PDCD6 programmed cell death 6 [Homo sapiens] - Gene

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Summary

Official Symbol: PDCD6provided by HGNC
Official Full Name: programmed cell death 6provided by HGNC
Primary source: HGNC:8765
See related: Ensembl:ENSG00000249915; HPRD:03035; MIM:601057; Vega:OTTHUMG00000090283
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
Also known as: ALG-2; PEF1B; MGC9123; FLJ46208; MGC111017; MGC119050
Summary: This gene encodes a calcium-binding protein belonging to the penta-EF-hand protein family. Calcium binding is important for homodimerization and for conformational changes required for binding to other protein partners. This gene product participates in T cell receptor-, Fas-, and glucocorticoid-induced programmed cell death. In mice deficient for this gene product, however, apoptosis was not blocked suggesting this gene product is functionally redundant. [provided by RefSeq, Jul 2008]

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Genomic context

Location :: 5p15.33

Sequence :: Chromosome: 5; NC_000005.9 (271736..315089)

See PDCD6 in Epigenomics, MapViewer

Chromosome 5 - NC_000005.9 Genomic Context describing neighboring genes

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Genomic regions, transcripts, and products

Genomic Sequence

Go to nucleotideGraphics FASTA GenBank

Go to reference sequence details

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Bibliography

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

PDCD6 seems to play an important role in ovarian cancer progression.
Title: PDCD6 is an independent predictor of progression free survival in epithelial ovarian cancer.
PDCD6 exerts its anti-tumor potency by activating the p53-p21 protein for G1 phase of cell cycle progression and apoptosis
Title: PDCD6 additively cooperates with anti-cancer drugs through activation of NF-κB pathways.
PDCD6 may have a role in advanced gastric cancer
Title: Programmed cell death 6 (PDCD6) as a prognostic marker for gastric cancers.
programmed cell death 6 protein plays a significant role in modulating cellular angiogenesis
Title: Programmed cell death 6 (PDCD6) inhibits angiogenesis through PI3K/mTOR/p70S6K pathway by interacting of VEGFR-2.
ALG-2 acts as a Ca(2+) sensor that modulates the function of MCOLN1 along the late endosomal-lysosomal pathway.
Title: Identification of the penta-EF-hand protein ALG-2 as a Ca2+-dependent interactor of mucolipin-1.
lower mRNA expression levels of PDCD6 were correlated significantly with a poor overall survival in gastric cancer.
Title: Identification of prognostic biomarkers in gastric cancer using endoscopic biopsy samples.
A Ca(2+)/EF3-driven arginine switch mechanism for ALG-2 binding to Alix.
Title: Structural basis for Ca2+ -dependent formation of ALG-2/Alix peptide complex: Ca2+/EF3-driven arginine switch mechanism.
Results describe the crystallization and structural analysis of N-terminally truncated human ALG-2.
Title: Crystallization and X-ray diffraction analysis of N-terminally truncated human ALG-2.
Identification of Alix-type and Non-Alix-type ALG-2-binding sites in human phospholipid scramblase 3: differential binding to an alternatively spliced isoform and amino acid-substituted mutants
Title: Identification of Alix-type and Non-Alix-type ALG-2-binding sites in human phospholipid scramblase 3: differential binding to an alternatively spliced isoform and amino acid-substituted mutants.
Data show that ALG-2 is overexpressed in liver and lung neoplasms, and is mainly found in epithelial cells in the lung.
Title: Up-regulation of ALG-2 in hepatomas and lung cancer tissue.

Submit: New GeneRIF Correction See all (20)

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Phenotypes

Review eQTL and phenotype association data in this region using PheGenI

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Products	Interactant	Other Gene	Source	Pubs	Description
O75340	P50995	ANXA11	HPRD	PubMed
O75340	P20073	ANXA7	HPRD	PubMed
O75340	Q99829	CPNE1	HPRD	PubMed
O75340	Q96FN4	CPNE2	HPRD	PubMed
O75340	Q96A23	CPNE4	HPRD	PubMed
O75340	P25445	FAS	HPRD	PubMed
O75340	P48023	FASLG	HPRD	PubMed
O75340	Q9Y5Z4	HEBP2	HPRD	PubMed
O75340	P35858	IGFALS	HPRD	PubMed
O75340	Q99683	MAP3K5	HPRD	PubMed
O75340	Q8NDC0	MAPK1IP1L	HPRD	PubMed
O75340	O75340	PDCD6	HPRD	PubMed
O75340	Q8WUM4	PDCD6IP	HPRD	PubMed
O75340	Q9UBV8	PEF1	HPRD	PubMed
O75340	Q96B97	SH3KBP1	HPRD	PubMed
O75340	Q9Y584	TIMM22	HPRD	PubMed
BioGRID:115333	BioGRID:106808	ANXA11	BioGRID	PubMed	Far Western; Reconstituted Complex; Two-hybrid
BioGRID:115333	BioGRID:107463	CDKN2A	BioGRID	PubMed	Affinity Capture-MS
BioGRID:115333	BioGRID:106851	FAS	BioGRID	PubMed	Affinity Capture-Western; Reconstituted Complex; Two-hybrid
BioGRID:115333	BioGRID:109268	H2AFX	BioGRID	PubMed	Affinity Capture-MS
BioGRID:115333	BioGRID:117128	HEBP2	BioGRID	PubMed	Two-hybrid
BioGRID:115333	BioGRID:110381	MAP3K5	BioGRID	PubMed	Affinity Capture-Western; Co-localization; Reconstituted Complex
BioGRID:115333	BioGRID:125030	MAPK1IP1L	BioGRID	PubMed	Two-hybrid
BioGRID:115333	BioGRID:115333	PDCD6	BioGRID	PubMed	Two-hybrid
BioGRID:115333	BioGRID:115332	PDCD6IP	BioGRID	PubMed	Affinity Capture-Western; Reconstituted Complex; Two-hybrid
BioGRID:115333	BioGRID:139275	PEF1	BioGRID	PubMed	Affinity Capture-Western; Co-fractionation
BioGRID:115333	BioGRID:119029	SH3KBP1	BioGRID	PubMed	Reconstituted Complex
BioGRID:115333	BioGRID:113164	UBC	BioGRID	PubMed	Affinity Capture-MS
BioGRID:115333	BioGRID:116168	YWHAQ	BioGRID	PubMed	Affinity Capture-MS

