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Protein

Piwi-like protein Siwi

Gene

Siwi

Organism
Bombyx mori (Silk moth)
Status
Reviewed-Annotation score: -Experimental evidence at protein leveli

Functioni

Endoribonuclease that plays a central role during spermatogenesis by repressing transposable elements and preventing their mobilization, which is essential for the germline integrity (PubMed:19460866, PubMed:27693359). Plays an essential role in meiotic differentiation of spermatocytes, germ cell differentiation and in self-renewal of spermatogonial stem cells (PubMed:19460866, PubMed:25558067, PubMed:27693359). Its presence in oocytes suggests that it may participate in similar functions during oogenesis in females (PubMed:18191035). Acts via the piRNA metabolic process, which mediates the repression of transposable elements during meiosis by forming complexes composed of piRNAs and Piwi proteins and govern the methylation and subsequent repression of transposons (PubMed:19460866, PubMed:25558067, PubMed:27693359). Directly binds piRNAs, a class of 24 to 30 nucleotide RNAs that are generated by a Dicer-independent mechanism and are primarily derived from transposons and other repeated sequence elements (PubMed:19460866, PubMed:25558067, PubMed:27693359). Recognizes piRNAs containing a phosphate at the 5'-end and a 2'-O-methylation modification at the 3'-end (PubMed:27693359). Strongly prefers a uridine in the first position of their guide (g1U preference, also named 1U-bias) and a complementary adenosine in the target (t1A bias) (PubMed:24757166, PubMed:27693359). Plays a key role in the piRNA amplification loop, also named ping-pong amplification cycle: antisense piRNA-bound Siwi and sense piRNA-bound Ago3 reciprocally cleave complementary transcripts, to couple the amplification of piRNAs with the repression of transposable elements. In this process Siwi acts as a 'slicer-competent' piRNA endoribonuclease that cleaves primary piRNAs, which are then loaded onto Ago3 (PubMed:27693359). In this process, Siwi requires the RNA unwinding activity of the RNA helicase Vasa for the release of the cleavage products (PubMed:25558067).5 Publications

Cofactori

Mg2+1 Publication

Sites

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Metal bindingi645MagnesiumCombined sources1 Publication1
Active sitei670Combined sources1 Publication1
Active sitei708Combined sources1 Publication1
Active sitei740Combined sources1 Publication1
Active sitei874Combined sources1 Publication1
Metal bindingi899Magnesium; via carboxylateCombined sources1 Publication1

GO - Molecular functioni

  • endoribonuclease activity Source: UniProtKB
  • magnesium ion binding Source: UniProtKB
  • piRNA binding Source: UniProtKB

GO - Biological processi

Keywordsi

Molecular functionDevelopmental protein, Endonuclease, Hydrolase, Nuclease, RNA-binding
Biological processDifferentiation, Meiosis, RNA-mediated gene silencing, Spermatogenesis
LigandMetal-binding

Names & Taxonomyi

Protein namesi
Recommended name:
Piwi-like protein SiwiCurated (EC:3.1.26.-1 Publication)
Gene namesi
Name:Siwi1 Publication
OrganismiBombyx mori (Silk moth)
Taxonomic identifieri7091 [NCBI]
Taxonomic lineageiEukaryotaMetazoaEcdysozoaArthropodaHexapodaInsectaPterygotaNeopteraHolometabolaLepidopteraGlossataDitrysiaBombycoideaBombycidaeBombycinaeBombyx
Proteomesi
  • UP000005204 Componenti: Unassembled WGS sequence

Subcellular locationi

Keywords - Cellular componenti

Cytoplasm

Pathology & Biotechi

Mutagenesis

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Mutagenesisi602N → Q: Does not affect ability to recognize uridine at the first position of piRNAs (g1U preference, also named 1U-bias). 1 Publication1
Mutagenesisi607Y → E: Reduced piRNA-binding. 1 Publication1
Mutagenesisi607Y → L: Does not affect ability to recognize uridine at the first position of piRNAs (g1U preference, also named 1U-bias). 1 Publication1
Mutagenesisi611K → A: Reduced piRNA-binding. 1 Publication1
Mutagenesisi623Q → A: Reduced piRNA-binding. 1 Publication1
Mutagenesisi645Q → A: Reduced piRNA-binding. 1 Publication1
Mutagenesisi649K → A: Reduced piRNA-binding. 1 Publication1
Mutagenesisi670D → A: Abolished endoribonuclease activity. 1 Publication1
Mutagenesisi708E → A: Abolished endoribonuclease activity. 1 Publication1
Mutagenesisi740D → A: Abolished endoribonuclease activity. 1 Publication1
Mutagenesisi874H → A: Abolished endoribonuclease activity. 1 Publication1

