4XR7

Structure of the Saccharomyces cerevisiae PAN2-PAN3 core complex

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 [auth G]	UCH	e4xr7G2	A: a+b complex topology	X: Cysteine proteinases-like	H: Cysteine proteinases (From Topology)	T: Cysteine proteinases	F: UCH	ECOD (1.6)
A [auth G]	RNase_T	e4xr7G1	A: mixed a+b and a/b	X: Ribonuclease H-like	H: Ribonuclease H-like (From Topology)	T: Ribonuclease H-like	F: RNase_T	ECOD (1.6)
F [auth D]	UCH	e4xr7D1	A: a+b complex topology	X: Cysteine proteinases-like	H: Cysteine proteinases (From Topology)	T: Cysteine proteinases	F: UCH	ECOD (1.6)
F [auth D]	RNase_T	e4xr7D2	A: mixed a+b and a/b	X: Ribonuclease H-like	H: Ribonuclease H-like (From Topology)	T: Ribonuclease H-like	F: RNase_T	ECOD (1.6)
I [auth J]	UCH	e4xr7J2	A: a+b complex topology	X: Cysteine proteinases-like	H: Cysteine proteinases (From Topology)	T: Cysteine proteinases	F: UCH	ECOD (1.6)
I [auth J]	RNase_T	e4xr7J1	A: mixed a+b and a/b	X: Ribonuclease H-like	H: Ribonuclease H-like (From Topology)	T: Ribonuclease H-like	F: RNase_T	ECOD (1.6)
L [auth A]	UCH	e4xr7A1	A: a+b complex topology	X: Cysteine proteinases-like	H: Cysteine proteinases (From Topology)	T: Cysteine proteinases	F: UCH	ECOD (1.6)
L [auth A]	RNase_T	e4xr7A2	A: mixed a+b and a/b	X: Ribonuclease H-like	H: Ribonuclease H-like (From Topology)	T: Ribonuclease H-like	F: RNase_T	ECOD (1.6)
B [auth L]	F_UNCLASSIFIED	e4xr7L3	A: alpha arrays	X: Dimerization domain in caprin-1 and PAN3 (From Topology)	H: Dimerization domain in caprin-1 and PAN3 (From Topology)	T: Dimerization domain in caprin-1 and PAN3	F: F_UNCLASSIFIED	ECOD (1.6)
B [auth L]	Pkinase_Tyr	e4xr7L2	A: a+b complex topology	X: Protein kinase/SAICAR synthase/ATP-grasp (From Homology)	H: Protein kinase/SAICAR synthase/ATP-grasp	T: Protein kinase	F: Pkinase_Tyr	ECOD (1.6)
C [auth K]	F_UNCLASSIFIED	e4xr7K3	A: alpha arrays	X: Dimerization domain in caprin-1 and PAN3 (From Topology)	H: Dimerization domain in caprin-1 and PAN3 (From Topology)	T: Dimerization domain in caprin-1 and PAN3	F: F_UNCLASSIFIED	ECOD (1.6)
C [auth K]	Pkinase_Tyr	e4xr7K2	A: a+b complex topology	X: Protein kinase/SAICAR synthase/ATP-grasp (From Homology)	H: Protein kinase/SAICAR synthase/ATP-grasp	T: Protein kinase	F: Pkinase_Tyr	ECOD (1.6)
D [auth E]	F_UNCLASSIFIED	e4xr7E2	A: alpha arrays	X: Dimerization domain in caprin-1 and PAN3 (From Topology)	H: Dimerization domain in caprin-1 and PAN3 (From Topology)	T: Dimerization domain in caprin-1 and PAN3	F: F_UNCLASSIFIED	ECOD (1.6)
D [auth E]	Pkinase_Tyr	e4xr7E1	A: a+b complex topology	X: Protein kinase/SAICAR synthase/ATP-grasp (From Homology)	H: Protein kinase/SAICAR synthase/ATP-grasp	T: Protein kinase	F: Pkinase_Tyr	ECOD (1.6)
E [auth F]	F_UNCLASSIFIED	e4xr7F3	A: alpha arrays	X: Dimerization domain in caprin-1 and PAN3 (From Topology)	H: Dimerization domain in caprin-1 and PAN3 (From Topology)	T: Dimerization domain in caprin-1 and PAN3	F: F_UNCLASSIFIED	ECOD (1.6)
E [auth F]	Pkinase_Tyr	e4xr7F2	A: a+b complex topology	X: Protein kinase/SAICAR synthase/ATP-grasp (From Homology)	H: Protein kinase/SAICAR synthase/ATP-grasp	T: Protein kinase	F: Pkinase_Tyr	ECOD (1.6)
G [auth H]	F_UNCLASSIFIED	e4xr7H3	A: alpha arrays	X: Dimerization domain in caprin-1 and PAN3 (From Topology)	H: Dimerization domain in caprin-1 and PAN3 (From Topology)	T: Dimerization domain in caprin-1 and PAN3	F: F_UNCLASSIFIED	ECOD (1.6)
