2FFL | pdb_00002ffl

Crystal Structure of Dicer from Giardia intestinalis

External Resource: Annotation

Domain Annotation: ECOD Classification
Domain Annotation: CATH
Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
A	PAZ	e2fflA2	A: beta barrels	X: SH3	H: SH3	T: SH3	F: PAZ	ECOD (1.6)
A	Ribonucleas_3_3	e2fflA3	A: alpha arrays	X: RNase III catalytic domain-like (From Topology)	H: RNase III catalytic domain-like (From Topology)	T: RNase III catalytic domain-like	F: Ribonucleas_3_3	ECOD (1.6)
A	EUF08014	e2fflA4	A: alpha arrays	X: Giardia Dicer helical domain bridging RNase IIIa and RNase IIIb (From Topology)	H: Giardia Dicer helical domain bridging RNase IIIa and RNase IIIb (From Topology)	T: Giardia Dicer helical domain bridging RNase IIIa and RNase IIIb	F: EUF08014	ECOD (1.6)
A	EUF08458	e2fflA1	A: a+b two layers	X: Giardia Dicer N-terminal domain (From Topology)	H: Giardia Dicer N-terminal domain (From Topology)	T: Giardia Dicer N-terminal domain	F: EUF08458	ECOD (1.6)
B	PAZ	e2fflB1	A: beta barrels	X: SH3	H: SH3	T: SH3	F: PAZ	ECOD (1.6)
B	Ribonucleas_3_3	e2fflB2	A: alpha arrays	X: RNase III catalytic domain-like (From Topology)	H: RNase III catalytic domain-like (From Topology)	T: RNase III catalytic domain-like	F: Ribonucleas_3_3	ECOD (1.6)
B	EUF08014	e2fflB3	A: alpha arrays	X: Giardia Dicer helical domain bridging RNase IIIa and RNase IIIb (From Topology)	H: Giardia Dicer helical domain bridging RNase IIIa and RNase IIIb (From Topology)	T: Giardia Dicer helical domain bridging RNase IIIa and RNase IIIb	F: EUF08014	ECOD (1.6)
B	EUF08458	e2fflB5	A: a+b two layers	X: Giardia Dicer N-terminal domain (From Topology)	H: Giardia Dicer N-terminal domain (From Topology)	T: Giardia Dicer N-terminal domain	F: EUF08458	ECOD (1.6)
C	PAZ	e2fflC4	A: beta barrels	X: SH3	H: SH3	T: SH3	F: PAZ	ECOD (1.6)
C	Ribonucleas_3_3	e2fflC2	A: alpha arrays	X: RNase III catalytic domain-like (From Topology)	H: RNase III catalytic domain-like (From Topology)	T: RNase III catalytic domain-like	F: Ribonucleas_3_3	ECOD (1.6)
C	EUF08014	e2fflC1	A: alpha arrays	X: Giardia Dicer helical domain bridging RNase IIIa and RNase IIIb (From Topology)	H: Giardia Dicer helical domain bridging RNase IIIa and RNase IIIb (From Topology)	T: Giardia Dicer helical domain bridging RNase IIIa and RNase IIIb	F: EUF08014	ECOD (1.6)
C	EUF08458	e2fflC3	A: a+b two layers	X: Giardia Dicer N-terminal domain (From Topology)	H: Giardia Dicer N-terminal domain (From Topology)	T: Giardia Dicer N-terminal domain	F: EUF08458	ECOD (1.6)
D	PAZ	e2fflD4	A: beta barrels	X: SH3	H: SH3	T: SH3	F: PAZ	ECOD (1.6)
D	Ribonucleas_3_3	e2fflD2	A: alpha arrays	X: RNase III catalytic domain-like (From Topology)	H: RNase III catalytic domain-like (From Topology)	T: RNase III catalytic domain-like	F: Ribonucleas_3_3	ECOD (1.6)
D	EUF08014	e2fflD1	A: alpha arrays	X: Giardia Dicer helical domain bridging RNase IIIa and RNase IIIb (From Topology)	H: Giardia Dicer helical domain bridging RNase IIIa and RNase IIIb (From Topology)	T: Giardia Dicer helical domain bridging RNase IIIa and RNase IIIb	F: EUF08014	ECOD (1.6)
D	EUF08458	e2fflD3	A: a+b two layers	X: Giardia Dicer N-terminal domain (From Topology)	H: Giardia Dicer N-terminal domain (From Topology)	T: Giardia Dicer N-terminal domain	F: EUF08458	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	2.170.260.10	Mainly Beta	Beta Complex	paz domain	paz domain	CATH (4.3.0)
A	6.10.250.1440	Special	Helix non-globular	Single alpha-helices involved in coiled-coils or other helix-helix interfaces		CATH (4.3.0)
