Reviewed, UniProtKB/Swiss-Prot Q9SP32 (DICER_ARATH)

Names and origin

Protein names

Recommended name:
    Endoribonuclease Dicer homolog
    EC=3.1.26.-
Alternative name(s):
    Protein CARPEL FACTORY
    Protein SHORT INTEGUMENTS 1
    Protein SUSPENSOR 1

Gene names

Name:	CAF
Synonyms:	SIN1, SUS1
Ordered Locus Names:	At1g01040
ORF Names:	T25K16.4

Organism

Arabidopsis thaliana (Mouse-ear cress) [Complete proteome]

Taxonomic identifier

3702 [NCBI]

Taxonomic lineage

Eukaryota › Viridiplantae › Streptophyta › Embryophyta › Tracheophyta › Spermatophyta › Magnoliophyta › eudicotyledons › core eudicotyledons › rosids › eurosids II › Brassicales › Brassicaceae › Arabidopsis

Protein attributes

Sequence length	1909 AA.
Sequence status	Complete.
Sequence processing	The displayed sequence is not processed.
Protein existence	Evidence at protein level.

General annotation (Comments)

Function	Probably involved in cleaving double-stranded RNA in the RNA silencing pathway. It produces 20 to 23 bp dsRNAs (siRNAs and miRNAs) which target the selective destruction of homologous RNAs. Regulates by this way the early development of the embryo.
Cofactor	Magnesium or manganese By similarity.
Subunit structure	May interact with ARGONAUTE1 or PINHEAD through their common PAZ domains By similarity.
Subcellular location	Nucleus Potential.
Tissue specificity	Highly expressed in flowers and seeds and detected in leaves and stems. Found in ovule integuments, inflorescence and floral meristems, stigma of flowers until just before pollination, vasculature of the funiculus, and embryo. Ref.1 Ref.2
Developmental stage	Detected in the embryo, but not in the suspensor, up to the globular stage. Ref.2
Miscellaneous	Expression in the early embryo is from the maternally contributed genome.
Sequence similarities	Belongs to the helicase family. Dicer subfamily. Contains 1 Dicer dsRNA-binding fold domain. Contains 2 DRBM (double-stranded RNA-binding) domains. Contains 1 helicase ATP-binding domain. Contains 1 helicase C-terminal domain. Contains 1 PAZ domain. Contains 2 RNase III domains.
Sequence caution	The sequence AAF26461.1 differs from that shown. Reason: Erroneous gene model prediction.

Ontologies

Keywords
Biological process	RNA-mediated gene silencing
Cellular component	Nucleus
Domain	Repeat
Ligand	ATP-binding Magnesium Manganese Metal-binding Nucleotide-binding RNA-binding
Molecular function	Endonuclease Helicase Hydrolase Nuclease
Technical term	Complete proteome
Gene Ontology (GO)
Biological process	cytokinesis Ref.1 Inferred from mutant phenotype. Source: TAIR embryonic pattern specification Inferred from mutant phenotype. Source: TAIR flower development Traceable author statement. Source: TAIR mRNA cleavage involved in gene silencing by miRNA Inferred from mutant phenotype. Source: TAIR primary microRNA processing Traceable author statement. Source: TAIR production of lsiRNA involved in RNA interference Inferred from mutant phenotype. Source: TAIR production of ta-siRNAs involved in RNA interference Inferred from mutant phenotype. Source: TAIR vegetative to reproductive phase transition Inferred from mutant phenotype. Source: TAIR virus induced gene silencing Inferred from mutant phenotype. Source: TAIR
Cellular component	nuclear dicing body Inferred from direct assay. Source: TAIR
Molecular function	ATP binding Inferred from electronic annotation. Source: UniProtKB-KW ATP-dependent helicase activity Inferred from electronic annotation. Source: InterPro double-stranded RNA binding Inferred from direct assay. Source: TAIR magnesium ion binding Inferred from electronic annotation. Source: UniProtKB-KW manganese ion binding Inferred from electronic annotation. Source: UniProtKB-KW protein binding Inferred from physical interaction. Source: IntAct ribonuclease III activity Inferred from electronic annotation. Source: InterPro
Complete GO annotation...