G [auth H]	Pkinase_Tyr	e4xr7H2	A: a+b complex topology	X: Protein kinase/SAICAR synthase/ATP-grasp (From Homology)	H: Protein kinase/SAICAR synthase/ATP-grasp	T: Protein kinase	F: Pkinase_Tyr	ECOD (1.6)
H [auth I]	F_UNCLASSIFIED	e4xr7I3	A: alpha arrays	X: Dimerization domain in caprin-1 and PAN3 (From Topology)	H: Dimerization domain in caprin-1 and PAN3 (From Topology)	T: Dimerization domain in caprin-1 and PAN3	F: F_UNCLASSIFIED	ECOD (1.6)
H [auth I]	Pkinase_Tyr	e4xr7I2	A: a+b complex topology	X: Protein kinase/SAICAR synthase/ATP-grasp (From Homology)	H: Protein kinase/SAICAR synthase/ATP-grasp	T: Protein kinase	F: Pkinase_Tyr	ECOD (1.6)
J [auth C]	F_UNCLASSIFIED	e4xr7C2	A: alpha arrays	X: Dimerization domain in caprin-1 and PAN3 (From Topology)	H: Dimerization domain in caprin-1 and PAN3 (From Topology)	T: Dimerization domain in caprin-1 and PAN3	F: F_UNCLASSIFIED	ECOD (1.6)
J [auth C]	Pkinase_Tyr	e4xr7C1	A: a+b complex topology	X: Protein kinase/SAICAR synthase/ATP-grasp (From Homology)	H: Protein kinase/SAICAR synthase/ATP-grasp	T: Protein kinase	F: Pkinase_Tyr	ECOD (1.6)
K [auth B]	F_UNCLASSIFIED	e4xr7B2	A: alpha arrays	X: Dimerization domain in caprin-1 and PAN3 (From Topology)	H: Dimerization domain in caprin-1 and PAN3 (From Topology)	T: Dimerization domain in caprin-1 and PAN3	F: F_UNCLASSIFIED	ECOD (1.6)
K [auth B]	Pkinase_Tyr	e4xr7B1	A: a+b complex topology	X: Protein kinase/SAICAR synthase/ATP-grasp (From Homology)	H: Protein kinase/SAICAR synthase/ATP-grasp	T: Protein kinase	F: Pkinase_Tyr	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A [auth G]	3.90.70.10	Alpha Beta	Alpha-Beta Complex	Cathepsin B	Chain A	CATH (4.3.0)
F [auth D]	3.90.70.10	Alpha Beta	Alpha-Beta Complex	Cathepsin B	Chain A	CATH (4.3.0)
I [auth J]	3.90.70.10	Alpha Beta	Alpha-Beta Complex	Cathepsin B	Chain A	CATH (4.3.0)
L [auth A]	3.90.70.10	Alpha Beta	Alpha-Beta Complex	Cathepsin B	Chain A	CATH (4.3.0)
B [auth L]	1.10.510.10	Mainly Alpha	Orthogonal Bundle	Transferase(Phosphotransferase)	domain 1	CATH (4.3.0)
B [auth L]	1.10.287.3700	Mainly Alpha	Orthogonal Bundle	Helix Hairpins		CATH (4.3.0)
C [auth K]	1.10.510.10	Mainly Alpha	Orthogonal Bundle	Transferase(Phosphotransferase)	domain 1	CATH (4.3.0)
C [auth K]	1.10.287.3700	Mainly Alpha	Orthogonal Bundle	Helix Hairpins		CATH (4.3.0)
D [auth E]	1.10.510.10	Mainly Alpha	Orthogonal Bundle	Transferase(Phosphotransferase)	domain 1	CATH (4.3.0)
D [auth E]	1.10.287.3700	Mainly Alpha	Orthogonal Bundle	Helix Hairpins		CATH (4.3.0)
E [auth F]	1.10.510.10	Mainly Alpha	Orthogonal Bundle	Transferase(Phosphotransferase)	domain 1	CATH (4.3.0)
E [auth F]	1.10.287.3700	Mainly Alpha	Orthogonal Bundle	Helix Hairpins		CATH (4.3.0)
G [auth H]	1.10.510.10	Mainly Alpha	Orthogonal Bundle	Transferase(Phosphotransferase)	domain 1	CATH (4.3.0)
G [auth H]	1.10.287.3700	Mainly Alpha	Orthogonal Bundle	Helix Hairpins		CATH (4.3.0)
H [auth I]	1.10.510.10	Mainly Alpha	Orthogonal Bundle	Transferase(Phosphotransferase)	domain 1	CATH (4.3.0)
H [auth I]	1.10.287.3700	Mainly Alpha	Orthogonal Bundle	Helix Hairpins		CATH (4.3.0)
J [auth C]	1.10.510.10	Mainly Alpha	Orthogonal Bundle	Transferase(Phosphotransferase)	domain 1	CATH (4.3.0)
J [auth C]	1.10.287.3700	Mainly Alpha	Orthogonal Bundle	Helix Hairpins		CATH (4.3.0)
K [auth B]	1.10.510.10	Mainly Alpha	Orthogonal Bundle	Transferase(Phosphotransferase)	domain 1	CATH (4.3.0)
K [auth B]	1.10.287.3700	Mainly Alpha	Orthogonal Bundle	Helix Hairpins		CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A [auth G], F [auth D], I [auth J], L [auth A]	PF00929	Exonuclease (RNase_T)	Exonuclease	-	Family
