Q5SWZ9 (PLD6_MOUSE) Reviewed, UniProtKB/Swiss-Prot

Names and origin

Protein names

Recommended name:
Mitochondrial cardiolipin hydrolase
EC=3.1.-.-

Alternative name(s):
Choline phosphatase 6
Mitochondrial phospholipase
Short name=MitoPLD
Phosphatidylcholine-hydrolyzing phospholipase D6
Phospholipase D6
Short name=PLD 6
Protein zucchini homolog
Short name=mZuc

Gene names

Name:

Pld6

Organism

Mus musculus (Mouse) [Reference proteome]

Taxonomic identifier

10090 [NCBI]

Taxonomic lineage

cellular organisms › Eukaryota › Opisthokonta › Metazoa › Eumetazoa › Bilateria › Deuterostomia › Chordata › Craniata › Vertebrata › Gnathostomata › Teleostomi › Euteleostomi › Sarcopterygii › Tetrapoda › Amniota › Mammalia › Theria › Eutheria › Euarchontoglires › Glires › Rodentia › Sciurognathi › Muroidea › Muridae › Murinae › Mus › Mus

Protein attributes

Sequence length	221 AA.
Sequence status	Complete.
Protein existence	Evidence at protein level

General annotation (Comments)

Function	Regulates mitochondrial shape through facilitating mitochondrial fusion. During spermatogenesis, plays a critical role in PIWI-interacting RNA (piRNA) biogenesis. piRNAs provide essential protection against the activity of mobile genetic elements. piRNA-mediated transposon silencing is thus critical for maintaining genome stability, in particular in germline cells when transposons are mobilized as a consequence of wide-spread genomic demethylation. Has been proposed to act as a cardiolipin hydrolase to generate phosphatidic acid at mitochondrial surface (Ref.5). Although it cannot be excluded that it can act as a phospholipase in some circumstances, it should be noted that cardiolipin hydrolase activity is either undetectable in vitro (Ref.7 and Ref.6), or very low. In addition, cardiolipin is almost exclusively found on the inner mitochondrial membrane, while PLD6 localizes to the outer mitochondrial membrane, facing the cytosol. Has been shown to be a backbone-non-specific, single strand-specific nuclease, cleaving either RNA or DNA substrates with similar affinity (Ref.7 and Ref.6). Produces 5' phosphate and 3' hydroxyl termini, suggesting it could directly participate in the processing of primary piRNA transcripts. Ref.4 Ref.5 Ref.6 Ref.7
Enzyme regulation	SsDNA hydrolase activity does not depend upon, but it stimulated by, the presence of Ca2+ and Mn2+. Ref.7
Subunit structure	Homodimer. Ref.7
Subcellular location	Mitochondrion outer membrane; Single-pass membrane protein Ref.4.
Tissue specificity	Predominantly expressed in testis (at protein level). Also expressed at high levels in growing ovary. Ref.4
Developmental stage	Expressed in embryonic testis at 16.5 dpc (at protein level). Expressed at low levels in type A and B spermatogonia, increases 5-fold in spermatocytes undergoing meiosis (pachytene spermatocytes), and then decreases again in round spermatids. Expressed at low levels in testes in young mice, peaks from postnatal day 14 to day 29 with the onset of puberty andpersists in adulthood (at protein level). Ref.4 Ref.5
Domain	In contrast to other members of the phospholipase D family, contains only one PLD phosphodiesterase domain, suggesting that it has a single half-catalytic and requires homodimerization to form a complete active site By similarity.
Disruption phenotype	Mutant animals are born at the expected Mendelian ratio. Females show no discernible phenotype and are fertile. Males are sterile, because of meiotic arrest during spermatogenesis due to demethylation and subsequent derepression of transposable elements. Effects are caused by defects in primary piRNA biogenesis: in contrast to wild-type cells neither mitochondria nor associated meiotic nuage (named P granule) are aggregated. Ref.4 Ref.5
Sequence similarities	Belongs to the phospholipase D family. MitoPLD/Zucchini subfamily. Contains 1 C3H1-type zinc finger. Contains 1 PLD phosphodiesterase domain.

