ATP5D ATP synthase, H+ transporting, mitochondrial F1 complex, delta subunit [Homo sapiens (human)] - Gene

Summary

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Official Symbol: ATP5Dprovided by HGNC
Official Full Name: ATP synthase, H+ transporting, mitochondrial F1 complex, delta subunitprovided by HGNC
Primary source: HGNC:837
See related: Ensembl:ENSG00000099624; HPRD:04397; MIM:603150; Vega:OTTHUMG00000180143
Gene type: protein coding
RefSeq status: REVIEWED
Organism: Homo sapiens
Lineage: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Summary: This gene encodes a subunit of mitochondrial ATP synthase. Mitochondrial ATP synthase catalyzes ATP synthesis, utilizing an electrochemical gradient of protons across the inner membrane during oxidative phosphorylation. ATP synthase is composed of two linked multi-subunit complexes: the soluble catalytic core, F1, and the membrane-spanning component, Fo, comprising the proton channel. The catalytic portion of mitochondrial ATP synthase consists of 5 different subunits (alpha, beta, gamma, delta, and epsilon) assembled with a stoichiometry of 3 alpha, 3 beta, and a single representative of the other 3. The proton channel consists of three main subunits (a, b, c). This gene encodes the delta subunit of the catalytic core. Alternatively spliced transcript variants encoding the same isoform have been identified. [provided by RefSeq, Jul 2008]

Genomic context

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Location :: 19p13.3

Sequence :: Chromosome: 19; NC_000019.9 (1241749..1244824)

See ATP5D in Epigenomics, MapViewer

Chromosome 19 - NC_000019.9 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Genomic Sequence

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Go to reference sequence details

Bibliography

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GeneRIFs: Gene References Into Functions What's a GeneRIF?

Submit: New GeneRIF Correction

Phenotypes

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Find tests for this gene in the NIH Genetic Testing Registry (GTR)

Review eQTL and phenotype association data in this region using PheGenI

HIV-1 protein interactions

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Protein	Gene	Interaction	Pubs
Vpu, p16	vpu	HIV-1 Vpu is identified to have a physical interaction with ATP synthase, H+ transporting, mitochondrial F1 complex, delta subunit (ATP5D) in human HEK293 and/or Jurkat cell lines by using affinity tagging and purification mass spectrometry analyses	PubMed

Go to the HIV-1, Human Protein Interaction Database

Interactions

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Products	Interactant	Other Gene	Source	Pubs	Description
BioGRID:106998	BioGRID:106987	ATP5A1	BioGRID	PubMed	Co-fractionation
BioGRID:106998	BioGRID:106994	ATP5B	BioGRID	PubMed	Co-fractionation
BioGRID:106998	BioGRID:107000	ATP5F1	BioGRID	PubMed	Co-fractionation
BioGRID:106998	BioGRID:107452	CDK2	BioGRID	PubMed	Affinity Capture-MS
BioGRID:106998	BioGRID:110694	MYC	BioGRID	PubMed	Dosage Lethality
BioGRID:106998	BioGRID:113164	UBC	BioGRID	PubMed	Affinity Capture-MS
BioGRID:106998	BioGRID:1205543	vpu	BioGRID	PubMed	Affinity Capture-MS