Binary interactions

With	Entry	#Exp.	IntAct	Notes
At1g09700	O04492	3	EBI-632627,EBI-632620
At3g03300	Q680B0	1	EBI-632627,EBI-632653
At3g20560/K10D20.9	Q8W4D8	1	EBI-632627,EBI-2015534
At5g41070/MEE6_14	Q8GY79	1	EBI-632627,EBI-632672

Sequence annotation (Features)

	Feature key	Position(s)	Length	Description	Graphical view	Feature identifier
Molecule processing
	Chain	1 – 1909	1909	Endoribonuclease Dicer homolog		PRO_0000180472
Regions
	Domain	256 – 433	178	Helicase ATP-binding
	Domain	651 – 812	162	Helicase C-terminal
	Domain	840 – 935	96	Dicer dsRNA-binding fold
	Domain	1180 – 1318	139	PAZ
	Domain	1342 – 1518	177	RNase III 1
	Domain	1559 – 1707	149	RNase III 2
	Domain	1733 – 1796	64	DRBM 1
	Domain	1831 – 1906	76	DRBM 2
	Nucleotide binding	249 – 256	8	ATP Potential
	Motif	378 – 381	4	DECH box
Sites
	Metal binding	1597	1	Magnesium or manganese By similarity
	Metal binding	1693	1	Magnesium or manganese By similarity
	Metal binding	1696	1	Magnesium or manganese By similarity
	Site	1689	1	Important for activity By similarity
Experimental info
	Mutagenesis	415	1	P → S in sin1-1; impaired reproductive development.
	Mutagenesis	431	1	I → K in sin1-2; impaired reproductive development.
	Mutagenesis	1837 – 1843	7	NDICLRK → IAEIDPG in caf-1; converts the floral meristem to an indeterminate state.
	Mutagenesis	1844 – 1909	66	Missing in caf-1; converts the floral meristem to an indeterminate state.
	Sequence conflict	148	1	S → F in AAF03534. Ref.1
	Sequence conflict	988	1	Y → H in AAF03534. Ref.1