A [auth G], F [auth D], I [auth J], L [auth A]	PF13423	Ubiquitin carboxyl-terminal hydrolase (UCH_1)	Ubiquitin carboxyl-terminal hydrolase	This is the ubiquitin carboxyl-terminal hydrolase domain found in a variety of proteins, including PAN2, one of the subunits of the poly(A)-specific nuclease (PAN) is a deadenylating enzyme involved in cytoplasmic mRNA turnover (consisting of PAN2 an ...	This is the ubiquitin carboxyl-terminal hydrolase domain found in a variety of proteins, including PAN2, one of the subunits of the poly(A)-specific nuclease (PAN) is a deadenylating enzyme involved in cytoplasmic mRNA turnover (consisting of PAN2 and PAN3), involved in the initial trimming of poly(A) tails [1-3].	Domain
B [auth L], C [auth K], D [auth E], E [auth F], G [auth H], B [auth L], C [auth K], D [auth E], E [auth F], G [auth H], H [auth I], J [auth C], K [auth B]	PF18101	Pan3 Pseudokinase domain (Pan3_PK)	Pan3 Pseudokinase domain	This is a pseudokinase (PK) domain found in PAB-dependent poly(A)-specific ribonuclease subunit pan3. PAN3 proteins contain three prominent regions: an unstructured N-terminal region (N-term), a central PK domain, and a highly conserved C-terminal d ...	This is a pseudokinase (PK) domain found in PAB-dependent poly(A)-specific ribonuclease subunit pan3. PAN3 proteins contain three prominent regions: an unstructured N-terminal region (N-term), a central PK domain, and a highly conserved C-terminal domain (C-term). The PAN3 PK domain has retained its ATP binding capacity, and this function is required for mRNA degradation in vivo. Analysis of Pan3 amino acids sequences show that, despite of retaining the general structural characteristics of protein kinases, the PK domain has substitutions in all the conserved motifs that are critical for kinase activity, such as in the catalytic VAIK and HRD motifs and in the Mg2+ binding DFG motif. However, the PAN3 PK domain has been shown to bind ATP. Furthermore, similar to other kinases, the ATP-binding site is located in the cleft between the N- and C-lobes of the kinase fold, however, the ATP-binding pocket is wider than that of typical kinases [3].	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A [auth G], F [auth D], I [auth J], L [auth A]	PAB-dependent poly(A)-specific ribonuclease subunit PAN2	binding organic cyclic compound binding nucleic acid binding 3'-5'-RNA exonuclease activity catalytic activity, acting on RNA RNA exonuclease activity, producing 5'-phosphomonoesters catalytic activity, acting on a nucleic acid 3'-5' exonuclease activity RNA exonuclease activity RNA nuclease activity hydrolase activity poly(A)-specific ribonuclease activity exonuclease activity, active with either ribo- or deoxyribonucleic acids and producing 5'-phosphomonoesters nuclease activity binding organic cyclic compound binding nucleic acid binding 3'-5'-RNA exonuclease activity catalytic activity, acting on RNA RNA exonuclease activity, producing 5'-phosphomonoesters catalytic activity, acting on a nucleic acid 3'-5' exonuclease activity RNA exonuclease activity RNA nuclease activity hydrolase activity poly(A)-specific ribonuclease activity exonuclease activity, active with either ribo- or deoxyribonucleic acids and producing 5'-phosphomonoesters nuclease activity hydrolase activity, acting on ester bonds exonuclease activity catalytic activity cation binding ion binding metal ion binding small molecule