Ontologies

Keywords
Biological process	Differentiation Lipid degradation Lipid metabolism Meiosis Spermatogenesis
Cellular component	Membrane Mitochondrion Mitochondrion outer membrane
Coding sequence diversity	Alternative splicing
Domain	Transmembrane Transmembrane helix Zinc-finger
Ligand	Metal-binding Zinc
Molecular function	Endonuclease Hydrolase Nuclease
Technical term	3D-structure Complete proteome Reference proteome
Gene Ontology (GO)
Biological_process	DNA methylation involved in gamete generation Inferred from mutant phenotype Ref.4. Source: UniProtKB P granule organization Inferred from mutant phenotype Ref.5. Source: UniProtKB lipid catabolic process Inferred from electronic annotation. Source: UniProtKB-KW meiosis Inferred from mutant phenotype Ref.4Ref.5. Source: UniProtKB mitochondrial fusion Inferred from sequence or structural similarity. Source: UniProtKB piRNA metabolic process Inferred from mutant phenotype Ref.4Ref.5. Source: UniProtKB spermatid development Inferred from mutant phenotype Ref.4Ref.5. Source: UniProtKB
Cellular_component	endoplasmic reticulum membrane Traceable author statement. Source: Reactome integral to membrane Inferred from electronic annotation. Source: UniProtKB-KW mitochondrial outer membrane Inferred from direct assay Ref.4. Source: UniProtKB
Molecular_function	cardiolipin hydrolase activity Inferred from sequence or structural similarity. Source: UniProtKB protein homodimerization activity Inferred from sequence or structural similarity. Source: UniProtKB
Complete GO annotation...

Alternative products

This entry describes 2 isoforms produced by alternative splicing. [Align] [Select]

Isoform 1 (identifier: Q5SWZ9-1)

This isoform has been chosen as the 'canonical' sequence. All positional information in this entry refers to it. This is also the sequence that appears in the downloadable versions of the entry.

Isoform 2 (identifier: Q5SWZ9-2)

The sequence of this isoform differs from the canonical sequence as follows:
     139-147: AGIQVRHDQ → GYRYGTTRT
     148-221: Missing.

Sequence annotation (Features)

Feature key

Position(s)

Length

Description

Graphical view

Feature identifier

Molecule processing

Chain

1 – 221

221

Mitochondrial cardiolipin hydrolase

PRO_0000325911

Regions

Topological domain

1 – 4

4

Mitochondrial intermembrane Potential

Transmembrane

5 – 27

23

Helical; Potential

Topological domain

28 – 221

194

Cytoplasmic Potential

Domain

148 – 175

28

PLD phosphodiesterase

Zinc finger

44 – 75

32

C3H1-type; atypical

Region

1 – 38

38

Required for mitochondrial localization

Sites

Active site

153

1

Potential

Active site

155

1

Potential

Active site

160

1

Potential

Natural variations

Alternative sequence

139 – 147

9

AGIQVRHDQ → GYRYGTTRT in isoform 2.

VSP_032474

Alternative sequence

148 – 221

74

Missing in isoform 2.

VSP_032475

Experimental info

Mutagenesis

153

1

H → N: Loss of nuclease activity. Ref.7

Secondary structure

1

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221

Helix Strand Turn

Details...

Beta strand

38 – 44

7

Turn

51 – 55

5

Beta strand

68 – 70

3

Helix

76 – 85

10

Beta strand

88 – 96

9

Helix

101 – 112

12

Beta strand

116 – 123

8

Helix

132 – 138

7

Beta strand

142 – 145

4

Beta strand

148 – 150

3

Beta strand

155 – 159

5

Turn

160 – 162

3

Beta strand

163 – 168

6

Helix

173 – 178

6

Beta strand

181 – 186

6

Helix

189 – 205

17

Sequences

	Sequence		Length	Mass (Da)
	Isoform 1 [UniParc]. Last modified December 21, 2004. Version 1. Checksum: A7A2E813281B924E	FASTA	221	25,041
	10 20 30 40 50 60 MGRSSWRLVF AAGAGLALAL EALPWLMRWL LAGRRPRREV LFFPSQVTCT EALLQAPGLP 70 80 90 100 110 120 PGPSGCPCSL PHSESSLSRL LRALLAARSS LELCLFAFSS PQLGRAVQLL HQRGVRVRVI 130 140 150 160 170 180 TDCDYMALNG SQIGLLRKAG IQVRHDQDLG YMHHKFAIVD KKVLITGSLN WTTQAIQNNR 190 200 210 220 ENVLIMEDTE YVRLFLEEFE RIWEEFDPTK YSFFPQKHRG H
	Isoform 2 [UniParc]. Checksum: C89BFBDAE7BA570D	FASTA	147	16,108
	10 20 30 40 50 60 MGRSSWRLVF AAGAGLALAL EALPWLMRWL LAGRRPRREV LFFPSQVTCT EALLQAPGLP 70 80 90 100 110 120 PGPSGCPCSL PHSESSLSRL LRALLAARSS LELCLFAFSS PQLGRAVQLL HQRGVRVRVI 130 140 TDCDYMALNG SQIGLLRKGY RYGTTRT