Function	Evidence Code	Pubs
binding, bridging	IMP Inferred from Mutant Phenotype more info	PubMed
calcium ion binding	IEA Inferred from Electronic Annotation more info
calcium ion binding	ISS Inferred from Sequence or Structural Similarity more info
calcium-dependent protein binding	IEA Inferred from Electronic Annotation more info
calcium-dependent protein binding	IPI Inferred from Physical Interaction more info	PubMed
protein binding	IPI Inferred from Physical Interaction more info	PubMed
protein dimerization activity	IPI Inferred from Physical Interaction more info	PubMed
protein homodimerization activity	IEA Inferred from Electronic Annotation more info

Process	Evidence Code	Pubs
activation of cysteine-type endopeptidase activity involved in apoptotic process	IEA Inferred from Electronic Annotation more info
cellular response to stress	IDA Inferred from Direct Assay more info
induction of apoptosis by extracellular signals	TAS Traceable Author Statement more info	PubMed
intracellular protein transport	IDA Inferred from Direct Assay more info
response to calcium ion	IEA Inferred from Electronic Annotation more info
response to calcium ion	ISS Inferred from Sequence or Structural Similarity more info

Component	Evidence Code	Pubs
cytoplasm	IDA Inferred from Direct Assay more info
cytoplasm	IEA Inferred from Electronic Annotation more info
cytoplasmic vesicle	IDA Inferred from Direct Assay more info
endoplasmic reticulum	IDA Inferred from Direct Assay more info	PubMed
endoplasmic reticulum membrane	IEA Inferred from Electronic Annotation more info
membrane	IEA Inferred from Electronic Annotation more info
microsome	IEA Inferred from Electronic Annotation more info
nuclear membrane	IEA Inferred from Electronic Annotation more info
nucleus	IDA Inferred from Direct Assay more info	PubMed
soluble fraction	IEA Inferred from Electronic Annotation more info

General protein information

Preferred Names: programmed cell death protein 6

Names: programmed cell death protein 6; apoptosis-linked gene-2; apoptosis-linked gene 2 protein; probable calcium-binding protein ALG-2

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NCBI Reference Sequences (RefSeq)

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_013232.3 → NP_037364.1 programmed cell death protein 6

Status: REVIEWED

Source sequence(s)

AK223366, BC012384

Consensus CDS

CCDS3854.1

UniProtKB/Swiss-Prot

O75340

UniProtKB/TrEMBL

Q53FC3

Related

ENSP00000264933, OTTHUMP00000115318, ENST00000264933, OTTHUMT00000206609

Conserved Domains (3) summary

cd00051
Location:98 – 154
Blast Score: 129

EFh; EF-hand, calcium binding motif; A diverse superfamily of calcium sensors and calcium signal modulators; most examples in this alignment model have 2 active canonical EF hands. Ca2+ binding induces a conformational change in the EF-hand motif, leading to ...

pfam13499
Location:100 – 155
Blast Score: 107

EF_hand_5; EF-hand domain pair

pfam13833
Location:40 – 90
Blast Score: 79

EF_hand_6; EF-hand domain pair

RefSeqs of Annotated Genomes: Build 37.3

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

Reference GRCh37.p5 Primary Assembly

Genomic

NC_000005.9 Reference GRCh37.p5 Primary Assembly

Range

271736..315089

Download

GenBank, FASTA, Sequence Viewer (Graphics)

Alternate HuRef

Genomic

AC_000137.1 Alternate HuRef

Range

258986..302543

Download

GenBank, FASTA, Sequence Viewer (Graphics)

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Related Sequences

Nucleotide		Protein
Heading	Accession and Version	Protein
genomic	AC021087.5 (127212..156676)	None
genomic	AC118458.2 (37214..51099)	None
genomic	CH471235.1	EAW50991.1
mRNA	AF035606.1	AAC27697.1
mRNA	AK001917.1	None
mRNA	AK128087.1	BAC87267.1
mRNA	AK223366.1	BAD97086.1
mRNA	AK295082.1	BAG58124.1
mRNA	AK308872.1	None
mRNA	AK310347.1	None
mRNA	AK315370.1	BAG37763.1
mRNA	BC012384.1	AAH12384.1
mRNA	BC028242.1	None
mRNA	BC050597.1	AAH50597.1
mRNA	BC106706.2	AAI06707.1
mRNA	BC110291.1	AAI10292.1
mRNA	BI553617.1	None
mRNA	BT020072.1	AAV38875.1
mRNA	U58773.1	AAF14336.1
other-genetic	DQ891163.2	ABM82089.1
other-genetic	DQ894344.2	ABM85270.1

Protein Accession	Links
Protein Accession	GenPept Link	UniProtKB Link
O75340.1	GenPept	UniProtKB/Swiss-Prot:O75340
Q2YDC2	GenPept	UniProtKB/TrEMBL:Q2YDC2
Q53FC3	GenPept	UniProtKB/TrEMBL:Q53FC3
Q6ZRP2	GenPept	UniProtKB/TrEMBL:Q6ZRP2
Q86W51	GenPept	UniProtKB/TrEMBL:Q86W51