binding	regulation of cellular process negative regulation of biological process negative regulation of cellular metabolic process regulation of primary metabolic process nucleobase-containing compound metabolic process positive regulation of metabolic process post-transcriptional regulation of gene expression regulation of RNA metabolic process organic substance biosynthetic process positive regulation of macromolecule metabolic process regulation of nucleobase-containing compound metabolic process regulation of biological quality RNA catabolic process mRNA catabolic process regulation of cellular process negative regulation of biological process negative regulation of cellular metabolic process regulation of primary metabolic process nucleobase-containing compound metabolic process positive regulation of metabolic process post-transcriptional regulation of gene expression regulation of RNA metabolic process organic substance biosynthetic process positive regulation of macromolecule metabolic process regulation of nucleobase-containing compound metabolic process regulation of biological quality RNA catabolic process mRNA catabolic process regulation of biological process positive regulation of nucleobase-containing compound metabolic process cellular metabolic process negative regulation of metabolic process positive regulation of mRNA metabolic process regulation of cellular metabolic process primary metabolic process negative regulation of cellular biosynthetic process nucleobase-containing compound catabolic process nuclear-transcribed mRNA poly(A) tail shortening positive regulation of RNA metabolic process regulation of gene expression organic cyclic compound metabolic process negative regulation of gene expression biosynthetic process negative regulation of macromolecule biosynthetic process nucleic acid catabolic process regulation of macromolecule biosynthetic process metabolic process macromolecule metabolic process regulation of metabolic process nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay catabolic process cellular biosynthetic process positive regulation of biological process RNA metabolic process macromolecule catabolic process mRNA destabilization organic substance metabolic process regulation of mRNA catabolic process negative regulation of cellular process negative regulation of macromolecule metabolic process regulation of biosynthetic process nuclear-transcribed mRNA catabolic process RNA destabilization biological regulation regulation of macromolecule metabolic process regulation of catabolic process gene expression macromolecule biosynthetic process mRNA metabolic process nucleic acid metabolic process organic cyclic compound catabolic process regulation of cellular biosynthetic process positive regulation of catabolic process regulation of mRNA stability negative regulation of biosynthetic process positive regulation of mRNA catabolic process regulation of RNA stability cellular process regulation of mRNA metabolic process organic substance catabolic process mRNA processing RNA processing cellular response to stimulus postreplication repair response to stimulus DNA metabolic process cellular response to stress DNA damage response response to stress DNA repair	protein-containing complex intracellular anatomical structure PAN complex cytoplasm cellular anatomical entity cytoplasmic ribonucleoprotein granule ribonucleoprotein granule intracellular organelle organelle intracellular non-membrane-bounded organelle supramolecular complex P-body non-membrane-bounded organelle
