B3DLA6

SS
Gene name
dicer1
Protein name
Endoribonuclease Dicer
Names
EC 3.1.26.3
Species
Xenopus tropicalis (Western clawed frog) (Silurana tropicalis)
KEGG Pathway
xtr:100170154
EC number
3.1.26.3: Endoribonucleases producing 5'-phosphomonoesters
Protein Class

Descriptions

Dicer, a member of the Ribonuclease III family of enzymes, processes double-stranded RNA substrates into ~21-27 nucleotide products that trigger sequence-directed gene silencing by RNA interference (RNAi). The N-terminal domain of Dicer, which is homologous to DExD/H-box helicases, substantially attenuates the rate of substrate cleavage. Deletion or mutation of this domain activates human Dicer. Modest stimulation of catalysis by the full-length Dicer enzyme was observed in the presence of the TAR-RNA binding protein (TRBP), which physically interacts with the DExD/H-box domain. Thus, the DExD/H-box domain likely disrupts the functionality of the Dicer active site until a structural rearrangement occurs, perhaps upon assembly with its molecular partners

Autoinhibitory domains (AIDs)

0-595 (DExD/H-box helicase domain) SS

Target domain

1253-1379 (RNase IIIa domain);1637-1795 (RNase IIIb domain)

Relief mechanism

Partner binding

Assay

Accessory elements

No accessory elements

References

Autoinhibited structure

Activated structure

1 structures for B3DLA6

Entry ID Method Resolution Chain Position Source
AF-B3DLA6-F1 Predicted AlphaFoldDB

No variants for B3DLA6

Variant ID(s) Position Change Description Diseaes Association Provenance
No variants for B3DLA6

No associated diseases with B3DLA6

11 regional properties for B3DLA6

Type Name Position InterPro Accession
domain Ribonuclease III domain 1249 - 1570 IPR000999-1
domain Ribonuclease III domain 1637 - 1818 IPR000999-2
domain Helicase, C-terminal domain-like 424 - 593 IPR001650
domain PAZ domain 882 - 1060 IPR003100
domain Dicer dimerisation domain 621 - 713 IPR005034
domain DEAD/DEAH box helicase domain 36 - 199 IPR011545
domain Helicase superfamily 1/2, ATP-binding domain 30 - 233 IPR014001
domain Double-stranded RNA-binding domain 1820 - 1885 IPR014720
domain Dicer, double-stranded RNA-binding domain 1801 - 1889 IPR044441
domain Dicer, platform domain 752 - 877 IPR048512
domain Dicer, partner-binding domain 258 - 356 IPR048513

Functions

Description
EC Number 3.1.26.3 Endoribonucleases producing 5'-phosphomonoesters
Subcellular Localization
  • Cytoplasm
PANTHER Family
PANTHER Subfamily
PANTHER Protein Class
PANTHER Pathway Category No pathway information available

4 GO annotations of cellular component

Name Definition
cytoplasm The contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
nucleus A membrane-bounded organelle of eukaryotic cells in which chromosomes are housed and replicated. In most cells, the nucleus contains all of the cell's chromosomes except the organellar chromosomes, and is the site of RNA synthesis and processing. In some species, or in specialized cell types, RNA metabolism or DNA replication may be absent.
RISC complex A ribonucleoprotein complex that contains members of the Argonaute family of proteins, small interfering RNAs (siRNAs) or microRNAs (miRNAs), and miRNA or siRNA-complementary mRNAs, in addition to a number of accessory factors. The RISC complex is involved in posttranscriptional repression of gene expression through downregulation of translation or induction of mRNA degradation.
RISC-loading complex A trimeric protein complex required for the formation of a mature RNA-induced silencing complex (RISC). In humans the complex is composed of the endonuclease Dicer (DICER1), TRBP (TARBP2) and the Argonaute protein Ago2 (EIF2C2/AGO2). Within the complex, Dicer and TRBP are required to process precursor miRNAs (pre-miRNAs) to mature miRNAs and then load them onto Ago2. Ago2 bound to the mature miRNA constitutes the minimal RISC and may subsequently dissociate from Dicer and TRBP. This complex has endoribonuclease activity.