Pathways from BioSystems

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Alzheimer's disease, organism-specific biosystem (from KEGG)
Alzheimer's disease, organism-specific biosystemAlzheimer's disease (AD) is a chronic disorder that slowly destroys neurons and causes serious cognitive disability. AD is associated with senile plaques and neurofibrillary tangles (NFTs). Amyloid-b...
Alzheimer's disease, conserved biosystem (from KEGG)
Alzheimer's disease, conserved biosystemAlzheimer's disease (AD) is a chronic disorder that slowly destroys neurons and causes serious cognitive disability. AD is associated with senile plaques and neurofibrillary tangles (NFTs). Amyloid-b...
Electron Transport Chain, organism-specific biosystem (from WikiPathways)
Electron Transport Chain, organism-specific biosystemAn electron transport chain(ETC) couples a chemical reaction between an electron donor (such as NADH) and an electron acceptor (such as O2) to the transfer of H+ ions across a membrane, through a set...
F-type ATPase, eukaryotes, organism-specific biosystem (from KEGG)
F-type ATPase, eukaryotes, organism-specific biosystemStructural complex; Energy metabolism; ATP synthesis
Formation of ATP by chemiosmotic coupling, organism-specific biosystem (from REACTOME)
Formation of ATP by chemiosmotic coupling, organism-specific biosystemThe re-entry of protons into the mitochondrial matrix through Complex V causes conformational changes which result in ATP synthesis. Complex V (ATP synthase) is composed of 3 parts; an F1 catalytic c...
Huntington's disease, organism-specific biosystem (from KEGG)
Huntington's disease, organism-specific biosystemHuntington disease (HD) is an autosomal-dominant neurodegenerative disorder that primarily affects medium spiny striatal neurons (MSN). The symptoms are choreiform, involuntary movements, personality...
Huntington's disease, conserved biosystem (from KEGG)
Huntington's disease, conserved biosystemHuntington disease (HD) is an autosomal-dominant neurodegenerative disorder that primarily affects medium spiny striatal neurons (MSN). The symptoms are choreiform, involuntary movements, personality...
Metabolism, organism-specific biosystem (from REACTOME)
Metabolism, organism-specific biosystemMetabolic processes in human cells generate energy through the oxidation of molecules consumed in the diet and mediate the synthesis of diverse essential molecules not taken in the diet as well as th...
Oxidative phosphorylation, organism-specific biosystem (from WikiPathways)
Oxidative phosphorylation, organism-specific biosystem
Oxidative phosphorylation
Oxidative phosphorylation, organism-specific biosystem (from KEGG)
Oxidative phosphorylation, organism-specific biosystem
Oxidative phosphorylation
Oxidative phosphorylation, conserved biosystem (from KEGG)
Oxidative phosphorylation, conserved biosystem
Oxidative phosphorylation
Parkinson's disease, organism-specific biosystem (from KEGG)
Parkinson's disease, organism-specific biosystemParkinson's disease (PD) is a progressive neurodegenerative movement disorder that results primarily from the death of dopaminergic neurons in the substantia nigra. Mutations in alpha-synuclein, UCHL...
Respiratory electron transport, ATP synthesis by chemiosmotic coupling, and heat production by uncoupling proteins., organism-specific biosystem (from REACTOME)
Respiratory electron transport, ATP synthesis by chemiosmotic coupling, and heat production by uncoupling proteins., organism-specific biosystemOxidation of fatty acids and pyruvate in the mitochondrial matrix yield large amounts of NADH. The respiratory electron transport chain couples the re-oxidation of this NADH to NAD+ to the export of ...
The citric acid (TCA) cycle and respiratory electron transport, organism-specific biosystem (from REACTOME)
The citric acid (TCA) cycle and respiratory electron transport, organism-specific biosystemThe metabolism of pyruvate provides one source of acetyl-CoA which enters the citric acid (TCA, tricarboxylic acid) cycle to generate energy and the reducing equivalent NADH. These reducing equivalen...

General gene information

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Markers

sY3084 (e-PCR)
- UniSTS:515126

D11S3114 (e-PCR)
- UniSTS:152207

RH80863 (e-PCR)
- UniSTS:87265

Homology

Homologs of the ATP5D gene: The ATP5D gene is conserved in chimpanzee, Rhesus monkey, dog, cow, mouse, rat, chicken, zebrafish, fruit fly, mosquito, C.elegans, S.cerevisiae, K.lactis, E.gossypii, S.pombe, M.oryzae, and N.crassa.
Map Viewer (Mouse, Rat)
OrthoDB: The Hierarchical Catalog of Eukaryotic Orthologs

Gene Ontology Provided by GOA

Function	Evidence Code	Pubs
contributes_to ADP binding	NAS Non-traceable Author Statement more info	PubMed
contributes_to ATP binding	NAS Non-traceable Author Statement more info	PubMed
contributes_to ATPase activity	IDA Inferred from Direct Assay more info	PubMed
proton-transporting ATP synthase activity, rotational mechanism	IEA Inferred from Electronic Annotation more info
proton-transporting ATPase activity, rotational mechanism	IEA Inferred from Electronic Annotation more info
transmembrane transporter activity	IC Inferred by Curator more info	PubMed
transporter activity	NAS Non-traceable Author Statement more info	PubMed

Process	Evidence Code	Pubs
ATP biosynthetic process	NAS Non-traceable Author Statement more info	PubMed
ATP catabolic process	NAS Non-traceable Author Statement more info	PubMed
mitochondrial ATP synthesis coupled proton transport	IC Inferred by Curator more info	PubMed
mitochondrial ATP synthesis coupled proton transport	NAS Non-traceable Author Statement more info	PubMed
mitochondrial ATP synthesis coupled proton transport	TAS Traceable Author Statement more info
oxidative phosphorylation	NAS Non-traceable Author Statement more info	PubMed
respiratory electron transport chain	TAS Traceable Author Statement more info
response to copper ion	NAS Non-traceable Author Statement more info	PubMed
small molecule metabolic process	TAS Traceable Author Statement more info

