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Protein

ATP-binding cassette sub-family D member 4

Gene

ABCD4

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

Functioni

May be involved in intracellular processing of vitamin B12 (cobalamin). Could play a role in the lysosomal release of vitamin B12 into the cytoplasm.1 Publication

Regions

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Nucleotide bindingi421 – 4288ATPPROSITE-ProRule annotation

GO - Molecular functioni

  • ATPase activity, coupled to transmembrane movement of substances Source: UniProtKB
  • ATP binding Source: UniProtKB

GO - Biological processi

  • cobalamin metabolic process Source: UniProtKB
  • small molecule metabolic process Source: Reactome
  • transmembrane transport Source: UniProtKB
  • vitamin metabolic process Source: Reactome
  • water-soluble vitamin metabolic process Source: Reactome
Complete GO annotation...

Keywords - Biological processi

Transport

Keywords - Ligandi

ATP-binding, Nucleotide-binding

Enzyme and pathway databases

ReactomeiREACT_163862. Cobalamin (Cbl, vitamin B12) transport and metabolism.

Protein family/group databases

TCDBi3.A.1.203.9. the atp-binding cassette (abc) superfamily.

Names & Taxonomyi

Protein namesi
Recommended name:
ATP-binding cassette sub-family D member 4
Alternative name(s):
PMP70-related protein
Short name:
P70R
Peroxisomal membrane protein 1-like
Short name:
PXMP1-L
Peroxisomal membrane protein 69
Short name:
PMP69
Gene namesi
Name:ABCD4
Synonyms:PXMP1L
OrganismiHomo sapiens (Human)
Taxonomic identifieri9606 [NCBI]
Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresPrimatesHaplorrhiniCatarrhiniHominidaeHomo
ProteomesiUP000005640 Componenti: Chromosome 14

Organism-specific databases

HGNCiHGNC:68. ABCD4.

Subcellular locationi

Topology

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Transmembranei43 – 6321HelicalPROSITE-ProRule annotationAdd
BLAST
Transmembranei76 – 9621HelicalPROSITE-ProRule annotationAdd
BLAST
Transmembranei190 – 21021HelicalPROSITE-ProRule annotationAdd
BLAST
Transmembranei279 – 29921HelicalPROSITE-ProRule annotationAdd
BLAST
Transmembranei314 – 33421HelicalPROSITE-ProRule annotationAdd
BLAST

GO - Cellular componenti

  • ATP-binding cassette (ABC) transporter complex Source: UniProtKB
  • endoplasmic reticulum membrane Source: Ensembl
  • integral component of membrane Source: UniProtKB
  • lysosomal membrane Source: Reactome
  • peroxisomal membrane Source: UniProtKB-SubCell
  • peroxisome Source: UniProtKB
Complete GO annotation...

Keywords - Cellular componenti

Membrane, Peroxisome

Pathology & Biotechi

Involvement in diseasei

Methylmalonic aciduria and homocystinuria type cblJ (MAHCJ)1 Publication

The disease is caused by mutations affecting the gene represented in this entry.

Disease descriptionA disorder of cobalamin metabolism characterized by decreased levels of the coenzymes adenosylcobalamin (AdoCbl) and methylcobalamin (MeCbl). Clinical features include feeding difficulties, poor growth, hypotonia, lethargy, anemia, and developmental delay.

See also OMIM:614857
Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Natural varianti319 – 3191Y → C in MAHCJ. 1 Publication
Corresponds to variant rs201777056 [ dbSNP | Ensembl ].
VAR_069097

Keywords - Diseasei

Disease mutation

Organism-specific databases

MIMi614857. phenotype.
Orphaneti369955. Methylmalonic acidemia with homocystinuria, type cblJ.
PharmGKBiPA24403.

Polymorphism and mutation databases

BioMutaiABCD4.

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 606606ATP-binding cassette sub-family D member 4PRO_0000093312Add
BLAST

Proteomic databases

MaxQBiO14678.
PaxDbiO14678.
PRIDEiO14678.

PTM databases

PhosphoSiteiO14678.

Expressioni

Tissue specificityi

Ubiquitous.

Gene expression databases

BgeeiO14678.
CleanExiHS_ABCD4.
ExpressionAtlasiO14678. baseline and differential.
GenevisibleiO14678. HS.

