P05090 (APOD_HUMAN) Reviewed, UniProtKB/Swiss-Prot

Names and origin

Protein names

Recommended name:
Apolipoprotein D
Short name=Apo-D
Short name=ApoD

Gene names

Name:

APOD

Organism

Homo sapiens (Human)

Taxonomic identifier

9606 [NCBI]

Taxonomic lineage

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

Protein attributes

Sequence length	189 AA.
Sequence status	Complete.
Sequence processing	The displayed sequence is further processed into a mature form.
Protein existence	Evidence 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.
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 process	Transport
Cellular component	Secreted
Coding sequence diversity	Polymorphism
Domain	Signal
Ligand	Lipid-binding
PTM	Disulfide bond Glycoprotein Pyrrolidone carboxylic acid
Technical term	3D-structure Complete proteome Direct protein sequencing Reference proteome
Gene Ontology (GO)
Biological process	lipid metabolic process Traceable author statement. Source: ProtInc
Cellular component	extracellular space Inferred from direct assay. Source: BHF-UCL
Molecular function	lipid binding Inferred from electronic annotation. Source: UniProtKB-KW lipid transporter activity Traceable author statement. Source: ProtInc protein binding Inferred from physical interaction Ref.9. Source: UniProtKB
Complete GO annotation...

Sequence annotation (Features)

Feature key

Position(s)

Length

Description

Graphical view

Feature identifier

Molecule processing

Signal peptide

1 – 20

20

Ref.9

Chain

21 – 189

169

Apolipoprotein D

PRO_0000017872

Amino acid modifications

Modified residue

21

1

Pyrrolidone carboxylic acid Ref.1

Glycosylation

65

1

N-linked (GlcNAc...) Ref.9 Ref.14 Ref.17

Glycosylation

98

1

N-linked (GlcNAc...) (complex) Ref.9 Ref.12 Ref.13 Ref.14 Ref.15 Ref.17

Disulfide bond

28 ↔ 134

Ref.9

Disulfide bond

61 ↔ 185

Ref.9

Disulfide bond

136

Interchain (with C-29 in APOA2) Ref.9

Natural variations

Natural variant

15

1

F → S. Ref.18
Corresponds to variant rs5952 [ dbSNP | Ensembl ].

VAR_011931

Natural variant

115

1

S → L. Ref.18
Corresponds to variant rs5954 [ dbSNP | Ensembl ].

VAR_011932

Natural variant

178

1

T → K. Ref.18
Corresponds to variant rs5955 [ dbSNP | Ensembl ].

VAR_011933

Secondary structure

1

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189

Helix Strand Turn

Details...

Beta strand

23 – 27

5

Helix

39 – 42

4

Beta strand

44 – 51

8

Helix

55 – 57

3

Beta strand

59 – 67

9

Beta strand

75 – 81

7

Beta strand

87 – 101

15

Beta strand

103 – 107

5

Beta strand

115 – 123

9

Beta strand

125 – 137

13

Turn

138 – 140

3

Beta strand

141 – 154

14

Helix

157 – 167

11

Beta strand

168 – 171

4

Helix

174 – 176

3

Sequences

	Sequence		Length	Mass (Da)
	P05090 [UniParc]. Last modified August 13, 1987. Version 1. Checksum: 0EAA6DE03D5E71A8	FASTA	189	21,276
	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

