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P05090 (APOD_HUMAN) Reviewed, UniProtKB/Swiss-Prot

Last modified July 9, 2014. Version 165. 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:
Apolipoprotein D

Short name=Apo-D
Short name=ApoD
Gene names
Name:APOD
OrganismHomo sapiens (Human) [Reference proteome]
Taxonomic identifier9606 [NCBI]
Taxonomic lineageEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresPrimatesHaplorrhiniCatarrhiniHominidaeHomo

Protein attributes

Sequence length189 AA.
Sequence statusComplete.
Sequence processingThe displayed sequence is further processed into a mature form.
Protein existenceEvidence at protein level

General annotation (Comments)

Function

APOD occurs in the macromolecular complex with lecithin-cholesterol acyltransferase. It is probably involved in the transport and binding of bilin. Appears to be able to transport a variety of ligands in a number of different contexts.

Subunit structure

Homodimer. In plasma, also exists as a disulfide-linked heterodimer with APOA2. Ref.9

Subcellular location

Secreted.

Tissue specificity

Expressed in liver, intestine, pancreas, kidney, placenta, adrenal, spleen, fetal brain tissue and tears.

Post-translational modification

N-glycosylatd. N-glycan heterogeneity at Asn-65: Hex5HexNAc4 (major) and Hex6HexNAc5 (minor); at Asn-98: Hex5HexNAc4 (minor), dHex1Hex5HexNAc4 (major), dHex1Hex6HexNAc5 (minor) and dHex1Hex7HexNAc6 (minor).

Miscellaneous

APOD is primarily localized in HDL (60-65%), with most of the remainder in VHDL and only trace amounts in VLDL and LDL.

Sequence similarities

Belongs to the calycin superfamily. Lipocalin family.

Ontologies

Keywords
   Biological processTransport
   Cellular componentSecreted
   Coding sequence diversityPolymorphism
   DomainSignal
   LigandLipid-binding
   PTMDisulfide bond
Glycoprotein
Pyrrolidone carboxylic acid
   Technical term3D-structure
Complete proteome
Direct protein sequencing
Reference proteome
Gene Ontology (GO)
   Biological_processaging