References

	« Hide 'large scale' referencesShow 'large scale' references »
[1]	"The transcriptional landscape of the mammalian genome." Carninci P., Kasukawa T., Katayama S., Gough J., Frith M.C., Maeda N., Oyama R., Ravasi T., Lenhard B., Wells C., Kodzius R., Shimokawa K., Bajic V.B., Brenner S.E., Batalov S., Forrest A.R., Zavolan M., Davis M.J. , Wilming L.G., Aidinis V., Allen J.E., Ambesi-Impiombato A., Apweiler R., Aturaliya R.N., Bailey T.L., Bansal M., Baxter L., Beisel K.W., Bersano T., Bono H., Chalk A.M., Chiu K.P., Choudhary V., Christoffels A., Clutterbuck D.R., Crowe M.L., Dalla E., Dalrymple B.P., de Bono B., Della Gatta G., di Bernardo D., Down T., Engstrom P., Fagiolini M., Faulkner G., Fletcher C.F., Fukushima T., Furuno M., Futaki S., Gariboldi M., Georgii-Hemming P., Gingeras T.R., Gojobori T., Green R.E., Gustincich S., Harbers M., Hayashi Y., Hensch T.K., Hirokawa N., Hill D., Huminiecki L., Iacono M., Ikeo K., Iwama A., Ishikawa T., Jakt M., Kanapin A., Katoh M., Kawasawa Y., Kelso J., Kitamura H., Kitano H., Kollias G., Krishnan S.P., Kruger A., Kummerfeld S.K., Kurochkin I.V., Lareau L.F., Lazarevic D., Lipovich L., Liu J., Liuni S., McWilliam S., Madan Babu M., Madera M., Marchionni L., Matsuda H., Matsuzawa S., Miki H., Mignone F., Miyake S., Morris K., Mottagui-Tabar S., Mulder N., Nakano N., Nakauchi H., Ng P., Nilsson R., Nishiguchi S., Nishikawa S., Nori F., Ohara O., Okazaki Y., Orlando V., Pang K.C., Pavan W.J., Pavesi G., Pesole G., Petrovsky N., Piazza S., Reed J., Reid J.F., Ring B.Z., Ringwald M., Rost B., Ruan Y., Salzberg S.L., Sandelin A., Schneider C., Schoenbach C., Sekiguchi K., Semple C.A., Seno S., Sessa L., Sheng Y., Shibata Y., Shimada H., Shimada K., Silva D., Sinclair B., Sperling S., Stupka E., Sugiura K., Sultana R., Takenaka Y., Taki K., Tammoja K., Tan S.L., Tang S., Taylor M.S., Tegner J., Teichmann S.A., Ueda H.R., van Nimwegen E., Verardo R., Wei C.L., Yagi K., Yamanishi H., Zabarovsky E., Zhu S., Zimmer A., Hide W., Bult C., Grimmond S.M., Teasdale R.D., Liu E.T., Brusic V., Quackenbush J., Wahlestedt C., Mattick J.S., Hume D.A., Kai C., Sasaki D., Tomaru Y., Fukuda S., Kanamori-Katayama M., Suzuki M., Aoki J., Arakawa T., Iida J., Imamura K., Itoh M., Kato T., Kawaji H., Kawagashira N., Kawashima T., Kojima M., Kondo S., Konno H., Nakano K., Ninomiya N., Nishio T., Okada M., Plessy C., Shibata K., Shiraki T., Suzuki S., Tagami M., Waki K., Watahiki A., Okamura-Oho Y., Suzuki H., Kawai J., Hayashizaki Y. Science 309:1559-1563(2005) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] (ISOFORM 2). Strain: C57BL/6J. Tissue: Egg and Testis.
[2]	"Lineage-specific biology revealed by a finished genome assembly of the mouse." Church D.M., Goodstadt L., Hillier L.W., Zody M.C., Goldstein S., She X., Bult C.J., Agarwala R., Cherry J.L., DiCuccio M., Hlavina W., Kapustin Y., Meric P., Maglott D., Birtle Z., Marques A.C., Graves T., Zhou S. , Teague B., Potamousis K., Churas C., Place M., Herschleb J., Runnheim R., Forrest D., Amos-Landgraf J., Schwartz D.C., Cheng Z., Lindblad-Toh K., Eichler E.E., Ponting C.P. PLoS Biol. 7:E1000112-E1000112(2009) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA]. Strain: C57BL/6J.
[3]	"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] (ISOFORM 2), NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] OF 1-195 (ISOFORM 1). Tissue: Brain.
[4]	"MITOPLD is a mitochondrial protein essential for nuage formation and piRNA biogenesis in the mouse germline." Watanabe T., Chuma S., Yamamoto Y., Kuramochi-Miyagawa S., Totoki Y., Toyoda A., Hoki Y., Fujiyama A., Shibata T., Sado T., Noce T., Nakano T., Nakatsuji N., Lin H., Sasaki H. Dev. Cell 20:364-375(2011) [PubMed] [Europe PMC] [Abstract] Cited for: FUNCTION, DISRUPTION PHENOTYPE, SUBCELLULAR LOCATION, TOPOLOGY, TISSUE SPECIFICITY, DEVELOPMENTAL STAGE.
[5]	"piRNA-associated germline nuage formation and spermatogenesis require MitoPLD profusogenic mitochondrial-surface lipid signaling." Huang H., Gao Q., Peng X., Choi S.Y., Sarma K., Ren H., Morris A.J., Frohman M.A. Dev. Cell 20:376-387(2011) [PubMed] [Europe PMC] [Abstract] Cited for: FUNCTION, DEVELOPMENTAL STAGE, DISRUPTION PHENOTYPE.
[6]	"Structure and function of Zucchini endoribonuclease in piRNA biogenesis." Nishimasu H., Ishizu H., Saito K., Fukuhara S., Kamatani M.K., Bonnefond L., Matsumoto N., Nishizawa T., Nakanaga K., Aoki J., Ishitani R., Siomi H., Siomi M.C., Nureki O. Nature 491:284-287(2012) [PubMed] [Europe PMC] [Abstract] Cited for: FUNCTION AS A NUCLEASE, LACK OF CARDIOLIPIN HYDROLASE ACTIVITY.
[7]	"The structural biochemistry of Zucchini implicates it as a nuclease in piRNA biogenesis." Ipsaro J.J., Haase A.D., Knott S.R., Joshua-Tor L., Hannon G.J. Nature 491:279-283(2012) [PubMed] [Europe PMC] [Abstract] Cited for: X-RAY CRYSTALLOGRAPHY (1.75 ANGSTROMS) OF 31-221, FUNCTION AS A NUCLEASE, LACK OF CARDIOLIPIN HYDROLASE ACTIVITY, HOMODIMERIZATION, ENZYME REGULATION, MUTAGENESIS OF HIS-153.
+	Additional computationally mapped references.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ

