3PIF | pdb_00003pif

Crystal structure of the 5'->3' exoribonuclease Xrn1, E178Q mutant in Complex with Manganese

External Resource: Annotation

Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
Domain Annotation: CATH
Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
D	SCOP2B Superfamily	5' to 3' exonuclease, C-terminal subdomain	8105320	3000537	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	5' to 3' exonuclease, C-terminal subdomain	8105320	3000537	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	PIN domain-like	8105319	3001041	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	PIN domain-like	8105319	3001041	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	5' to 3' exonuclease, C-terminal subdomain	8105320	3000537	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	5' to 3' exonuclease, C-terminal subdomain	8105320	3000537	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	PIN domain-like	8105319	3001041	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	5' to 3' exonuclease, C-terminal subdomain	8105320	3000537	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	5' to 3' exonuclease, C-terminal subdomain	8105320	3000537	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	5' to 3' exonuclease, C-terminal subdomain	8105320	3000537	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	PIN domain-like	8105319	3001041	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	5' to 3' exonuclease, C-terminal subdomain	8105320	3000537	SCOP2B (2022-06-29)

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
D	KOG2045_4th	e3pifD5	A: beta barrels	X: SH3	H: SH3	T: SH3	F: KOG2045_4th	ECOD (1.6)
D	KOG2045_1st	e3pifD3	A: beta barrels	X: SH3	H: SH3	T: SH3	F: KOG2045_1st	ECOD (1.6)
D	KOG2045_2nd	e3pifD4	A: beta barrels	X: SH3	H: SH3	T: SH3	F: KOG2045_2nd	ECOD (1.6)
D	KOG2044	e3pifD7	A: alpha arrays	X: Helical domain in 5'->3' exoribonucleases (From Topology)	H: Helical domain in 5'->3' exoribonucleases (From Topology)	T: Helical domain in 5'->3' exoribonucleases	F: KOG2044	ECOD (1.6)
D	XRN1	e3pifD6	A: a+b two layers	X: R3H domain-like	H: R3H-like domain in 5'->3' exoribonucleases (From Topology)	T: R3H-like domain in 5'->3' exoribonucleases	F: XRN1	ECOD (1.6)
D	UNK_F_TYPE	e3pifD8	A: a+b three layers	X: C-terminal segment in 5'->3' exoribonucleases (From Topology)	H: C-terminal segment in 5'->3' exoribonucleases (From Topology)	T: C-terminal segment in 5'->3' exoribonucleases	F: UNK_F_TYPE	ECOD (1.6)
D	XRN_N	e3pifD1	A: a/b three-layered sandwiches	X: HAD domain-like	H: HAD domain-related	T: PIN domain-like	F: XRN_N	ECOD (1.6)
C	KOG2045_4th	e3pifC2	A: beta barrels	X: SH3	H: SH3	T: SH3	F: KOG2045_4th	ECOD (1.6)
C	KOG2045_1st	e3pifC7	A: beta barrels	X: SH3	H: SH3	T: SH3	F: KOG2045_1st	ECOD (1.6)
C	KOG2045_2nd	e3pifC6	A: beta barrels	X: SH3	H: SH3	T: SH3	F: KOG2045_2nd	ECOD (1.6)
C	KOG2044	e3pifC8	A: alpha arrays	X: Helical domain in 5'->3' exoribonucleases (From Topology)	H: Helical domain in 5'->3' exoribonucleases (From Topology)	T: Helical domain in 5'->3' exoribonucleases	F: KOG2044	ECOD (1.6)
C	XRN1	e3pifC3	A: a+b two layers	X: R3H domain-like	H: R3H-like domain in 5'->3' exoribonucleases (From Topology)	T: R3H-like domain in 5'->3' exoribonucleases	F: XRN1	ECOD (1.6)
C	UNK_F_TYPE	e3pifC9	A: a+b three layers	X: C-terminal segment in 5'->3' exoribonucleases (From Topology)	H: C-terminal segment in 5'->3' exoribonucleases (From Topology)	T: C-terminal segment in 5'->3' exoribonucleases	F: UNK_F_TYPE	ECOD (1.6)
C	XRN_N	e3pifC5	A: a/b three-layered sandwiches	X: HAD domain-like	H: HAD domain-related	T: PIN domain-like	F: XRN_N	ECOD (1.6)