References

	« Hide 'large scale' referencesShow '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: 3453108] [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: 2439269] [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. , 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: 14702039] [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. , 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: 15489334] [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: 7918467] [Abstract] Cited for: PROTEIN SEQUENCE OF 21-189, DISULFIDE BONDS, 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: 8549691] [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: 2244881] [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: 14760718] [Abstract] Cited for: GLYCOSYLATION [LARGE SCALE ANALYSIS] AT ASN-98, MASS SPECTROMETRY. 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: 16335952] [Abstract] Cited for: GLYCOSYLATION [LARGE SCALE ANALYSIS] AT ASN-98, MASS SPECTROMETRY. 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: 19159218] [Abstract] Cited for: GLYCOSYLATION [LARGE SCALE ANALYSIS] AT ASN-65 AND ASN-98, MASS SPECTROMETRY. Tissue: Liver.
[15]	"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: 19838169] [Abstract] Cited for: GLYCOSYLATION [LARGE SCALE ANALYSIS] AT ASN-98, STRUCTURE OF CARBOHYDRATES, MASS SPECTROMETRY. Tissue: Cerebrospinal fluid.
[16]	"Is apolipoprotein D a mammalian bilin-binding protein?" Peitsch M.C., Boguski M.S. New Biol. 2:197-206(1990) [PubMed: 2083249] [Abstract] Cited for: 3D-STRUCTURE MODELING, BILIN-BINDING.
[17]	"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: 7613477] [Abstract] Cited for: GLYCOSYLATION AT ASN-65 AND ASN-98.
[18]	"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: 10391209] [Abstract] Cited for: VARIANTS SER-15; LEU-115 AND LYS-178.
[19]	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.

IPI

IPI00006662.

PIR

LPHUD. A26958.

RefSeq

NP_001638.1. NM_001647.3.

UniGene

Hs.522555.

3D structure databases

PDBe
RCSB PDB
PDBj

Entry	Method	Resolution (Å)	Chain	Positions	PDBsum
2APD	model	-	A	21-189	[»]
2HZQ	X-ray	1.80	A	23-189	[»]
2HZR	X-ray	1.80	A	23-189	[»]

ProteinModelPortal

P05090.

SMR

P05090. Positions 23-188.

ModBase

Search...

Protein-protein interaction databases

IntAct

P05090. 2 interactions.

MINT

MINT-1396020.

STRING

P05090.

Polymorphism databases

DMDM

114034.

2D gel databases

SWISS-2DPAGE

P05090.

Proteomic databases

PeptideAtlas

P05090.

PRIDE

P05090.

Protocols and materials databases

StructuralBiologyKnowledgebase

Search...

Genome annotation databases

Ensembl

ENST00000343267; ENSP00000345179; ENSG00000189058.

GeneID

347.

KEGG

hsa:347.

UCSC

uc003fur.1. human.

Organism-specific databases

CTD

347.

GeneCards

GC03M195295.

H-InvDB

HIX0003987.

HGNC

HGNC:612. APOD.

MIM

107740. gene.

neXtProt

NX_P05090.

PharmGKB

PA24900.

GenAtlas

Search...

Phylogenomic databases

eggNOG

prNOG04250.

GeneTree

ENSGT00510000046981.

HOVERGEN

HBG018734.

InParanoid

P05090.

OrthoDB

EOG4G7C0M.

PhylomeDB

P05090.

Gene expression databases

ArrayExpress

P05090.

Bgee

P05090.

CleanEx

HS_APOD.

Genevestigator

P05090.

GermOnline

ENSG00000189058. Homo sapiens.

Family and domain databases

InterPro

IPR002969. ApolipopD.
IPR012674. Calycin.
IPR011038. Calycin-like.
IPR002345. Lipocalin.
IPR022271. Lipocalin_ApoD.
IPR022272. Lipocalin_CS.
IPR000566. Lipocln_cytosolic_FA-bd_dom.
[Graphical view]

Gene3D

G3DSA:2.40.128.20. Calycin. 1 hit.

Pfam

PF00061. Lipocalin. 1 hit.
[Graphical view]

PIRSF

PIRSF036893. Lipocalin_ApoD. 1 hit.

PRINTS

PR01219. APOLIPOPROTD.
PR00179. LIPOCALIN.

SUPFAM

SSF50814. Calycin. 1 hit.

PROSITE

PS00213. LIPOCALIN. 1 hit.
[Graphical view]

ProtoNet

Search...

Other

NextBio

1431.

SOURCE

Search...

Entry information

Entry name

APOD_HUMAN

Accession

Primary (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:	January 25, 2012
This is version 140 of the entry and version 1 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation program

Chordata Protein Annotation Program

Disclaimer

Any 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.