Component	Evidence Code	Pubs
mitochondrial inner membrane	ISS Inferred from Sequence or Structural Similarity more info
mitochondrial matrix	TAS Traceable Author Statement more info
mitochondrial proton-transporting ATP synthase complex	IDA Inferred from Direct Assay more info	PubMed
mitochondrial proton-transporting ATP synthase complex	NAS Non-traceable Author Statement more info	PubMed
mitochondrial proton-transporting ATP synthase complex, catalytic core F(1)	NAS Non-traceable Author Statement more info	PubMed
mitochondrion	NAS Non-traceable Author Statement more info	PubMed

General protein information

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Preferred Names: ATP synthase subunit delta, mitochondrial

Names: ATP synthase subunit delta, mitochondrial; F-ATPase delta subunit; mitochondrial ATP synthase, delta subunit; mitochondrial ATP synthase complex delta-subunit precusor

NP_001001975.1

EC 3.6.1.14

NP_001678.1

EC 3.6.1.14

NCBI Reference Sequences (RefSeq)

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RefSeqs maintained independently of Annotated Genomes

These reference sequences exist independently of genome builds. Explain

These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

mRNA and Protein(s)

NM_001001975.1 → NP_001001975.1 ATP synthase subunit delta, mitochondrial precursor

Status: REVIEWED

Description

Transcript Variant: This variant (2) lacks a segment in the 3' UTR, compared to variant 1. Both variants encode the same isoform.

Source sequence(s)

BC018817, X63423

Consensus CDS

CCDS12058.1

UniProtKB/Swiss-Prot

P30049

Related

ENSP00000378995, ENST00000395633

Conserved Domains (2) summary

COG0355
Location:36 – 167
Blast Score: 190

AtpC; F0F1-type ATP synthase, epsilon subunit (mitochondrial delta subunit) [Energy production and conversion]

cd12152
Location:38 – 162
Blast Score: 287

F1-ATPase_delta; mitochondrial ATP synthase delta subunit
NM_001687.4 → NP_001678.1 ATP synthase subunit delta, mitochondrial precursor

Status: REVIEWED

Description

Transcript Variant: This variant (1) represents the longer transcript. Both variants encode the same isoform.

Source sequence(s)

BC018817, X63422

Consensus CDS

CCDS12058.1

UniProtKB/Swiss-Prot

P30049

Related

ENSP00000215375, OTTHUMP00000263448, ENST00000215375, OTTHUMT00000449958

Conserved Domains (2) summary

COG0355
Location:36 – 167
Blast Score: 190

AtpC; F0F1-type ATP synthase, epsilon subunit (mitochondrial delta subunit) [Energy production and conversion]

cd12152
Location:38 – 162
Blast Score: 287

F1-ATPase_delta; mitochondrial ATP synthase delta subunit

RefSeqs of Annotated Genomes: Homo sapiens Annotation Release 104

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCh37.p10 Primary Assembly

Genomic

NC_000019.9 Reference GRCh37.p10 Primary Assembly

Range

1241749..1244824

Download

GenBank, FASTA, Sequence Viewer (Graphics)

Alternate HuRef

Genomic

AC_000151.1 Alternate HuRef

Range

1016668..1019743

Download

GenBank, FASTA, Sequence Viewer (Graphics)

Alternate CHM1_1.0

Genomic

NC_018930.1 Alternate CHM1_1.0

Range

1169756..1172831

Download

GenBank, FASTA, Sequence Viewer (Graphics)

Nucleotide		Protein
Heading	Accession and Version	Protein
genomic	ABBA01002634.1 (3591..6666)	None
genomic	AC004221.2	AAC04304.1
genomic	AMYH01009235.1 (3639..6714)	None
genomic	CH471139.2	EAW69531.1
		EAW69532.1
		EAW69533.1
		EAW69534.1
mRNA	AK094357.1	None
mRNA	BC002389.2	AAH02389.1
mRNA	BC004426.1	AAH04426.1
mRNA	BC018079.1	AAH18079.1
mRNA	BC018817.2	None
mRNA	BC050458.1	None
mRNA	BC058927.1	None
mRNA	CR542218.1	CAG47014.1
mRNA	S87916.1	AAA08055.1
mRNA	S87918.1	ABB76284.1
mRNA	X63422.1	CAA45016.1
mRNA	X63423.1	CAA45017.1