Non-traceable author statement PubMed 20023409. Source: UniProtKB

angiogenesis

Non-traceable author statement PubMed 21705670. Source: UniProtKB

brain development

Inferred from sequence or structural similarity. Source: UniProtKB

glucose metabolic process

Inferred from direct assay PubMed 19176353. Source: UniProtKB

lipid metabolic process

Inferred from direct assay PubMed 19176353. Source: UniProtKB

lipid transport

Non-traceable author statement Ref.1. Source: GOC

negative regulation of T cell migration

Inferred from direct assay PubMed 18842892. Source: UniProtKB

negative regulation of cytokine production involved in inflammatory response

Inferred from direct assay PubMed 18842892. Source: UniProtKB

negative regulation of focal adhesion assembly

Inferred from mutant phenotype PubMed 21705670. Source: UniProtKB

negative regulation of lipoprotein lipid oxidation

Inferred from direct assay PubMed 18419796. Source: UniProtKB

negative regulation of monocyte chemotactic protein-1 production

Inferred from direct assay PubMed 18842892. Source: UniProtKB

negative regulation of platelet-derived growth factor receptor signaling pathway

Inferred from direct assay PubMed 14551159. Source: UniProtKB

negative regulation of protein import into nucleus

Inferred from direct assay PubMed 14551159. Source: UniProtKB

negative regulation of smooth muscle cell proliferation

Inferred from direct assay PubMed 14551159. Source: UniProtKB

negative regulation of smooth muscle cell-matrix adhesion

Inferred from mutant phenotype PubMed 21705670. Source: UniProtKB

peripheral nervous system axon regeneration

Inferred from sequence or structural similarity. Source: UniProtKB

response to axon injury

Inferred from sequence or structural similarity. Source: UniProtKB

response to drug

Inferred from sequence or structural similarity. Source: UniProtKB

response to reactive oxygen species

Inferred from direct assay PubMed 18419796. Source: UniProtKB

tissue regeneration

Inferred from sequence or structural similarity. Source: UniProtKB

   Cellular_componentcytosolic ribosome

Inferred from sequence or structural similarity. Source: UniProtKB

dendrite

Inferred from sequence or structural similarity. Source: UniProtKB

endoplasmic reticulum

Inferred from sequence or structural similarity. Source: UniProtKB

extracellular region

Non-traceable author statement PubMed 14718574. Source: UniProtKB

extracellular space

Inferred from direct assay PubMed 21705670. Source: UniProtKB

extracellular vesicular exosome

Inferred from direct assay PubMed 19056867PubMed 23376485. Source: UniProt

neuronal cell body

Inferred from sequence or structural similarity. Source: UniProtKB

perinuclear region of cytoplasm

Inferred from direct assay PubMed 14551159. Source: UniProtKB

   Molecular_functioncholesterol binding

Inferred from direct assay PubMed 9278274. Source: UniProtKB

lipid transporter activity

Non-traceable author statement Ref.1. Source: UniProtKB

protein binding

Inferred from physical interaction Ref.9. Source: UniProtKB

Complete GO annotation...

Sequence annotation (Features)

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifier

Molecule processing

Signal peptide1 – 2020 Ref.9
Chain21 – 189169Apolipoprotein D
PRO_0000017872

Amino acid modifications

Modified residue211Pyrrolidone carboxylic acid Ref.1
Glycosylation651N-linked (GlcNAc...) (complex) Ref.9 Ref.14 Ref.17 Ref.19
Glycosylation981N-linked (GlcNAc...) (complex) Ref.9 Ref.12 Ref.13 Ref.14 Ref.15 Ref.16 Ref.17 Ref.19
Disulfide bond28 ↔ 134 Ref.9
Disulfide bond61 ↔ 185 Ref.9
Disulfide bond136Interchain (with C-29 in APOA2) Ref.9

Natural variations

Natural variant151F → S. Ref.20
Corresponds to variant rs5952 [ dbSNP | Ensembl ].
VAR_011931
Natural variant1151S → L. Ref.20
Corresponds to variant rs5954 [ dbSNP | Ensembl ].
VAR_011932
Natural variant1781T → K. Ref.20
Corresponds to variant rs5955 [ dbSNP | Ensembl ].
VAR_011933

Secondary structure

......................... 189
Helix Strand Turn

Details...

Sequences

Sequence LengthMass (Da)Tools
P05090 [UniParc].

Last modified August 13, 1987. Version 1.
Checksum: 0EAA6DE03D5E71A8

FASTA18921,276
        10         20         30         40         50         60 
MVMLLLLLSA LAGLFGAAEG QAFHLGKCPN PPVQENFDVN KYLGRWYEIE KIPTTFENGR 

        70         80         90        100        110        120 
CIQANYSLME NGKIKVLNQE LRADGTVNQI EGEATPVNLT EPAKLEVKFS WFMPSAPYWI 

       130        140        150        160        170        180 
LATDYENYAL VYSCTCIIQL FHVDFAWILA RNPNLPPETV DSLKNILTSN NIDVKKMTVT 