A	1.10.1520.10	Mainly Alpha	Orthogonal Bundle	Ribonuclease iii, N-terminal Endonuclease Domain	Chain A	CATH (4.3.0)
A	1.10.1740.150	Mainly Alpha	Orthogonal Bundle	Rna Polymerase Sigma Factor	Chain: A	CATH (4.3.0)
B	2.170.260.10	Mainly Beta	Beta Complex	paz domain	paz domain	CATH (4.3.0)
B	6.10.250.1440	Special	Helix non-globular	Single alpha-helices involved in coiled-coils or other helix-helix interfaces		CATH (4.3.0)
B	1.10.1520.10	Mainly Alpha	Orthogonal Bundle	Ribonuclease iii, N-terminal Endonuclease Domain	Chain A	CATH (4.3.0)
B	1.10.1740.150	Mainly Alpha	Orthogonal Bundle	Rna Polymerase Sigma Factor	Chain: A	CATH (4.3.0)
C	2.170.260.10	Mainly Beta	Beta Complex	paz domain	paz domain	CATH (4.3.0)
C	6.10.250.1440	Special	Helix non-globular	Single alpha-helices involved in coiled-coils or other helix-helix interfaces		CATH (4.3.0)
C	1.10.1520.10	Mainly Alpha	Orthogonal Bundle	Ribonuclease iii, N-terminal Endonuclease Domain	Chain A	CATH (4.3.0)
C	1.10.1740.150	Mainly Alpha	Orthogonal Bundle	Rna Polymerase Sigma Factor	Chain: A	CATH (4.3.0)
D	2.170.260.10	Mainly Beta	Beta Complex	paz domain	paz domain	CATH (4.3.0)
D	6.10.250.1440	Special	Helix non-globular	Single alpha-helices involved in coiled-coils or other helix-helix interfaces		CATH (4.3.0)
D	1.10.1520.10	Mainly Alpha	Orthogonal Bundle	Ribonuclease iii, N-terminal Endonuclease Domain	Chain A	CATH (4.3.0)
D	1.10.1740.150	Mainly Alpha	Orthogonal Bundle	Rna Polymerase Sigma Factor	Chain: A	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B, C, D	PF02170	PAZ domain (PAZ)	PAZ domain	This domain is named PAZ after the proteins Piwi Argonaut and Zwille. This domain is found in two families of proteins that are involved in post-transcriptional gene silencing. These are the Piwi family and the Dicer family, that includes the Carpel ...	This domain is named PAZ after the proteins Piwi Argonaut and Zwille. This domain is found in two families of proteins that are involved in post-transcriptional gene silencing. These are the Piwi family and the Dicer family, that includes the Carpel factory protein. The function of the domains is unknown but has been suggested to mediate complex formation between proteins of the Piwi and Dicer families by hetero-dimerisation. The three-dimensional structure of this domain has been solved [2-4]. The PAZ domain is composed of two subdomains. One subdomain is similar to the OB fold, albeit with a different topology. The OB-fold is well known as a single-stranded nucleic acid binding fold. The second subdomain is composed of a beta-hairpin followed by an alpha-helix. The PAZ domains shows low-affinity nucleic acid binding and appears to interact with the 3' ends of single-stranded regions of RNA in the cleft between the two subdomains. PAZ can bind the characteristic two-base 3' overhangs of siRNAs, indicating that although PAZ may not be a primary nucleic acid binding site in Dicer or RISC, it may contribute to the specific and productive incorporation of siRNAs and miRNAs into the RNAi pathway.	Domain
A, B, C, D	PF00636	Ribonuclease III domain (Ribonuclease_3)	Ribonuclease III domain	-	Family