6 GO annotations of molecular function

Name Definition
ATP binding Binding to ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
deoxyribonuclease I activity Catalysis of the endonucleolytic cleavage of DNA to 5'-phosphodinucleotide and 5'-phosphooligonucleotide end products.
helicase activity Catalysis of the reaction
metal ion binding Binding to a metal ion.
ribonuclease III activity Catalysis of the endonucleolytic cleavage of RNA with 5'-phosphomonoesters and 3'-OH termini; makes two staggered cuts in both strands of dsRNA, leaving a 3' overhang of 2 nt.
RNA binding Binding to an RNA molecule or a portion thereof.

4 GO annotations of biological process

Name Definition
apoptotic DNA fragmentation The cleavage of DNA during apoptosis, which usually occurs in two stages
global gene silencing by mRNA cleavage A posttranscriptional gene silencing pathway that involves the cleavage of mRNAs in a non-gene-specific manner.
pre-miRNA processing A process involved in the conversion of a pre-microRNA transcript into a mature microRNA molecule.
siRNA processing A process leading to the generation of a functional small interfering RNA (siRNA). Includes the cleavage of double-stranded RNA to form small interfering RNA molecules (siRNAs) of 21-23 nucleotides. May also include amplification of the siRNA by RNA-directed RNA polymerase.