DQVNCPKLS 

« Hide

References

« Hide 'large scale' references
[1]"Cloning and expression of human apolipoprotein D cDNA."
Drayna D.T., Fielding C., McLean J.W., Baer B., Castro G., Chen E., Comstock L., Henzel W., Kohr W., Rhee L., Wion K.L., Lawn R.M.
J. Biol. Chem. 261:16535-16539(1986) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [MRNA].
[2]"Human apolipoprotein D gene: gene sequence, chromosome localization, and homology to the alpha 2u-globulin superfamily."
Drayna D.T., McLean J.W., Wion K.L., Trent J.M., Drabkin H.A., Lawn R.M.
DNA 6:199-204(1987) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
[3]"Cloning of human full open reading frames in Gateway(TM) system entry vector (pDONR201)."
Ebert L., Schick M., Neubert P., Schatten R., Henze S., Korn B.
Submitted (JUN-2004) to the EMBL/GenBank/DDBJ databases
Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
[4]"Cloning of human full open reading frames in Gateway(TM) system entry vector (pDONR201)."
Halleck A., Ebert L., Mkoundinya M., Schick M., Eisenstein S., Neubert P., Kstrang K., Schatten R., Shen B., Henze S., Mar W., Korn B., Zuo D., Hu Y., LaBaer J.
Submitted (JUN-2004) to the EMBL/GenBank/DDBJ databases
Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
[5]"Cloning of human full-length CDSs in BD Creator(TM) system donor vector."
Kalnine N., Chen X., Rolfs A., Halleck A., Hines L., Eisenstein S., Koundinya M., Raphael J., Moreira D., Kelley T., LaBaer J., Lin Y., Phelan M., Farmer A.
Submitted (OCT-2004) to the EMBL/GenBank/DDBJ databases
Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
[6]"Complete sequencing and characterization of 21,243 full-length human cDNAs."
Ota T., Suzuki Y., Nishikawa T., Otsuki T., Sugiyama T., Irie R., Wakamatsu A., Hayashi K., Sato H., Nagai K., Kimura K., Makita H., Sekine M., Obayashi M., Nishi T., Shibahara T., Tanaka T., Ishii S. expand/collapse author list , Yamamoto J., Saito K., Kawai Y., Isono Y., Nakamura Y., Nagahari K., Murakami K., Yasuda T., Iwayanagi T., Wagatsuma M., Shiratori A., Sudo H., Hosoiri T., Kaku Y., Kodaira H., Kondo H., Sugawara M., Takahashi M., Kanda K., Yokoi T., Furuya T., Kikkawa E., Omura Y., Abe K., Kamihara K., Katsuta N., Sato K., Tanikawa M., Yamazaki M., Ninomiya K., Ishibashi T., Yamashita H., Murakawa K., Fujimori K., Tanai H., Kimata M., Watanabe M., Hiraoka S., Chiba Y., Ishida S., Ono Y., Takiguchi S., Watanabe S., Yosida M., Hotuta T., Kusano J., Kanehori K., Takahashi-Fujii A., Hara H., Tanase T.-O., Nomura Y., Togiya S., Komai F., Hara R., Takeuchi K., Arita M., Imose N., Musashino K., Yuuki H., Oshima A., Sasaki N., Aotsuka S., Yoshikawa Y., Matsunawa H., Ichihara T., Shiohata N., Sano S., Moriya S., Momiyama H., Satoh N., Takami S., Terashima Y., Suzuki O., Nakagawa S., Senoh A., Mizoguchi H., Goto Y., Shimizu F., Wakebe H., Hishigaki H., Watanabe T., Sugiyama A., Takemoto M., Kawakami B., Yamazaki M., Watanabe K., Kumagai A., Itakura S., Fukuzumi Y., Fujimori Y., Komiyama M., Tashiro H., Tanigami A., Fujiwara T., Ono T., Yamada K., Fujii Y., Ozaki K., Hirao M., Ohmori Y., Kawabata A., Hikiji T., Kobatake N., Inagaki H., Ikema Y., Okamoto S., Okitani R., Kawakami T., Noguchi S., Itoh T., Shigeta K., Senba T., Matsumura K., Nakajima Y., Mizuno T., Morinaga M., Sasaki M., Togashi T., Oyama M., Hata H., Watanabe M., Komatsu T., Mizushima-Sugano J., Satoh T., Shirai Y., Takahashi Y., Nakagawa K., Okumura K., Nagase T., Nomura N., Kikuchi H., Masuho Y., Yamashita R., Nakai K., Yada T., Nakamura Y., Ohara O., Isogai T., Sugano S.
Nat. Genet. 36:40-45(2004) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
Tissue: Cerebellum.
[7]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 (SEP-2005) to the EMBL/GenBank/DDBJ databases
Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
[8]"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].
Tissue: Skin.
[9]"Structure of human apolipoprotein D: locations of the intermolecular and intramolecular disulfide links."
Yang C.-Y., Gu Z.-W., Blanco-Vaca F., Gaskell S.J., Yang M., Massey J.B., Gotto A.M. Jr., Pownall H.J.
Biochemistry 33:12451-12455(1994) [PubMed] [Europe PMC] [Abstract]
Cited for: PROTEIN SEQUENCE OF 21-189, DISULFIDE BONDS, PYROGLUTAMATE FORMATION AT GLN-21, GLYCOSYLATION AT ASN-65 AND ASN-98.
Tissue: Plasma.