B	KOG2045_4th	e3pifB4	A: beta barrels	X: SH3	H: SH3	T: SH3	F: KOG2045_4th	ECOD (1.6)
B	KOG2045_1st	e3pifB2	A: beta barrels	X: SH3	H: SH3	T: SH3	F: KOG2045_1st	ECOD (1.6)
B	KOG2045_2nd	e3pifB3	A: beta barrels	X: SH3	H: SH3	T: SH3	F: KOG2045_2nd	ECOD (1.6)
B	KOG2044	e3pifB7	A: alpha arrays	X: Helical domain in 5'->3' exoribonucleases (From Topology)	H: Helical domain in 5'->3' exoribonucleases (From Topology)	T: Helical domain in 5'->3' exoribonucleases	F: KOG2044	ECOD (1.6)
B	XRN1	e3pifB1	A: a+b two layers	X: R3H domain-like	H: R3H-like domain in 5'->3' exoribonucleases (From Topology)	T: R3H-like domain in 5'->3' exoribonucleases	F: XRN1	ECOD (1.6)
B	UNK_F_TYPE	e3pifB8	A: a+b three layers	X: C-terminal segment in 5'->3' exoribonucleases (From Topology)	H: C-terminal segment in 5'->3' exoribonucleases (From Topology)	T: C-terminal segment in 5'->3' exoribonucleases	F: UNK_F_TYPE	ECOD (1.6)
B	XRN_N	e3pifB6	A: a/b three-layered sandwiches	X: HAD domain-like	H: HAD domain-related	T: PIN domain-like	F: XRN_N	ECOD (1.6)
A	KOG2045_4th	e3pifA4	A: beta barrels	X: SH3	H: SH3	T: SH3	F: KOG2045_4th	ECOD (1.6)
A	KOG2045_1st	e3pifA6	A: beta barrels	X: SH3	H: SH3	T: SH3	F: KOG2045_1st	ECOD (1.6)
A	KOG2045_2nd	e3pifA3	A: beta barrels	X: SH3	H: SH3	T: SH3	F: KOG2045_2nd	ECOD (1.6)
A	KOG2044	e3pifA7	A: alpha arrays	X: Helical domain in 5'->3' exoribonucleases (From Topology)	H: Helical domain in 5'->3' exoribonucleases (From Topology)	T: Helical domain in 5'->3' exoribonucleases	F: KOG2044	ECOD (1.6)
A	XRN1	e3pifA2	A: a+b two layers	X: R3H domain-like	H: R3H-like domain in 5'->3' exoribonucleases (From Topology)	T: R3H-like domain in 5'->3' exoribonucleases	F: XRN1	ECOD (1.6)
A	UNK_F_TYPE	e3pifA8	A: a+b three layers	X: C-terminal segment in 5'->3' exoribonucleases (From Topology)	H: C-terminal segment in 5'->3' exoribonucleases (From Topology)	T: C-terminal segment in 5'->3' exoribonucleases	F: UNK_F_TYPE	ECOD (1.6)
A	XRN_N	e3pifA5	A: a/b three-layered sandwiches	X: HAD domain-like	H: HAD domain-related	T: PIN domain-like	F: XRN_N	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
D	3.30.1370.250	Alpha Beta	2-Layer Sandwich	Ribosomal Protein S8	Chain: A, domain 1	CATH (4.3.0)
C	3.30.1370.250	Alpha Beta	2-Layer Sandwich	Ribosomal Protein S8	Chain: A, domain 1	CATH (4.3.0)
B	3.40.50.12390	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold		CATH (4.3.0)
B	1.25.40.1050	Mainly Alpha	Alpha Horseshoe	Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat		CATH (4.3.0)
B	3.30.1370.250	Alpha Beta	2-Layer Sandwich	Ribosomal Protein S8	Chain: A, domain 1	CATH (4.3.0)
B	2.170.260.40	Mainly Beta	Beta Complex	paz domain		CATH (4.3.0)
B	2.30.30.30	Mainly Beta	Roll	SH3 type barrels.		CATH (4.3.0)
B	6.10.140.950	Special	Helix non-globular	Helix Hairpins		CATH (4.3.0)
B	6.10.250.1110	Special	Helix non-globular	Single alpha-helices involved in coiled-coils or other helix-helix interfaces		CATH (4.3.0)
B	2.30.30.750	Mainly Beta	Roll	SH3 type barrels.		CATH (4.3.0)
A	3.30.1370.250	Alpha Beta	2-Layer Sandwich	Ribosomal Protein S8	Chain: A, domain 1	CATH (utative)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B, C, D	PF18334	Exoribonuclease Xrn1 D2/D3 domain (XRN1_D2_D3)	Exoribonuclease Xrn1 D2/D3 domain	This domain can be found in 5' to 3' exoribonuclease 1 (XRN1) which belong to a family of conserved enzymes in eukaryotes and have important functions in transcription, RNA metabolism, and RNA interference. Xrn1 in fungi and animals is primarily cyto ...	