B [auth L], C [auth K], D [auth E], E [auth F], G [auth H], B [auth L], C [auth K], D [auth E], E [auth F], G [auth H], H [auth I], J [auth C], K [auth B]	PAB-dependent poly(A)-specific ribonuclease subunit PAN3	binding adenyl ribonucleotide binding nucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding nucleoside phosphate binding ion binding purine nucleotide binding organic cyclic compound binding anion binding adenyl nucleotide binding ATP binding heterocyclic compound binding carbohydrate derivative binding binding adenyl ribonucleotide binding nucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding nucleoside phosphate binding ion binding purine nucleotide binding organic cyclic compound binding anion binding adenyl nucleotide binding ATP binding heterocyclic compound binding carbohydrate derivative binding ribonucleotide binding small molecule binding catalytic activity, acting on a protein kinase activity protein kinase activity transferase activity catalytic activity phosphotransferase activity, alcohol group as acceptor transferase activity, transferring phosphorus-containing groups RNA binding poly(A) binding poly-purine tract binding nucleic acid binding single-stranded RNA binding cation binding metal ion binding	cellular response to stimulus response to stimulus primary metabolic process DNA metabolic process nucleic acid metabolic process nucleobase-containing compound metabolic process organic cyclic compound metabolic process organic substance metabolic process cellular response to stress DNA damage response response to stress metabolic process cellular process macromolecule metabolic process cellular response to stimulus response to stimulus primary metabolic process DNA metabolic process nucleic acid metabolic process nucleobase-containing compound metabolic process organic cyclic compound metabolic process organic substance metabolic process cellular response to stress DNA damage response response to stress metabolic process cellular process macromolecule metabolic process DNA repair regulation of cellular process negative regulation of biological process negative regulation of cellular metabolic process regulation of primary metabolic process positive regulation of metabolic process post-transcriptional regulation of gene expression regulation of RNA metabolic process organic substance biosynthetic process positive regulation of macromolecule metabolic process regulation of nucleobase-containing compound metabolic process regulation of biological quality RNA catabolic process mRNA catabolic process regulation of biological process positive regulation of nucleobase-containing compound metabolic process cellular metabolic process negative regulation of metabolic process positive regulation of mRNA metabolic process regulation of cellular metabolic process negative regulation of cellular biosynthetic process nucleobase-containing compound catabolic process nuclear-transcribed mRNA poly(A) tail shortening positive regulation of RNA metabolic process regulation of gene expression negative regulation of gene expression biosynthetic process negative regulation of macromolecule biosynthetic process nucleic acid catabolic process regulation of macromolecule biosynthetic process regulation of metabolic process nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay catabolic process cellular