Sequences

	Sequence		Length	Mass (Da)
	Q9SP32-1 [UniParc]. Last modified September 19, 2003. Version 2. Checksum: EAA944F0C0C81D4C	FASTA	1,909	213,574
	10 20 30 40 50 60 MVMEDEPREA TIKPSYWLDA CEDISCDLID DLVSEFDPSS VAVNESTDEN GVINDFFGGI 70 80 90 100 110 120 DHILDSIKNG GGLPNNGVSD TNSQINEVTV TPQVIAKETV KENGLQKNGG KRDEFSKEEG 130 140 150 160 170 180 DKDRKRARVC SYQSERSNLS GRGHVNNSRE GDRFMNRKRT RNWDEAGNNK KKRECNNYRR 190 200 210 220 230 240 DGRDREVRGY WERDKVGSNE LVYRSGTWEA DHERDVKKVS GGNRECDVKA EENKSKPEER 250 260 270 280 290 300 KEKVVEEQAR RYQLDVLEQA KAKNTIAFLE TGAGKTLIAI LLIKSVHKDL MSQNRKMLSV 310 320 330 340 350 360 FLVPKVPLVY QQAEVIRNQT CFQVGHYCGE MGQDFWDSRR WQREFESKQV LVMTAQILLN 370 380 390 400 410 420 ILRHSIIRME TIDLLILDEC HHAVKKHPYS LVMSEFYHTT PKDKRPAIFG MTASPVNLKG 430 440 450 460 470 480 VSSQVDCAIK IRNLETKLDS TVCTIKDRKE LEKHVPMPSE IVVEYDKAAT MWSLHETIKQ 490 500 510 520 530 540 MIAAVEEAAQ ASSRKSKWQF MGARDAGAKD ELRQVYGVSE RTESDGAANL IHKLRAINYT 550 560 570 580 590 600 LAELGQWCAY KVGQSFLSAL QSDERVNFQV DVKFQESYLS EVVSLLQCEL LEGAAAEKVA 610 620 630 640 650 660 AEVGKPENGN AHDEMEEGEL PDDPVVSGGE HVDEVIGAAV ADGKVTPKVQ SLIKLLLKYQ 670 680 690 700 710 720 HTADFRAIVF VERVVAALVL PKVFAELPSL SFIRCASMIG HNNSQEMKSS QMQDTISKFR 730 740 750 760 770 780 DGHVTLLVAT SVAEEGLDIR QCNVVMRFDL AKTVLAYIQS RGRARKPGSD YILMVERGNV 790 800 810 820 830 840 SHAAFLRNAR NSEETLRKEA IERTDLSHLK DTSRLISIDA VPGTVYKVEA TGAMVSLNSA 850 860 870 880 890 900 VGLVHFYCSQ LPGDRYAILR PEFSMEKHEK PGGHTEYSCR LQLPCNAPFE ILEGPVCSSM 910 920 930 940 950 960 RLAQQAVCLA ACKKLHEMGA FTDMLLPDKG SGQDAEKADQ DDEGEPVPGT ARHREFYPEG 970 980 990 1000 1010 1020 VADVLKGEWV SSGKEVCESS KLFHLYMYNV RCVDFGSSKD PFLSEVSEFA ILFGNELDAE 1030 1040 1050 1060 1070 1080 VLSMSMDLYV ARAMITKASL AFKGSLDITE NQLSSLKKFH VRLMSIVLDV DVEPSTTPWD 1090 1100 1110 1120 1130 1140 PAKAYLFVPV TDNTSMEPIK GINWELVEKI TKTTAWDNPL QRARPDVYLG TNERTLGGDR 1150 1160 1170 1180 1190 1200 REYGFGKLRH NIVFGQKSHP TYGIRGAVAS FDVVRASGLL PVRDAFEKEV EEDLSKGKLM 1210 1220 1230 1240 1250 1260 MADGCMVAED LIGKIVTAAH SGKRFYVDSI CYDMSAETSF PRKEGYLGPL EYNTYADYYK 1270 1280 1290 1300 1310 1320 QKYGVDLNCK QQPLIKGRGV SYCKNLLSPR FEQSGESETV LDKTYYVFLP PELCVVHPLS 1330 1340 1350 1360 1370 1380 GSLIRGAQRL PSIMRRVESM LLAVQLKNLI SYPIPTSKIL EALTAASCQE TFCYERAELL 1390 1400 1410 1420 1430 1440 GDAYLKWVVS RFLFLKYPQK HEGQLTRMRQ QMVSNMVLYQ FALVKGLQSY IQADRFAPSR 1450 1460 1470 1480 1490 1500 WSAPGVPPVF DEDTKDGGSS FFDEEQKPVS EENSDVFEDG EMEDGELEGD LSSYRVLSSK 1510 1520 1530 1540 1550 1560 TLADVVEALI GVYYVEGGKI AANHLMKWIG IHVEDDPDEV DGTLKNVNVP ESVLKSIDFV 1570 1580 1590 1600 1610 1620 GLERALKYEF KEKGLLVEAI THASRPSSGV SCYQRLEFVG DAVLDHLITR HLFFTYTSLP 1630 1640 1650 1660 1670 1680 PGRLTDLRAA AVNNENFARV AVKHKLHLYL RHGSSALEKQ IREFVKEVQT ESSKPGFNSF 1690 1700 1710 1720 1730 1740 GLGDCKAPKV LGDIVESIAG AIFLDSGKDT TAAWKVFQPL LQPMVTPETL PMHPVRELQE 1750 1760 1770 1780 1790 1800 RCQQQAEGLE YKASRSGNTA TVEVFIDGVQ VGVAQNPQKK MAQKLAARNA LAALKEKEIA 1810 1820 1830 1840 1850 1860 ESKEKHINNG NAGEDQGENE NGNKKNGHQP FTRQTLNDIC LRKNWPMPSY RCVKEGGPAH 1870 1880 1890 1900 AKRFTFGVRV NTSDRGWTDE CIGEPMPSVK KAKDSAAVLL LELLNKTFS