A, B, C, D	PF17895	Giardia Dicer N-terminal domain (Dicer_N)	Giardia Dicer N-terminal domain	This is the N-terminal domain found in dicer proteins from Giardia intestinalis. The N-terminal region (i.e. the platform domain) forms a flat surface composed of antiparallel beta sheet and three alpha helices. This surface contains a large positive ...	This is the N-terminal domain found in dicer proteins from Giardia intestinalis. The N-terminal region (i.e. the platform domain) forms a flat surface composed of antiparallel beta sheet and three alpha helices. This surface contains a large positively charged region that could interact directly with the negatively charged phosphodiester backbone of the modeled dsRNA helix [1].	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B, C, D	Dicer	ribonuclease III activity double-stranded RNA-specific ribonuclease activity endonuclease activity RNA endonuclease activity, producing 5'-phosphomonoesters catalytic activity, acting on RNA catalytic activity, acting on a nucleic acid RNA nuclease activity hydrolase activity nuclease activity hydrolase activity, acting on ester bonds RNA endonuclease activity catalytic activity RNA binding binding ribonuclease III activity double-stranded RNA-specific ribonuclease activity endonuclease activity RNA endonuclease activity, producing 5'-phosphomonoesters catalytic activity, acting on RNA catalytic activity, acting on a nucleic acid RNA nuclease activity hydrolase activity nuclease activity hydrolase activity, acting on ester bonds RNA endonuclease activity catalytic activity RNA binding binding nucleic acid binding nucleoside phosphate binding nucleotide binding heterocyclic compound binding small molecule binding cation binding ion binding metal ion binding	regulation of biosynthetic process regulation of biological process regulation of cellular process negative regulation of metabolic process biological regulation negative regulation of biological process regulation of macromolecule metabolic process gene expression macromolecule biosynthetic process regulatory ncRNA-mediated gene silencing regulation of gene expression negative regulation of gene expression biosynthetic process negative regulation of biosynthetic process negative regulation of macromolecule biosynthetic process regulation of biosynthetic process regulation of biological process regulation of cellular process negative regulation of metabolic process biological regulation negative regulation of biological process regulation of macromolecule metabolic process gene expression macromolecule biosynthetic process regulatory ncRNA-mediated gene silencing regulation of gene expression negative regulation of gene expression biosynthetic process negative regulation of biosynthetic process negative regulation of macromolecule biosynthetic process negative regulation of cellular process regulation of macromolecule biosynthetic process metabolic process cellular process macromolecule metabolic process regulation of metabolic process negative regulation of macromolecule metabolic process RNA metabolic process primary metabolic process nucleobase-containing compound biosynthetic process nucleic acid metabolic process RNA biosynthetic process nucleobase-containing compound metabolic process nucleic acid biosynthetic process RNA processing	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B, C, D	IPR036085	PAZ domain superfamily	Homologous Superfamily
A, B, C, D	IPR000999	Ribonuclease III domain	Domain
A, B, C, D	IPR041279	Giardia dicer, N-terminal	Domain
A, B, C, D	IPR003100	PAZ domain	Domain
A, B, C, D	IPR036389	Ribonuclease III, endonuclease domain superfamily	Homologous Superfamily

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.