AK077214 mRNA. Translation: BAC36687.1.
AK139586 mRNA. Translation: BAE24077.1.
AL596204 Genomic DNA. Translation: CAI24298.1.
BC119245 mRNA. Translation: AAI19246.1.
BC145052 mRNA. Translation: AAI45053.1.

IPI

IPI00225919.
IPI00889236.

RefSeq

NP_898962.2. NM_183139.2.

UniGene

Mm.344651.

3D structure databases

PDBe
RCSB PDB
PDBj

Entry	Method	Resolution (Å)	Chain	Positions	PDBsum
4GGJ	X-ray	1.75	A	31-221	[»]
4GGK	X-ray	2.10	A	31-221	[»]

ProteinModelPortal

Q5SWZ9.

SMR

Q5SWZ9. Positions 35-209.

ModBase

Search...

Protein-protein interaction databases

DIP

DIP-59982N.

STRING

10090.ENSMUSP00000115503.

PTM databases

PhosphoSite

Q5SWZ9.

Proteomic databases

PaxDb

Q5SWZ9.

PRIDE

Q5SWZ9.

Protocols and materials databases

StructuralBiologyKnowledgebase

Search...

Genome annotation databases

Ensembl

ENSMUST00000125307; ENSMUSP00000115503; ENSMUSG00000043648.

GeneID

194908.

KEGG

mmu:194908.

UCSC

uc007jev.1. mouse.
uc011xvp.1. mouse.

Organism-specific databases

CTD

201164.

MGI

MGI:2687283. Pld6.

Phylogenomic databases

eggNOG

COG1502.

GeneTree

ENSGT00390000004368.

HOGENOM

HOG000082679.

HOVERGEN

HBG108267.

InParanoid

Q5SWZ9.

OMA

CPCSLPH.

OrthoDB

EOG402WTD.

Enzyme and pathway databases

Reactome

REACT_112621. Metabolism.

Gene expression databases

Bgee

Q5SWZ9.

Genevestigator

Q5SWZ9.

Family and domain databases

InterPro

IPR025202. PLD-like_dom.
IPR001736. PLipase_D/transphosphatidylase.
[Graphical view]

Pfam

PF13091. PLDc_2. 1 hit.
[Graphical view]

SMART

SM00155. PLDc. 1 hit.
[Graphical view]

PROSITE

PS50035. PLD. 1 hit.
PS50103. ZF_C3H1. False negative.
[Graphical view]

ProtoNet

Search...

Other

NextBio

371672.

SOURCE

Search...

Entry information

Entry name

PLD6_MOUSE

Accession

Primary (citable) accession number: Q5SWZ9
Secondary accession number(s): B7ZN71, Q3UTA3, Q8BVM0

Entry history

Integrated into UniProtKB/Swiss-Prot:	March 18, 2008
Last sequence update:	December 21, 2004
Last modified:	May 1, 2013
This is version 69 of the entry and version 1 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation program

Chordata Protein Annotation Program