References

	« Hide 'large scale' referencesShow 'large scale' references »
[1]	"Disruption of an RNA helicase/RNase III gene in Arabidopsis causes unregulated cell division in floral meristems." Jacobsen S.E., Running M.P., Meyerowitz E.M. Development 126:5231-5243(1999) [PubMed: 10556049] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [MRNA], TISSUE SPECIFICITY, MUTANT CAF-1. Strain: cv. Wassilewskija.
[2]	"SHORT INTEGUMENTS1/SUSPENSOR1/CARPEL FACTORY, a Dicer homolog, is a maternal effect gene required for embryo development in Arabidopsis." Golden T.A., Schauer S.E., Lang J.D., Pien S., Mushegian A.R., Grossniklaus U., Meinke D.W., Ray A. Plant Physiol. 130:808-822(2002) [PubMed: 12376646] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA / MRNA], TISSUE SPECIFICITY, DEVELOPMENTAL STAGE, MUTANTS SIN1-1 AND SIN1-2. Strain: cv. Landsberg erecta.
[3]	"Sequence and analysis of chromosome 1 of the plant Arabidopsis thaliana." Theologis A., Ecker J.R., Palm C.J., Federspiel N.A., Kaul S., White O., Alonso J., Altafi H., Araujo R., Bowman C.L., Brooks S.Y., Buehler E., Chan A., Chao Q., Chen H., Cheuk R.F., Chin C.W., Chung M.K. , Conn L., Conway A.B., Conway A.R., Creasy T.H., Dewar K., Dunn P., Etgu P., Feldblyum T.V., Feng J.-D., Fong B., Fujii C.Y., Gill J.E., Goldsmith A.D., Haas B., Hansen N.F., Hughes B., Huizar L., Hunter J.L., Jenkins J., Johnson-Hopson C., Khan S., Khaykin E., Kim C.J., Koo H.L., Kremenetskaia I., Kurtz D.B., Kwan A., Lam B., Langin-Hooper S., Lee A., Lee J.M., Lenz C.A., Li J.H., Li Y.-P., Lin X., Liu S.X., Liu Z.A., Luros J.S., Maiti R., Marziali A., Militscher J., Miranda M., Nguyen M., Nierman W.C., Osborne B.I., Pai G., Peterson J., Pham P.K., Rizzo M., Rooney T., Rowley D., Sakano H., Salzberg S.L., Schwartz J.R., Shinn P., Southwick A.M., Sun H., Tallon L.J., Tambunga G., Toriumi M.J., Town C.D., Utterback T., Van Aken S., Vaysberg M., Vysotskaia V.S., Walker M., Wu D., Yu G., Fraser C.M., Venter J.C., Davis R.W. Nature 408:816-820(2000) [PubMed: 11130712] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA]. Strain: cv. Columbia.
+	Additional computationally mapped references.

Cross-references

Sequence databases
EMBLGenBankDDBJ	AF187317 mRNA. Translation: AAF03534.1. AF292941 Genomic DNA. Translation: AAG38020.1. AF292940 mRNA. Translation: AAG38019.1. AC007323 Genomic DNA. Translation: AAF26461.1. Sequence problems.
IPI	IPI00541769.
RefSeq	NP_171612.1.
UniGene	At.22088
3D structure databases
ModBase	Search...
Protein-protein interaction databases
IntAct	Q9SP32. 4 interactions.
STRING	Q9SP32.
Proteomic databases
PRIDE	Q9SP32.
Genome annotation databases
GeneID	839574.
GenomeReviews	Gene locus AT1G01040 in contig CT485782_GR.
KEGG	ath:AT1G01040.
NMPDR	fig|3702.1.peg.206.
Organism-specific databases
TAIR	At1g01040.
Phylogenomic databases
OMA	NTIAFLE
Gene expression databases
ArrayExpress	Q9SP32.
Genevestigator	Q9SP32.
GermOnline	AT1G01040. Arabidopsis thaliana.
Family and domain databases
InterPro	IPR014001. DEAD-like_N. IPR005034. Dicer_dsRNA_binding_fold. IPR001650. DNA/RNA_helicase_C. IPR011545. DNA/RNA_helicase_DEAD/DEAH_N. IPR001159. Ds-RNA_bd. IPR014720. dsRNA-bd-like. IPR014021. Helicase_SF1/SF2_ATP-bd. IPR003100. PAZ. IPR000999. RNase_III. [Graphical view]
Gene3D	G3DSA:3.30.160.20. dsRNA-bd-like. 1 hit. G3DSA:1.10.1520.10. RNase_III. 2 hits.
Pfam	PF00270. DEAD. 1 hit. PF00035. dsrm. 2 hits. PF03368. dsRNA_bind. 1 hit. PF00271. Helicase_C. 1 hit. PF02170. PAZ. 1 hit. PF00636. Ribonuclease_3. 2 hits. [Graphical view]
SMART	SM00487. DEXDc. 1 hit. SM00358. DSRM. 2 hits. SM00490. HELICc. 1 hit. SM00535. RIBOc. 2 hits. [Graphical view]
PROSITE	PS51327. DICER_DSRBF. 1 hit. PS50137. DS_RBD. 2 hits. PS51192. HELICASE_ATP_BIND_1. 1 hit. PS51194. HELICASE_CTER. 1 hit. PS50821. PAZ. 1 hit. PS00517. RNASE_3_1. 1 hit. PS50142. RNASE_3_2. 2 hits. [Graphical view]
ProtoNet	Search...

Entry information

Entry name

DICER_ARATH

Accession

Primary (citable) accession number: Q9SP32
Secondary accession number(s): Q9FDY6, Q9MAN0

Entry history

Integrated into UniProtKB/Swiss-Prot:	September 19, 2003
Last sequence update:	September 19, 2003
Last modified:	November 24, 2009
This is version 72 of the entry and version 2 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation project

PPAP (Plant Proteome Annotation Project)