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_00004393551 – 899Piwi-like protein SiwiAdd BLAST899

Post-translational modificationi

Arginine methylation is required for the interaction with Tudor domain-containing protein Papi/TDRKH (PubMed:23970546, PubMed:26919431).2 Publications

Keywords - PTMi

Methylation

Proteomic databases

PRIDEiA8D8P8

Expressioni

Tissue specificityi

Highly expressed in the larval testis, pupal ovary and adult eggs.1 Publication

Interactioni

Subunit structurei

Interacts (when symmetrically methylated) with Papi/TDRKH (PubMed:23970546, PubMed:26919431). Interacts with Vasa (PubMed:25558067).3 Publications

Protein-protein interaction databases

STRINGi7091.BGIBMGA010644-TA

Structurei

Secondary structure

1899
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details

3D structure databases

ProteinModelPortaliA8D8P8
SMRiA8D8P8
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Domaini339 – 427PAZPROSITE-ProRule annotationAdd BLAST89
Domaini594 – 885PiwiPROSITE-ProRule annotationAdd BLAST292

Region

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Regioni130 – 168L0 region1 PublicationAdd BLAST39
Regioni169 – 241N region1 PublicationAdd BLAST73
Regioni242 – 318L1 region1 PublicationAdd BLAST77
Regioni428 – 527L2 region1 PublicationAdd BLAST100
Regioni528 – 658MID region1 PublicationAdd BLAST131

Compositional bias

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Compositional biasi23 – 67Pro-richPROSITE-ProRule annotationAdd BLAST45

Domaini

Shows a strong structural resemblance to the argonaute/Ago subfamily. The domains (N, PAZ, MID and PIWI) and linkers (L0, L1, and L2) assemble into a typical bi-lobed (N-PAZ lobe and MID-PIWI lobe) architecture, in which the 5' and 3' ends of the bound piRNA are anchored by the MID-PIWI and PAZ domains, respectively. However, the relative orientation of these two lobes differs significantly between Siwi and the Ago-clade proteins: the N-PAZ lobe in Siwi rotates significantly downward. Additional hinge motions between N and PAZ domains exist, due to a distinct set of contacts at the interface. Three out of the four residues in the DEDH catalytic tetrad are well-preserved. The fourth, Glu-708, is located in a disordered loop and likely joins the active site upon the guide-target RNA duplex formation. This 'unplugged' active site scheme is found in Agos of some bacteria.1 Publication

Sequence similaritiesi

Belongs to the argonaute family. Piwi subfamily.Curated

Phylogenomic databases

eggNOGiKOG1042 Eukaryota
ENOG410XNRH LUCA
InParanoidiA8D8P8
KOiK02156
OMAiYREHHGT

Family and domain databases

Gene3Di3.30.420.10, 1 hit
InterProiView protein in InterPro
IPR003100 PAZ_dom
IPR036085 PAZ_dom_sf
IPR003165 Piwi
IPR012337 RNaseH-like_sf
IPR036397 RNaseH_sf
PfamiView protein in Pfam
PF02170 PAZ, 1 hit
PF02171 Piwi, 1 hit
SMARTiView protein in SMART
SM00949 PAZ, 1 hit
SM00950 Piwi, 1 hit
SUPFAMiSSF101690 SSF101690, 1 hit
SSF53098 SSF53098, 1 hit
PROSITEiView protein in PROSITE
PS50821 PAZ, 1 hit
PS50822 PIWI, 1 hit

Sequencei

Sequence statusi: Complete.

