234 – 25421HelicalSequence AnalysisAdd
BLAST
Topological domaini255 – 2617CytoplasmicSequence Analysis

GO - Cellular componenti

  1. cell surface Source: UniProt
  2. endosome membrane Source: Ensembl
  3. extracellular vesicular exosome Source: UniProt
  4. integral component of membrane Source: UniProtKB-KW
  5. lysosomal membrane Source: Reactome
  6. membrane Source: UniProtKB
  7. MHC class II protein complex Source: UniProt
  8. multivesicular body Source: Ensembl
Complete GO annotation...

Keywords - Cellular componenti

Endosome, Lysosome, Membrane, MHC II

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Signal peptidei1 – 2626Sequence AnalysisAdd
BLAST
Chaini27 – 261235HLA class II histocompatibility antigen, DM alpha chainPRO_0000018958Add
BLAST

Amino acid modifications

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Glycosylationi41 – 411N-linked (GlcNAc...)Sequence Analysis
Disulfide bondi50 ↔ 105
Disulfide bondi147 ↔ 202

Keywords - PTMi

Disulfide bond, Glycoprotein

Proteomic databases

PaxDbiP28067.
PRIDEiP28067.

PTM databases

PhosphoSiteiP28067.

Expressioni

Gene expression databases

BgeeiP28067.
CleanExiHS_HLA-DMA.
ExpressionAtlasiP28067. baseline and differential.
GenevestigatoriP28067.

Organism-specific databases

HPAiHPA012750.

Interactioni

Subunit structurei

Heterodimer of an alpha chain (DMA) and a beta chain (DMB).2 Publications

Protein-protein interaction databases

DIPiDIP-6184N.
IntActiP28067. 7 interactions.
MINTiMINT-1539780.
STRINGi9606.ENSP00000408311.

Structurei

Secondary structure

1
261
Legend: HelixTurnBeta strand
Show more details
Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Beta strandi41 – 6323Combined sources
Beta strandi66 – 727Combined sources
Turni73 – 764Combined sources
Beta strandi77 – 826Combined sources
Helixi83 – 853Combined sources
Helixi87 – 893Combined sources
Helixi95 – 11016Combined sources
Turni114 – 1163Combined sources
Turni117 – 1193Combined sources
Beta strandi122 – 1243Combined sources
Beta strandi128 – 1358Combined sources
Beta strandi143 – 15513Combined sources
Beta strandi157 – 1637Combined sources
Beta strandi166 – 1683Combined sources
Beta strandi175 – 1795Combined sources
Turni180 – 1823Combined sources
Beta strandi183 – 19210Combined sources
Beta strandi200 – 2067Combined sources
Turni207 – 2104Combined sources
Beta strandi211 – 2177Combined sources

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
1HDMX-ray2.50A27-230[»]
2BC4X-ray2.27A/C27-229[»]
4FQXX-ray2.60C27-225[»]
4GBXX-ray3.00C27-225[»]
ProteinModelPortaliP28067.
SMRiP28067. Positions 38-230.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiP28067.

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Domaini121 – 21595Ig-like C1-typeAdd
BLAST

Region

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Regioni27 – 12498Alpha-1Add
BLAST
Regioni125 – 21793Alpha-2Add
BLAST
Regioni218 – 23316Connecting peptideSequence AnalysisAdd
BLAST

Sequence similaritiesi

Belongs to the MHC class II family.Curated

Keywords - Domaini

Signal, Transmembrane, Transmembrane helix

Phylogenomic databases

eggNOGiNOG43075.
HOGENOMiHOG000126882.
HOVERGENiHBG001688.
InParanoidiP28067.
PhylomeDBiP28067.
TreeFamiTF333797.

Family and domain databases

Gene3Di2.60.40.10. 1 hit.
3.10.320.10. 1 hit.
InterProiIPR007110. 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.
IPR001003. MHC_II_a_N.
[Graphical view]
PfamiPF07654. C1-set. 1 hit.
PF00993. MHC_II_alpha. 1 hit.
[Graphical view]
SMARTiSM00407. IGc1. 1 hit.
SM00920. MHC_II_alpha. 1 hit.
[Graphical view]
SUPFAMiSSF54452. SSF54452. 1 hit.
PROSITEiPS50835. IG_LIKE. 1 hit.
PS00290. IG_MHC. 1 hit.
[Graphical view]

Sequencei

Sequence statusi: Complete.