[10]"The human lacrimal gland synthesizes apolipoprotein D mRNA in addition to tear prealbumin mRNA, both species encoding members of the lipocalin superfamily."
Holzfeind P., Merschak P., Dieplinger H., Redl B.
Exp. Eye Res. 61:495-500(1995) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [MRNA] OF 92-189.
Tissue: Lacrimal gland.
[11]"Apolipoprotein D is the major protein component in cyst fluid from women with human breast gross cystic disease."
Balbin M., Freije J.M.P., Fueyo A., Sanchez L.M., Lopez-Otin C.
Biochem. J. 271:803-807(1990) [PubMed] [Europe PMC] [Abstract]
Cited for: PROTEIN SEQUENCE OF 128-187.
[12]"Screening for N-glycosylated proteins by liquid chromatography mass spectrometry."
Bunkenborg J., Pilch B.J., Podtelejnikov A.V., Wisniewski J.R.
Proteomics 4:454-465(2004) [PubMed] [Europe PMC] [Abstract]
Cited for: GLYCOSYLATION [LARGE SCALE ANALYSIS] AT ASN-98.
Tissue: Plasma.
[13]"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-98.
Tissue: Plasma.
[14]"Glycoproteomics analysis of human liver tissue by combination of multiple enzyme digestion and hydrazide chemistry."
Chen R., Jiang X., Sun D., Han G., Wang F., Ye M., Wang L., Zou H.
J. Proteome Res. 8:651-661(2009) [PubMed] [Europe PMC] [Abstract]
Cited for: GLYCOSYLATION [LARGE SCALE ANALYSIS] AT ASN-65 AND ASN-98.
Tissue: Liver.
[15]"A strategy for precise and large scale identification of core fucosylated glycoproteins."
Jia W., Lu Z., Fu Y., Wang H.P., Wang L.H., Chi H., Yuan Z.F., Zheng Z.B., Song L.N., Han H.H., Liang Y.M., Wang J.L., Cai Y., Zhang Y.K., Deng Y.L., Ying W.T., He S.M., Qian X.H.
Mol. Cell. Proteomics 8:913-923(2009) [PubMed] [Europe PMC] [Abstract]
Cited for: GLYCOSYLATION AT ASN-98.
[16]"Enrichment of glycopeptides for glycan structure and attachment site identification."
Nilsson J., Rueetschi U., Halim A., Hesse C., Carlsohn E., Brinkmalm G., Larson G.
Nat. Methods 6:809-811(2009) [PubMed] [Europe PMC] [Abstract]
Cited for: GLYCOSYLATION [LARGE SCALE ANALYSIS] AT ASN-98, STRUCTURE OF CARBOHYDRATES.
Tissue: Cerebrospinal fluid.
[17]"Human urinary glycoproteomics; attachment site specific analysis of N-and O-linked glycosylations by CID and ECD."
Halim A., Nilsson J., Ruetschi U., Hesse C., Larson G.
Mol. Cell. Proteomics 0:0-0(2011) [PubMed] [Europe PMC] [Abstract]
Cited for: GLYCOSYLATION AT ASN-65 AND ASN-98, STRUCTURE OF CARBOHYDRATES, IDENTIFICATION BY MASS SPECTROMETRY.
[18]"Is apolipoprotein D a mammalian bilin-binding protein?"
Peitsch M.C., Boguski M.S.
New Biol. 2:197-206(1990) [PubMed] [Europe PMC] [Abstract]
Cited for: 3D-STRUCTURE MODELING, BILIN-BINDING.
[19]"Site-specific detection and structural characterization of the glycosylation of human plasma proteins lecithin:cholesterol acyltransferase and apolipoprotein D using HPLC/electrospray mass spectrometry and sequential glycosidase digestion."
Schindler P.A., Settineri C.A., Collet X., Fielding C.J., Burlingame A.L.
Protein Sci. 4:791-803(1995) [PubMed] [Europe PMC] [Abstract]
Cited for: GLYCOSYLATION AT ASN-65 AND ASN-98.
[20]"Characterization of single-nucleotide polymorphisms in coding regions of human genes."
Cargill M., Altshuler D., Ireland J., Sklar P., Ardlie K., Patil N., Shaw N., Lane C.R., Lim E.P., Kalyanaraman N., Nemesh J., Ziaugra L., Friedland L., Rolfe A., Warrington J., Lipshutz R., Daley G.Q., Lander E.S.
Nat. Genet. 22:231-238(1999) [PubMed] [Europe PMC] [Abstract]
Cited for: VARIANTS SER-15; LEU-115 AND LYS-178.
[21]Erratum
Cargill M., Altshuler D., Ireland J., Sklar P., Ardlie K., Patil N., Shaw N., Lane C.R., Lim E.P., Kalyanaraman N., Nemesh J., Ziaugra L., Friedland L., Rolfe A., Warrington J., Lipshutz R., Daley G.Q., Lander E.S.
Nat. Genet. 23:373-373(1999)
+Additional computationally mapped references.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ
J02611 mRNA. Translation: AAB59517.1.
M16696 Genomic DNA. Translation: AAA51764.1.
BT019860 mRNA. Translation: AAV38663.1.
BT019861 mRNA. Translation: AAV38664.1.
CR456838 mRNA. Translation: CAG33119.1.
CR541773 mRNA. Translation: CAG46572.1.
AK312090 mRNA. Translation: BAG35026.1.
CH471052 Genomic DNA. Translation: EAW78023.1.
CH471052 Genomic DNA. Translation: EAW78024.1.
BC007402 mRNA. Translation: AAH07402.1.
S80440 mRNA. Translation: AAB35919.1.
CCDSCCDS33925.1.
PIRLPHUD. A26958.
RefSeqNP_001638.1. NM_001647.3.
UniGeneHs.522555.