This domain can be found in 5' to 3' exoribonuclease 1 (XRN1) which belong to a family of conserved enzymes in eukaryotes and have important functions in transcription, RNA metabolism, and RNA interference. Xrn1 in fungi and animals is primarily cytosolic, involved in degradation of decapped mRNAs, nonsense mediated decay, microRNA decay and is essential for proper development. The Xrn1 homolog in Drosophila, known as Pacman, is required for male fertility [1]. This entry relates to domain 2 and 3 combined which can be found in the 510-residue C-terminal extension found in XRN1 and not in XRN2/Rat1. Domain D2 is formed by two stretches of Xrn1, residues 915-960 and 1134-1151. The presence of domain (D3) is suggested based on structure. This domain is formed by residues 979-1109, in the insert of domain D2. It is suggested that domains D2-D4 may help maintain domain D1 Pfam:PF18332 in the correct conformation, thereby indirectly stabilising the conformation of the N-terminal segment Pfam:PF03159 [1].	Domain
A, B, C, D	PF18332	Exoribonuclease Xrn1 D1 domain (XRN1_D1)	Exoribonuclease Xrn1 D1 domain	This domain can be found in 5' to 3' exoribonuclease 1 (XRN1) which belong to a family of conserved enzymes in eukaryotes and have important functions in transcription, RNA metabolism, and RNA interference. Xrn1 in fungi and animals is primarily cyto ...	This domain can be found in 5' to 3' exoribonuclease 1 (XRN1) which belong to a family of conserved enzymes in eukaryotes and have important functions in transcription, RNA metabolism, and RNA interference. Xrn1 in fungi and animals is primarily cytosolic and is involved in degradation of decapped mRNAs, nonsense mediated decay, microRNA decay and is essential for proper development. The Xrn1 homolog in Drosophila, known as Pacman, is required for male fertility [1]. This domain (D1) along with 3 other domains, make up a 510-residue segment following the conserved regions found in XRNs but they are only present in XRN1 and are absent in Rat1/XRN2. The amino acid sequences of these four domains contain an excess of basic residues, suggesting that these domains might help in binding the RNA substrate. Mutational studies carried out in D1 domain show that the mutant forms had dramatically reduced nuclease activity towards ssDNA substrate indicating that domain D1 is required for Xrn1 nuclease activity [1].	Domain
A, B, C, D	PF18129	Xrn1 SH3-like domain (SH3_12)	Xrn1 SH3-like domain	This is the C-terminal SH3-like domain which can be found in the exoribonuclease Xrn1. Xrn1 is a 175 kDa processive exoribonuclease that is conserved from yeast to mammals which targets cytoplasmic RNA substrates marked by a 5' monophosphate for proc ...	This is the C-terminal SH3-like domain which can be found in the exoribonuclease Xrn1. Xrn1 is a 175 kDa processive exoribonuclease that is conserved from yeast to mammals which targets cytoplasmic RNA substrates marked by a 5' monophosphate for processive 5'-to-3' degradation. The Sh3-like domain in Xrn1 lacks the canonical SH3 residues normally involved in binding proline-rich peptide motifs and instead engages in non-canonical interactions with the catalytic domain. Additionally it is essential in maintaining the structural integrity of Xrn1, since partial truncation of this domain in yeast Xrn1 yields an inactive protein. There is a long loop projecting from the SH3-like domain that contacts the PAZ/Tudor domain, occluding the functional surface that binds RNA or peptide motifs containing methylated arginines, respectively, in canonical PAZ and Tudor domain [1].	Domain