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

P28067-1 [UniParc]FASTAAdd to Basket

« Hide

        10         20         30         40         50
MGHEQNQGAA LLQMLPLLWL LPHSWAVPEA PTPMWPDDLQ NHTFLHTVYC
60 70 80 90 100
QDGSPSVGLS EAYDEDQLFF FDFSQNTRVP RLPEFADWAQ EQGDAPAILF
110 120 130 140 150
DKEFCEWMIQ QIGPKLDGKI PVSRGFPIAE VFTLKPLEFG KPNTLVCFVS
160 170 180 190 200
NLFPPMLTVN WHDHSVPVEG FGPTFVSAVD GLSFQAFSYL NFTPEPSDIF
210 220 230 240 250
SCIVTHEIDR YTAIAYWVPR NALPSDLLEN VLCGVAFGLG VLGIIVGIVL
260
IIYFRKPCSG D
Length:261
Mass (Da):29,194
Last modified:August 1, 1992 - v1
Checksum:i1986C3C1989F02E9
GO

Polymorphismi

The following alleles of DMA are known: DMA*01:01, DMA*01:02, DMA*01:03 (DMA3.2) and DMA*01:04 (DMA3.4). The sequence shown is that of DMA*01:01.

Natural variant

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Natural varianti162 – 1621H → Q in allele DMA*01:03 and allele DMA*01:04.
VAR_016746
Natural varianti163 – 1631D → H in allele DMA*01:03 and allele DMA*01:04.
VAR_016747
Natural varianti166 – 1661V → I in allele DMA*01:02 and allele DMA*01:04.
Corresponds to variant rs1063478 [ dbSNP | Ensembl ].
VAR_016748
Natural varianti181 – 1811G → A in allele DMA*01:03.
Corresponds to variant rs6926628 [ dbSNP | Ensembl ].
VAR_016749
Natural varianti210 – 2101R → C in allele DMA*01:04.
Corresponds to variant rs17214044 [ dbSNP | Ensembl ].
VAR_016750
Natural varianti210 – 2101R → H in allele DMA*01:03.
Corresponds to variant rs41555121 [ dbSNP | Ensembl ].
VAR_016751
Natural varianti235 – 2351V → M.
Corresponds to variant rs9469319 [ dbSNP | Ensembl ].
VAR_056544

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
X62744 mRNA. Translation: CAA44606.1.
AL935042 Genomic DNA. No translation available.
Z24753 Genomic DNA. No translation available.
U04878 Genomic DNA. Translation: AAA56994.1.
U04877 Genomic DNA. Translation: AAA56993.1.
CCDSiCCDS4761.1.
PIRiI38490.
S17886.
UniGeneiHs.728759.

Genome annotation databases

EnsembliENST00000374843; ENSP00000363976; ENSG00000204257.
ENST00000383230; ENSP00000372717; ENSG00000243215.
ENST00000434337; ENSP00000407198; ENSG00000242361.
ENST00000441375; ENSP00000410591; ENSG00000239463.
ENST00000450601; ENSP00000392842; ENSG00000242685.
ENST00000452615; ENSP00000395349; ENSG00000243189.
ENST00000453490; ENSP00000404018; ENSG00000243719.

Polymorphism databases

DMDMi133158.

Keywords - Coding sequence diversityi

Polymorphism

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
X62744 mRNA. Translation: CAA44606.1 .
AL935042 Genomic DNA. No translation available.
Z24753 Genomic DNA. No translation available.
U04878 Genomic DNA. Translation: AAA56994.1 .
U04877 Genomic DNA. Translation: AAA56993.1 .
CCDSi CCDS4761.1.
PIRi I38490.
S17886.
UniGenei Hs.728759.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
Entry Method Resolution (Å) Chain Positions PDBsum
1HDM X-ray 2.50 A 27-230 [» ]
2BC4 X-ray 2.27 A/C 27-229 [» ]
4FQX X-ray 2.60 C 27-225 [» ]
4GBX X-ray 3.00 C 27-225 [» ]
ProteinModelPortali P28067.
SMRi P28067. Positions 38-230.
ModBasei Search...
MobiDBi Search...