3D structure databases

PDBe
RCSB-PDB
PDBj
EntryMethodResolution (Å)ChainPositionsPDBsum
2APDmodel-A21-189[»]
2HZQX-ray1.80A23-189[»]
2HZRX-ray1.80A23-189[»]
ProteinModelPortalP05090.
SMRP05090. Positions 23-188.
ModBaseSearch...
MobiDBSearch...

Protein-protein interaction databases

BioGrid106844. 11 interactions.
IntActP05090. 5 interactions.
MINTMINT-1396020.
STRING9606.ENSP00000345179.

PTM databases

PhosphoSiteP05090.

Polymorphism databases

DMDM114034.

2D gel databases

SWISS-2DPAGEP05090.

Proteomic databases

MaxQBP05090.
PaxDbP05090.
PeptideAtlasP05090.
PRIDEP05090.

Protocols and materials databases

DNASU347.
StructuralBiologyKnowledgebaseSearch...

Genome annotation databases

EnsemblENST00000343267; ENSP00000345179; ENSG00000189058.
GeneID347.
KEGGhsa:347.
UCSCuc003fur.2. human.

Organism-specific databases

CTD347.
GeneCardsGC03M195295.
HGNCHGNC:612. APOD.
MIM107740. gene.
neXtProtNX_P05090.
PharmGKBPA24900.
GenAtlasSearch...

Phylogenomic databases

eggNOGCOG3040.
HOGENOMHOG000061525.
HOVERGENHBG018734.
InParanoidP05090.
KOK03098.
PhylomeDBP05090.
TreeFamTF324836.

Gene expression databases

ArrayExpressP05090.
BgeeP05090.
CleanExHS_APOD.
GenevestigatorP05090.

Family and domain databases

Gene3D2.40.128.20. 1 hit.
InterProIPR026222. ApoD_vertbrte.
IPR002969. ApolipopD.
IPR012674. Calycin.
IPR011038. Calycin-like.
IPR002345. Lipocalin.
IPR022271. Lipocalin_ApoD.
IPR022272. Lipocalin_CS.
IPR000566. Lipocln_cytosolic_FA-bd_dom.
[Graphical view]
PfamPF00061. Lipocalin. 1 hit.
[Graphical view]
PIRSFPIRSF036893. Lipocalin_ApoD. 1 hit.
PRINTSPR02058. APODVERTBRTE.
PR01219. APOLIPOPROTD.
PR00179. LIPOCALIN.
SUPFAMSSF50814. SSF50814. 1 hit.
PROSITEPS00213. LIPOCALIN. 1 hit.
[Graphical view]
ProtoNetSearch...

Other

ChiTaRSAPOD. human.
EvolutionaryTraceP05090.
GeneWikiApolipoprotein_D.
GenomeRNAi347.
NextBio1431.
PROP05090.
SOURCESearch...

Entry information

Entry nameAPOD_HUMAN
AccessionPrimary (citable) accession number: P05090
Secondary accession number(s): B2R579, D3DNW6, Q6IBG6
Entry history
Integrated into UniProtKB/Swiss-Prot: August 13, 1987
Last sequence update: August 13, 1987
Last modified: July 9, 2014
This is version 165 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 3

Human chromosome 3: entries, gene names and cross-references to MIM