7 homologous proteins in AiPD

UniProt AC Gene Name Protein Name Species Evidence Code
Q6TUI4 DICER1 Endoribonuclease Dicer Bos taurus (Bovine) SS
Q25BN1 DICER1 Endoribonuclease Dicer Gallus gallus (Chicken) SS
Q9UPY3 DICER1 Endoribonuclease Dicer Homo sapiens (Human) EV
Q8R418 Dicer1 Endoribonuclease Dicer Mus musculus (Mouse) SS
Q6ATG6 Os05g0271300 Ribonuclease 3-like protein 2 Oryza sativa subsp japonica (Rice) PR
P34529 dcr-1 Endoribonuclease dcr-1 Caenorhabditis elegans PR
Q6TV19 dicer1 Endoribonuclease Dicer Danio rerio (Zebrafish) (Brachydanio rerio) SS
10 20 30 40 50 60
MAGLQLMTPA SSPMGPFFGL PWQQEAIHDN IYTPRKYQVE LLEAALDHNT IVCLNSGSGK
70 80 90 100 110 120
TFIAVLLSKE LSYQIRGDFS KNTKRTVFLV NSEKQVSQQV SAVRTHTDLK VGEYSDQEKT
130 140 150 160 170 180
QCWAKERWYL EFETHQVLVM TCHIFLNVLK SGNVSLSNIN LLVFDECHLA IQDHPYREIM
190 200 210 220 230 240
KICESCQPCP RILGLTASIL NGKCDPRDLE EKIQKLEEIL RSNAETATDL VVLDRYASQP
250 260 270 280 290 300
CEIVLDCGPY IDKSGLYQRL LNELDEALNF LIDCNISTHS KERDSTLISK QILSDCQTVL
310 320 330 340 350 360
LVLGPWCADK VAGMMVRELQ KYIKHEQEEL HRKFLLFTDT ILRKIHALCE EHFSPASLDM
370 380 390 400 410 420
KFVTPKVIKL LEILRKYKPY ERQQFESVEW YNNRNQDNYV SWSDSEDDDD EDEEIEEKEK
430 440 450 460 470 480
TETSFPSPFT NILCGIIFVE RRYTAVVLNR LIKEAGKQDP ELAYISSNFI TGHGIGKNQP
490 500 510 520 530 540
RNKQMEVEFR KQEEVLRKFR AHETNLLIAT SIVEEGVDIP KCNLVVRFDL PSEYRSYVQS
550 560 570 580 590 600
KGRARAPISN YIMLADSDKI KAFEEDLKTY KAIEKILRNK CSKSIDCGNT ESEPIVDDDE
610 620 630 640 650 660
IFPPYVLRQD DGSPRVTINT AIGHINRYCA RLPSDPFTHL APKCKTREFP DGLYRSTLYL
670 680 690 700 710 720
PINSPLRAPI VGPPMNCGRL ADRAVALICC KKLHEIGELD DHLMPVGKET VKYEEELDLH
730 740 750 760 770 780
DEEETSVPGR PGSTKRRQCY PKAIPECLRN SYPKPGQPCY LYVIGMVLTT PLPDELNFRR
790 800 810 820 830 840
RKLYPPEDTT RCFGILTAKP IPQIPHFPVY TRSGEVTISI ELKKSGFTLN LEQLELITRL
850 860 870 880 890 900
HQYIFSHILR LEKPALEFKP TVADCAYCVL PLNVVNDSGT LDIDFKFVED IEKSEARTGI
910 920 930 940 950 960
PNTQYSAESP FIFKLEDYQD AVIIPRQVIY RNFDQPHRFY VADVYTDLTP LSKFPSPEYE
970 980 990 1000 1010 1020
TFAEYYKTKY NLDLTNLNQP LLDVDHTSSR LNLLTPRHLN QKGKALPLSS AEKRKAKWES
1030 1040 1050 1060 1070 1080
LQNKQILVPE LCAIHPVPAS LWRKAVCLPS ILYRLHCLLT AEELRAQTAI DAGVGVKSLP
1090 1100 1110 1120 1130 1140
DDFRYPNLDF GWKRSIDSKT FISNQSSSSV ESESDCRLNK TTAPDSAASS AANSVIYMQI
1150 1160 1170 1180 1190 1200
NDQMSVNCTP PCQKSLSHLQ TVCFSDDYKA INGISCNGLT NGDWEAESAA CFQKDERITC
1210 1220 1230 1240 1250 1260
KQEIPEKSTS FHVQNLPKEN QPILKECTLS NSDGNVSKPT SDECPSTCTS DMHYDSGLSN
1270 1280 1290 1300 1310 1320
RHSSKTLGPN PGLILQALTL SNASDGFNLE RLEMLGDSFL KHAITTYLFC TYPDAHEGRL
1330 1340 1350 1360 1370 1380
SYMRSKKVSN CNLYRLGKKK GSPSRMVVSI FDPPVNWLPP GYIVNQDKNS DKWESNETSG
1390 1400 1410 1420 1430 1440
EDVMVNGKID EDFDDEEDED LMWRNPKEET DFDDDFLEYD QEHIKFIDSM LMGSGAFVKK
1450 1460 1470 1480 1490 1500
IPLSSFAPPD QNYEWRAPKK PPLESSQFPC DFDDFDYSSW DAMCYLDPSK AVEEDDFVVG
1510 1520 1530 1540 1550 1560
FWNPSEENCG ADAGKQSISY DLHTEQCIAD KSIADCVEAL LGCYLTSCGE RAAQLFLCSL
1570 1580 1590 1600 1610 1620
GLKVLPEVRK LVTNTNVISA SSSYQNSTRD NCTLTARTNT DLSSCKGIDY GYLKIPPRCM
1630 1640 1650 1660 1670 1680
FEHPDAEKTL DHLISGFENF EKKINYPFKN KAYLLQAFTH ASYHYNTITD CYQRLEFLGD
1690 1700 1710 1720 1730 1740
AILDYLITKH LYEDPRQHSP GVLTDLRSAL VNNTIFASLA VKYDYHKYFK AISPELFHVI
1750 1760 1770 1780 1790 1800
DDFVQFQLEK NEMQGMDSEL RRSEEDEEKE EDIEVPKAMG DIFESLAGAI YMDSGMSLET
1810 1820 1830 1840 1850 1860
VWHVYYPMMQ PLIEKFSANV PRSPVRELLE MEPETAKFSP AERTYDGKVR VTVEVVGKGK
1870 1880 1890
FKGVGRSYRI AKSAAARRAL RSLKANQSQV PNS