Organism-specific databases

HPAiHPA003396.

Interactioni

Subunit structurei

Homodimer or heterodimer.Curated

Protein-protein interaction databases

BioGridi111784. 9 interactions.
IntActiO14678. 4 interactions.
STRINGi9606.ENSP00000349396.

Structurei

3D structure databases

ProteinModelPortaliO14678.
SMRiO14678. Positions 274-595.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Domaini39 – 332294ABC transmembrane type-1PROSITE-ProRule annotationAdd
BLAST
Domaini389 – 603215ABC transporterPROSITE-ProRule annotationAdd
BLAST

Sequence similaritiesi

Contains 1 ABC transmembrane type-1 domain.PROSITE-ProRule annotation
Contains 1 ABC transporter domain.PROSITE-ProRule annotation

Keywords - Domaini

Transmembrane, Transmembrane helix

Phylogenomic databases

eggNOGiCOG4178.
GeneTreeiENSGT00390000003950.
HOGENOMiHOG000007546.
HOVERGENiHBG106060.
InParanoidiO14678.
KOiK05678.
OMAiVQMLADF.
OrthoDBiEOG72RMXS.
PhylomeDBiO14678.
TreeFamiTF105205.

Family and domain databases

Gene3Di3.40.50.300. 1 hit.
InterProiIPR003593. AAA+_ATPase.
IPR011527. ABC1_TM_dom.
IPR003439. ABC_transporter-like.
IPR017871. ABC_transporter_CS.
IPR027417. P-loop_NTPase.
[Graphical view]
PfamiPF06472. ABC_membrane_2. 1 hit.
PF00005. ABC_tran. 1 hit.
[Graphical view]
SMARTiSM00382. AAA. 1 hit.
[Graphical view]
SUPFAMiSSF52540. SSF52540. 1 hit.
SSF90123. SSF90123. 1 hit.
PROSITEiPS50929. ABC_TM1F. 1 hit.
PS00211. ABC_TRANSPORTER_1. 1 hit.
PS50893. ABC_TRANSPORTER_2. 1 hit.
[Graphical view]

Sequencei

Sequence statusi: Complete.

O14678-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MAVAGPAPGA GARPRLDLQF LQRFLQILKV LFPSWSSQNA LMFLTLLCLT
60 70 80 90 100
LLEQFVIYQV GLIPSQYYGV LGNKDLEGFK TLTFLAVMLI VLNSTLKSFD
110 120 130 140 150
QFTCNLLYVS WRKDLTEHLH RLYFRGRAYY TLNVLRDDID NPDQRISQDV
160 170 180 190 200
ERFCRQLSSM ASKLIISPFT LVYYTYQCFQ STGWLGPVSI FGYFILGTVV
210 220 230 240 250
NKTLMGPIVM KLVHQEKLEG DFRFKHMQIR VNAEPAAFYR AGHVEHMRTD
260 270 280 290 300
RRLQRLLQTQ RELMSKELWL YIGINTFDYL GSILSYVVIA IPIFSGVYGD
310 320 330 340 350
LSPAELSTLV SKNAFVCIYL ISCFTQLIDL STTLSDVAGY THRIGQLRET
360 370 380 390 400
LLDMSLKSQD CEILGESEWG LDTPPGWPAA EPADTAFLLE RVSISAPSSD
410 420 430 440 450
KPLIKDLSLK ISEGQSLLIT GNTGTGKTSL LRVLGGLWTS TRGSVQMLTD
460 470 480 490 500
FGPHGVLFLP QKPFFTDGTL REQVIYPLKE VYPDSGSADD ERILRFLELA
510 520 530 540 550
GLSNLVARTE GLDQQVDWNW YDVLSPGEMQ RLSFARLFYL QPKYAVLDEA
560 570 580 590 600
TSALTEEVES ELYRIGQQLG MTFISVGHRQ SLEKFHSLVL KLCGGGRWEL

MRIKVE
Length:606
Mass (Da):68,597
Last modified:January 1, 1998 - v1
Checksum:i2D88DEFED0EA0777
GO