A, B, C, D	PF17846	Xrn1 helical domain (XRN_M)	Xrn1 helical domain	This helical domain is part of the Xrn1 catalytic core [1]. Xrn1 is a cytoplasmic 5'-3' exonuclease that degrades decapped mRNAs.	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B, C, D	5'->3' EXORIBONUCLEASE (xrn1)	5'-3' RNA exonuclease activity 5'-3' exonuclease activity catalytic activity, acting on RNA catalytic activity, acting on a nucleic acid RNA exonuclease activity, producing 5'-phosphomonoesters RNA exonuclease activity RNA nuclease activity hydrolase activity hydrolase activity, acting on ester bonds nuclease activity exonuclease activity catalytic activity RNA binding binding 5'-3' RNA exonuclease activity 5'-3' exonuclease activity catalytic activity, acting on RNA catalytic activity, acting on a nucleic acid RNA exonuclease activity, producing 5'-phosphomonoesters RNA exonuclease activity RNA nuclease activity hydrolase activity hydrolase activity, acting on ester bonds nuclease activity exonuclease activity catalytic activity RNA binding binding nucleic acid binding cation binding ion binding metal ion binding small molecule binding	catabolic process RNA metabolic process primary metabolic process rRNA catabolic process nucleic acid metabolic process macromolecule catabolic process nucleobase-containing compound catabolic process nucleobase-containing compound metabolic process nucleic acid catabolic process metabolic process cellular process macromolecule metabolic process rRNA metabolic process RNA catabolic process catabolic process RNA metabolic process primary metabolic process rRNA catabolic process nucleic acid metabolic process macromolecule catabolic process nucleobase-containing compound catabolic process nucleobase-containing compound metabolic process nucleic acid catabolic process metabolic process cellular process macromolecule metabolic process rRNA metabolic process RNA catabolic process regulation of cellular process nuclear-transcribed mRNA catabolic process, nonsense-mediated decay negative regulation of biological process negative regulation of cellular process negative regulation of macromolecule metabolic process regulation of biosynthetic process mRNA catabolic process nuclear-transcribed mRNA catabolic process regulation of biological process negative regulation of metabolic process biological regulation regulation of macromolecule metabolic process gene expression macromolecule biosynthetic process mRNA metabolic process regulation of gene expression negative regulation of gene expression biosynthetic process negative regulation of biosynthetic process negative regulation of macromolecule biosynthetic process regulation of macromolecule biosynthetic process regulation of metabolic process	cellular anatomical structure intracellular anatomical structure cytoplasm membrane-bounded organelle intracellular organelle organelle nucleus intracellular membrane-bounded organelle

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B, C, D	IPR041106	Exoribonuclease Xrn1, D2/D3 domain	Domain
A, B, C, D	IPR014722	Large ribosomal subunit protein uL2, domain 2	Homologous Superfamily
A, B, C, D	IPR016494	5'-3' exoribonuclease 1	Family
A, B, C, D	IPR040992	5'-3' exoribonuclease 1, D1 domain	Domain
A, B, C, D	IPR047007	5'-3' exoribonuclease 1, D1 domain superfamily	Homologous Superfamily
A, B, C, D	IPR047008	5'-3' exoribonuclease 1, SH3-like domain superfamily	Homologous Superfamily
A, B, C, D	IPR027073	5'-3' exoribonuclease	Family
A, B, C, D	IPR041385	5'-3' exoribonuclease 1, SH3-like domain	Domain
A, B, C, D	IPR041412	Xrn1, helical domain	Domain
A, B, C, D	IPR004859	Xrn1, N-terminal	Domain