A8D8P8-1 [UniParc]FASTAAdd to basket
« Hide
        10         20         30         40         50
MSEPRGRGRA RGRAGRGGDG GGPAPRRPGE QAGPSQQSMP PGPRPQPPSG
60 70 80 90 100
WGPQSSVPPV RAGVPTPTAQ AGRASHRVTP TTHEHPGDID VQQRMQKLEL
110 120 130 140 150
GPHSSGGGDA SSVVGRGSRR GGGRVLPETI SILRTRPEAV TSKKGTSGTP
160 170 180 190 200
LDLLANYFTV ETTPKWGLYQ YHVDISPEED STGVRKALMR VHSKTLGGYL
210 220 230 240 250
FDGTVLYTVN RLHPDPMELY SDRKTDNERM RILIKLTCEV SPGDYHYIQI
260 270 280 290 300
FNIIIRKCFN LLKLQLMGRD YFDPEAKIDI PEFKLQIWPG YKTTINQYED
310 320 330 340 350
RLLLVTEIAH KVLRMDTVLQ MLSEYAATKG NNYKKIFLED VVGKIVMTDY
360 370 380 390 400
NKRTYRVDDV AWNVSPKSTF KMRDENITYI EYYYKKYNLR IQDPGQPLLI
410 420 430 440 450
SRSKPREIRA GLPELIYLVP ELCRQTGLSD EMRANFKLMR SLDVHTKIGP
460 470 480 490 500
DKRIEKLNNF NRRFTSTPEV VEELATWSLK LSKELVKIKG RQLPPENIIQ
510 520 530 540 550
ANNVKYPAGD TTEGWTRDMR SKHLLAIAQL NSWVVITPER QRRDTESFID
560 570 580 590 600
LIIKTGGGVG FRMRSPDLVV IRHDGPIEYA NMCEEVIARK NPALILCVLA
610 620 630 640 650
RNYADRYEAI KKKCTVDRAV PTQVVCARNM SSKSAMSIAT KVAIQINCKL
660 670 680 690 700
GGSPWTVDIP LPSLMVVGYD VCHDTRSKEK SFGAFVATLD KQMTQYYSIV
710 720 730 740 750
NAHTSGEELS SHMGFNIASA VKKFREKNGT YPARIFIYRD GVGDGQIPYV
760 770 780 790 800
HSHEVAEIKK KLAEIYAGVE IKLAFIIVSK RINTRIFVQR GRSGENPRPG
810 820 830 840 850
TVIDDVVTLP ERYDFYLVSQ NVREGTIAPT SYNVIEDTTG LNPDRIQRLT
860 870 880 890
YKLTHLYFNC SSQVRVPSVC QYAHKLAFLA ANSLHNQPHY SLNETLYFL
Length:899
Mass (Da):101,338
Last modified:November 13, 2007 - v1
Checksum:iDAF3AD4845AC9386
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AB332313 mRNA Translation: BAF73718.2
AB372006 mRNA Translation: BAF98574.1
EU143547 mRNA Translation: ABV60274.1
BABH01033344 Genomic DNA No translation available.
EU034629 mRNA Translation: ABS53348.1
RefSeqiNP_001098066.2, NM_001104596.2
XP_012545276.1, XM_012689822.1
UniGeneiBmo.2686

Genome annotation databases

EnsemblMetazoaiBGIBMGA010644-RA; BGIBMGA010644-TA; BGIBMGA010644
GeneIDi100125336
KEGGibmor:100125336

Similar proteinsi

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AB332313 mRNA Translation: BAF73718.2
AB372006 mRNA Translation: BAF98574.1
EU143547 mRNA Translation: ABV60274.1
BABH01033344 Genomic DNA No translation available.
EU034629 mRNA Translation: ABS53348.1
RefSeqiNP_001098066.2, NM_001104596.2
XP_012545276.1, XM_012689822.1
UniGeneiBmo.2686

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
5GUHX-ray2.40A1-899[»]
ProteinModelPortaliA8D8P8
SMRiA8D8P8
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

STRINGi7091.BGIBMGA010644-TA

Proteomic databases

PRIDEiA8D8P8

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblMetazoaiBGIBMGA010644-RA; BGIBMGA010644-TA; BGIBMGA010644
GeneIDi100125336
KEGGibmor:100125336

Organism-specific databases

CTDi100125336

Phylogenomic databases

eggNOGiKOG1042 Eukaryota
ENOG410XNRH LUCA
InParanoidiA8D8P8
KOiK02156
OMAiYREHHGT

Family and domain databases

Gene3Di3.30.420.10, 1 hit
InterProiView protein in InterPro
IPR003100 PAZ_dom
IPR036085 PAZ_dom_sf
IPR003165 Piwi
IPR012337 RNaseH-like_sf
IPR036397 RNaseH_sf
PfamiView protein in Pfam
PF02170 PAZ, 1 hit
PF02171 Piwi, 1 hit
SMARTiView protein in SMART
SM00949 PAZ, 1 hit
SM00950 Piwi, 1 hit
SUPFAMiSSF101690 SSF101690, 1 hit
SSF53098 SSF53098, 1 hit
PROSITEiView protein in PROSITE
PS50821 PAZ, 1 hit
PS50822 PIWI, 1 hit
ProtoNetiSearch...

Entry informationi

Entry nameiSIWI_BOMMO
AccessioniPrimary (citable) accession number: A8D8P8
Secondary accession number(s): A7BJS4, A7LM14
Entry historyiIntegrated into UniProtKB/Swiss-Prot: March 15, 2017
Last sequence update: November 13, 2007
Last modified: October 10, 2018
This is version 80 of the entry and version 1 of the sequence. See complete history.
Entry statusiReviewed (UniProtKB/Swiss-Prot)

Miscellaneousi

Keywords - Technical termi

3D-structure, Complete proteome, Reference proteome

Documents

  1. SIMILARITY comments
    Index of protein domains and families
  2. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
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Main funding by: National Institutes of Health

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