biosynthetic process positive regulation of biological process RNA metabolic process macromolecule catabolic process mRNA destabilization regulation of mRNA catabolic process negative regulation of cellular process negative regulation of macromolecule metabolic process regulation of biosynthetic process nuclear-transcribed mRNA catabolic process RNA destabilization biological regulation regulation of macromolecule metabolic process regulation of catabolic process gene expression macromolecule biosynthetic process mRNA metabolic process organic cyclic compound catabolic process regulation of cellular biosynthetic process positive regulation of catabolic process regulation of mRNA stability negative regulation of biosynthetic process positive regulation of mRNA catabolic process regulation of RNA stability regulation of mRNA metabolic process organic substance catabolic process mRNA processing RNA processing postreplication repair	protein-containing complex intracellular anatomical structure PAN complex cytoplasm cellular anatomical entity cytoplasmic ribonucleoprotein granule ribonucleoprotein granule intracellular organelle organelle intracellular non-membrane-bounded organelle supramolecular complex P-body non-membrane-bounded organelle

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A [auth G], F [auth D], I [auth J], L [auth A]	IPR036397	Ribonuclease H superfamily	Homologous Superfamily
A [auth G], F [auth D], I [auth J], L [auth A]	IPR028889	Ubiquitin specific protease domain	Domain
A [auth G], F [auth D], I [auth J], L [auth A]	IPR030843	PAN2-PAN3 deadenylation complex catalytic subunit PAN2	Family
A [auth G], F [auth D], I [auth J], L [auth A]	IPR028881	PAN2, UCH domain	Domain
A [auth G], F [auth D], I [auth J], L [auth A]	IPR048841	PAN2-PAN3 deadenylation complex catalytic subunit PAN2, N-terminal	Domain
A [auth G], F [auth D], I [auth J], L [auth A]	IPR011047	Quinoprotein alcohol dehydrogenase-like superfamily	Homologous Superfamily
A [auth G], F [auth D], I [auth J], L [auth A]	IPR038765	Papain-like cysteine peptidase superfamily	Homologous Superfamily
A [auth G], F [auth D], I [auth J], L [auth A]	IPR015943	WD40/YVTN repeat-like-containing domain superfamily	Homologous Superfamily
A [auth G], F [auth D], I [auth J], L [auth A]	IPR012337	Ribonuclease H-like superfamily	Homologous Superfamily
A [auth G], F [auth D], I [auth J], L [auth A]	IPR013520	Exonuclease, RNase T/DNA polymerase III	Domain
B [auth L], C [auth K], D [auth E], E [auth F], G [auth H], B [auth L], C [auth K], D [auth E], E [auth F], G [auth H], H [auth I], J [auth C], K [auth B]	IPR030844	PAN2-PAN3 deadenylation complex subunit PAN3	Family
B [auth L], C [auth K], D [auth E], E [auth F], G [auth H], B [auth L], C [auth K], D [auth E], E [auth F], G [auth H], H [auth I], J [auth C], K [auth B]	IPR000571	Zinc finger, CCCH-type	Domain
B [auth L], C [auth K], D [auth E], E [auth F], G [auth H], B [auth L], C [auth K], D [auth E], E [auth F], G [auth H], H [auth I], J [auth C], K [auth B]	IPR011009	Protein kinase-like domain superfamily	Homologous Superfamily
B [auth L], C [auth K], D [auth E], E [auth F], G [auth H], B [auth L], C [auth K], D [auth E], E [auth F], G [auth H], H [auth I], J [auth C], K [auth B]	IPR000719	Protein kinase domain	Domain
B [auth L], C [auth K], D [auth E], E [auth F], G [auth H], B [auth L], C [auth K], D [auth E], E [auth F], G [auth H], H [auth I], J [auth C], K [auth B]	IPR041332	Pan3 pseudokinase domain	Domain