Experimental Info

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Sequence conflicti594 – 5941G → V in BAF84021 (PubMed:14702039).Curated
Sequence conflicti606 – 6061E → D in CAG33385 (Ref. 6) Curated

Natural variant

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Natural varianti172 – 1721V → I.
Corresponds to variant rs34992370 [ dbSNP | Ensembl ].
VAR_048134
Natural varianti304 – 3041A → T.4 Publications
Corresponds to variant rs4148077 [ dbSNP | Ensembl ].
VAR_020778
Natural varianti319 – 3191Y → C in MAHCJ. 1 Publication
Corresponds to variant rs201777056 [ dbSNP | Ensembl ].
VAR_069097
Natural varianti350 – 3501T → R.
Corresponds to variant rs35073715 [ dbSNP | Ensembl ].
VAR_048135
Natural varianti368 – 3681E → K.4 Publications
Corresponds to variant rs3742801 [ dbSNP | Ensembl ].
VAR_020222

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
Y14318
, Y14319, Y14320, Y14321, Y14322, Y14323 Genomic DNA. Translation: CAA74699.1.
AF009746 mRNA. Translation: AAB83967.1.
BT007412 mRNA. Translation: AAP36080.1.
AK291332 mRNA. Translation: BAF84021.1.
CR457104 mRNA. Translation: CAG33385.1.
BC012815 mRNA. Translation: AAH12815.1.
CCDSiCCDS9828.1.
PIRiJC5604.
RefSeqiNP_005041.1. NM_005050.3.
UniGeneiHs.94395.

Genome annotation databases

EnsembliENST00000356924; ENSP00000349396; ENSG00000119688.
GeneIDi5826.
KEGGihsa:5826.
UCSCiuc001xpr.2. human.

Keywords - Coding sequence diversityi

Polymorphism

Cross-referencesi

Web resourcesi

ABCMdb

Database for mutations in ABC proteins

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
Y14318
, Y14319, Y14320, Y14321, Y14322, Y14323 Genomic DNA. Translation: CAA74699.1.
AF009746 mRNA. Translation: AAB83967.1.
BT007412 mRNA. Translation: AAP36080.1.
AK291332 mRNA. Translation: BAF84021.1.
CR457104 mRNA. Translation: CAG33385.1.
BC012815 mRNA. Translation: AAH12815.1.
CCDSiCCDS9828.1.
PIRiJC5604.
RefSeqiNP_005041.1. NM_005050.3.
UniGeneiHs.94395.

3D structure databases

ProteinModelPortaliO14678.
SMRiO14678. Positions 274-595.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi111784. 9 interactions.
IntActiO14678. 4 interactions.
STRINGi9606.ENSP00000349396.

Protein family/group databases

TCDBi3.A.1.203.9. the atp-binding cassette (abc) superfamily.

PTM databases

PhosphoSiteiO14678.

Polymorphism and mutation databases

BioMutaiABCD4.

Proteomic databases

MaxQBiO14678.
PaxDbiO14678.
PRIDEiO14678.

Protocols and materials databases

DNASUi5826.
Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsembliENST00000356924; ENSP00000349396; ENSG00000119688.
GeneIDi5826.
KEGGihsa:5826.
UCSCiuc001xpr.2. human.

Organism-specific databases

CTDi5826.
GeneCardsiGC14M074751.
GeneReviewsiABCD4.
HGNCiHGNC:68. ABCD4.
HPAiHPA003396.
MIMi603214. gene.
614857. phenotype.
neXtProtiNX_O14678.
Orphaneti369955. Methylmalonic acidemia with homocystinuria, type cblJ.
PharmGKBiPA24403.
GenAtlasiSearch...

Phylogenomic databases

eggNOGiCOG4178.
GeneTreeiENSGT00390000003950.
HOGENOMiHOG000007546.
HOVERGENiHBG106060.
InParanoidiO14678.
KOiK05678.
OMAiVQMLADF.
OrthoDBiEOG72RMXS.
PhylomeDBiO14678.
TreeFamiTF105205.

Enzyme and pathway databases

ReactomeiREACT_163862. Cobalamin (Cbl, vitamin B12) transport and metabolism.

Miscellaneous databases

ChiTaRSiABCD4. human.
GeneWikiiABCD4.
GenomeRNAii5826.
NextBioi22693.
PROiO14678.
SOURCEiSearch...