Protein-protein interaction databases

DIPi DIP-6184N.
IntActi P28067. 7 interactions.
MINTi MINT-1539780.
STRINGi 9606.ENSP00000408311.

PTM databases

PhosphoSitei P28067.

Polymorphism databases

DMDMi 133158.

Proteomic databases

PaxDbi P28067.
PRIDEi P28067.

Protocols and materials databases

Structural Biology Knowledgebase Search...

Genome annotation databases

Ensembli ENST00000374843 ; ENSP00000363976 ; ENSG00000204257 .
ENST00000383230 ; ENSP00000372717 ; ENSG00000243215 .
ENST00000434337 ; ENSP00000407198 ; ENSG00000242361 .
ENST00000441375 ; ENSP00000410591 ; ENSG00000239463 .
ENST00000450601 ; ENSP00000392842 ; ENSG00000242685 .
ENST00000452615 ; ENSP00000395349 ; ENSG00000243189 .
ENST00000453490 ; ENSP00000404018 ; ENSG00000243719 .

Organism-specific databases

GeneCardsi GC06M032933.
GC06Mi32899.
GC06Mj32838.
GC06Ml33070.
GC06Mm32949.
GC06Mn32845.
GC06Mo33006.
H-InvDB HIX0207683.
HGNCi HGNC:4934. HLA-DMA.
HPAi HPA012750.
MIMi 142855. gene.
neXtProti NX_P28067.
GenAtlasi Search...

Phylogenomic databases

eggNOGi NOG43075.
HOGENOMi HOG000126882.
HOVERGENi HBG001688.
InParanoidi P28067.
PhylomeDBi P28067.
TreeFami TF333797.

Enzyme and pathway databases

Reactomei REACT_121399. MHC class II antigen presentation.

Miscellaneous databases

ChiTaRSi HLA-DMA. human.
EvolutionaryTracei P28067.
PROi P28067.
SOURCEi Search...

Gene expression databases

Bgeei P28067.
CleanExi HS_HLA-DMA.
ExpressionAtlasi P28067. baseline and differential.
Genevestigatori P28067.

Family and domain databases

Gene3Di 2.60.40.10. 1 hit.
3.10.320.10. 1 hit.
InterProi IPR007110. 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.
IPR001003. MHC_II_a_N.
[Graphical view ]
Pfami PF07654. C1-set. 1 hit.
PF00993. MHC_II_alpha. 1 hit.
[Graphical view ]
SMARTi SM00407. IGc1. 1 hit.
SM00920. MHC_II_alpha. 1 hit.
[Graphical view ]
SUPFAMi SSF54452. SSF54452. 1 hit.
PROSITEi PS50835. IG_LIKE. 1 hit.
PS00290. IG_MHC. 1 hit.
[Graphical view ]
ProtoNeti Search...

Publicationsi

« Hide 'large scale' publications
  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 DMA*01:01).
  2. "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.
    , 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].
  3. "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 31-218 (ALLELE DMA*01:02).
  4. "Sequence analysis of two novel HLA-DMA alleles."
    Carrington M., Harding A.
    Immunogenetics 40:165-165(1994) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA] OF 125-217 (ALLELES DMA*01:03 AND DMA*01:04).
  5. "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.
  6. "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 27-230 IN COMPLEX WITH DMB, FUNCTION, SUBUNIT, DISULFIDE BONDS.
  7. Cited for: X-RAY CRYSTALLOGRAPHY (2.27 ANGSTROMS) OF 27-229 IN COMPLEX WITH DMB, FUNCTION, SUBUNIT, DISULFIDE BONDS.

Entry informationi

Entry nameiDMA_HUMAN
AccessioniPrimary (citable) accession number: P28067
Secondary accession number(s): Q29639, Q29640
Entry historyi
Integrated into UniProtKB/Swiss-Prot: August 1, 1992
Last sequence update: August 1, 1992
Last modified: November 26, 2014
This is version 144 of the entry and version 1 of the sequence. [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

3D-structure, Complete proteome, Reference proteome

Documents

  1. Human chromosome 6
    Human chromosome 6: 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. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
  6. SIMILARITY comments
    Index of protein domains and families

External Data

Dasty 3