Gene expression databases

BgeeiO14678.
CleanExiHS_ABCD4.
ExpressionAtlasiO14678. baseline and differential.
GenevisibleiO14678. HS.

Family and domain databases

Gene3Di3.40.50.300. 1 hit.
InterProiIPR003593. AAA+_ATPase.
IPR011527. ABC1_TM_dom.
IPR003439. ABC_transporter-like.
IPR017871. ABC_transporter_CS.
IPR027417. P-loop_NTPase.
[Graphical view]
PfamiPF06472. ABC_membrane_2. 1 hit.
PF00005. ABC_tran. 1 hit.
[Graphical view]
SMARTiSM00382. AAA. 1 hit.
[Graphical view]
SUPFAMiSSF52540. SSF52540. 1 hit.
SSF90123. SSF90123. 1 hit.
PROSITEiPS50929. ABC_TM1F. 1 hit.
PS00211. ABC_TRANSPORTER_1. 1 hit.
PS50893. ABC_TRANSPORTER_2. 1 hit.
[Graphical view]
ProtoNetiSearch...

Publicationsi

« Hide 'large scale' publications
  1. "Primary structure of human PMP69, a putative peroxisomal ABC-transporter."
    Holzinger A., Kammerer S., Roscher A.A.
    Biochem. Biophys. Res. Commun. 237:152-157(1997) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [MRNA].
  2. "Genomic organization and chromosomal localization of the human peroxisomal membrane protein-1-like protein (PXMP1-L) gene encoding a peroxisomal ABC transporter."
    Holzinger A., Roscher A.A., Landgraf P., Lichtner P., Kammerer S.
    FEBS Lett. 426:238-242(1998) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA / MRNA].
  3. "Identification of a fourth half ABC transporter in the human peroxisomal membrane."
    Shani N., Jimenez-Sanchez G., Steel G., Dean M., Valle D.
    Hum. Mol. Genet. 6:1925-1931(1997) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [MRNA].
  4. "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 (MAY-2003) to the EMBL/GenBank/DDBJ databases
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA], VARIANTS THR-304 AND LYS-368.
  5. "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] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
    Tissue: Tongue.
  6. "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], VARIANTS THR-304 AND LYS-368.
  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], VARIANTS THR-304 AND LYS-368.
    Tissue: Muscle.
  8. Cited for: FUNCTION, VARIANT MAHCJ CYS-319.
  9. "Catalog of 605 single-nucleotide polymorphisms (SNPs) among 13 genes encoding human ATP-binding cassette transporters: ABCA4, ABCA7, ABCA8, ABCD1, ABCD3, ABCD4, ABCE1, ABCF1, ABCG1, ABCG2, ABCG4, ABCG5, and ABCG8."
    Iida A., Saito S., Sekine A., Mishima C., Kitamura Y., Kondo K., Harigae S., Osawa S., Nakamura Y.
    J. Hum. Genet. 47:285-310(2002) [PubMed] [Europe PMC] [Abstract]
    Cited for: VARIANTS THR-304 AND LYS-368.

Entry informationi

Entry nameiABCD4_HUMAN
AccessioniPrimary (citable) accession number: O14678
Secondary accession number(s): A8K5L7, Q6IAQ0, Q96E75
Entry historyi
Integrated into UniProtKB/Swiss-Prot: May 30, 2000
Last sequence update: January 1, 1998
Last modified: July 22, 2015
This is version 139 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

Complete proteome, Reference proteome

Documents

  1. Human chromosome 14
    Human chromosome 14: 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. SIMILARITY comments
    Index of protein domains and families

External Data

Dasty 3

Similar proteinsi

Links to similar proteins from the UniProt Reference Clusters (UniRef) at 100%, 90% and 50% sequence identity:
100%UniRef100 combines identical sequences and sub-fragments with 11 or more residues from any organism into Uniref entry.
90%UniRef90 is built by clustering UniRef100 sequences that have at least 90% sequence identity to, and 80% overlap with, the longest sequence (a.k.a seed sequence).
50%UniRef50 is built by clustering UniRef90 seed sequences that have at least 50% sequence identity to, and 80% overlap with, the longest sequence in the cluster.