2YCB | pdb_00002ycb

Structure of the archaeal beta-CASP protein with N-terminal KH domains from Methanothermobacter thermautotrophicus

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)
B	SCOP2B Superfamily	Prokaryotic type KH domain (KH-domain type II)	8103570	3001043	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Metallo-hydrolase/oxidoreductase	8103572	3001057	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Prokaryotic type KH domain (KH-domain type II)	8103569	3001043	SCOP2B (2022-06-29)
A	SCOP2 Family	Prokaryotic type KH domain (KH-domain type II)	8046635	4001200	SCOP2 (2022-06-29)
A	SCOP2 Family	Prokaryotic type KH domain (KH-domain type II)	8103568	4001200	SCOP2 (2022-06-29)
A	SCOP2 Family	beta-CASP RNA-metabolising hydrolases	8103571	4000432	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	Prokaryotic type KH domain (KH-domain type II)	8103569	3001043	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	Prokaryotic type KH domain (KH-domain type II)	8103570	3001043	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	Metallo-hydrolase/oxidoreductase	8103572	3001057	SCOP2 (2022-06-29)

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
B	KH_7	e2ycbB3	A: a+b two layers	X: Alpha-lytic protease prodomain-like	H: KH-domains	T: Prokaryotic type KH domain (KH-domain type II)	F: KH_7	ECOD (1.6)
B	Lactamase_B_6	e2ycbB1	A: a+b four layers	X: Metallo-hydrolase/oxidoreductase (From Topology)	H: Metallo-hydrolase/oxidoreductase (From Topology)	T: Metallo-hydrolase/oxidoreductase	F: Lactamase_B_6	ECOD (1.6)
B	Beta-Casp	e2ycbB2	A: a/b three-layered sandwiches	X: P-loop domains-like	H: P-loop domains-related	T: P-loop containing nucleoside triphosphate hydrolases	F: Beta-Casp	ECOD (1.6)
A	KH_7	e2ycbA1	A: a+b two layers	X: Alpha-lytic protease prodomain-like	H: KH-domains	T: Prokaryotic type KH domain (KH-domain type II)	F: KH_7	ECOD (1.6)
A	Lactamase_B_6	e2ycbA4	A: a+b four layers	X: Metallo-hydrolase/oxidoreductase (From Topology)	H: Metallo-hydrolase/oxidoreductase (From Topology)	T: Metallo-hydrolase/oxidoreductase	F: Lactamase_B_6	ECOD (1.6)
A	Beta-Casp	e2ycbA3	A: a/b three-layered sandwiches	X: P-loop domains-like	H: P-loop domains-related	T: P-loop containing nucleoside triphosphate hydrolases	F: Beta-Casp	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
B	3.30.300.230	Alpha Beta	2-Layer Sandwich	GMP Synthetase	Chain A, domain 3	CATH (4.3.0)
B	3.30.300.20	Alpha Beta	2-Layer Sandwich	GMP Synthetase	Chain A, domain 3	CATH (4.3.0)
B	3.60.15.10	Alpha Beta	4-Layer Sandwich	Metallo-beta-lactamase	Chain A	CATH (4.3.0)
B	3.40.50.10890	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold		CATH (4.3.0)
A	3.30.300.230	Alpha Beta	2-Layer Sandwich	GMP Synthetase	Chain A, domain 3	CATH (4.3.0)
A	3.30.300.20	Alpha Beta	2-Layer Sandwich	GMP Synthetase	Chain A, domain 3	CATH (4.3.0)
A	3.60.15.10	Alpha Beta	4-Layer Sandwich	Metallo-beta-lactamase	Chain A	CATH (4.3.0)
A	3.40.50.10890	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold		CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B	PF07521	Zn-dependent metallo-hydrolase RNA specificity domain (RMMBL)	Zn-dependent metallo-hydrolase RNA specificity domain	-	Motif
A, B	PF16661	Metallo-beta-lactamase superfamily domain (Lactamase_B_6)	Metallo-beta-lactamase superfamily domain	This family is part of the metallo-beta-lactamase superfamily.	Domain
A, B	PF17214	Transcription termination factor FttA, KH domain (KH_TffA)	Transcription termination factor FttA, KH domain	This entry represents the KH domain found at the N terminus of transcription termination factor FttA and similar archaeal proteins [2]. FttA is a single-stranded endoribonuclease (endoRNase) that mediates cleavage at the RNA exit channel of RNA polym ...	This entry represents the KH domain found at the N terminus of transcription termination factor FttA and similar archaeal proteins [2]. FttA is a single-stranded endoribonuclease (endoRNase) that mediates cleavage at the RNA exit channel of RNA polymerase (RNAP); the 5'-3' exonuclease activity of this protein degrades the nascent RNA released from RNAP. It terminates transcription on the whole genome, a process that is linked to FttA-mediated RNA cleavage and does not require NTP hydrolysis [2]. It also has weak activity 5'-3' exodeoxyribonuclease activity on ssDNA [2].	Domain
A, B	PF10996	Beta-Casp domain (Beta-Casp)	Beta-Casp domain	The beta-CASP domain is found C terminal to the beta-lactamase domain in pre-mRNA 3'-end-processing endonuclease. The active site of this enzyme is located at the interface of these two domains [1].	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B	CLEAVAGE AND POLYADENYLATION SPECIFICITY FACTOR	hydrolase activity, acting on ester bonds nuclease activity catalytic activity, acting on a nucleic acid hydrolase activity exonuclease activity catalytic activity DNA binding binding nucleic acid binding catalytic activity, acting on RNA RNA nuclease activity endonuclease activity RNA endonuclease activity cation binding hydrolase activity, acting on ester bonds nuclease activity catalytic activity, acting on a nucleic acid hydrolase activity exonuclease activity catalytic activity DNA binding binding nucleic acid binding catalytic activity, acting on RNA RNA nuclease activity endonuclease activity RNA endonuclease activity cation binding transition metal ion binding zinc ion binding ion binding metal ion binding small molecule binding RNA binding identical protein binding protein binding	RNA metabolic process primary metabolic process nucleobase-containing compound biosynthetic process gene expression DNA-templated transcription termination macromolecule biosynthetic process nucleic acid metabolic process RNA biosynthetic process nucleobase-containing compound metabolic process DNA-templated transcription nucleic acid biosynthetic process biosynthetic process metabolic process cellular process RNA metabolic process primary metabolic process nucleobase-containing compound biosynthetic process gene expression DNA-templated transcription termination macromolecule biosynthetic process nucleic acid metabolic process RNA biosynthetic process nucleobase-containing compound metabolic process DNA-templated transcription nucleic acid biosynthetic process biosynthetic process metabolic process cellular process macromolecule metabolic process	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B	IPR019975	Transcription termination factor CPSF1, archaea	Family
A, B	IPR001279	Metallo-beta-lactamase	Domain
A, B	IPR009019	K homology domain superfamily, prokaryotic type	Homologous Superfamily
A, B	IPR022712	Beta-Casp domain	Domain
A, B	IPR004087	K Homology domain	Domain
A, B	IPR050698	RNA Processing Metallo-Beta-Lactamase	Family
A, B	IPR033769	Transcription termination factor FttA, KH domain	Domain
A, B	IPR015946	K homology domain-like, alpha/beta	Homologous Superfamily
A, B	IPR011108	Zn-dependent metallo-hydrolase, RNA specificity domain	Domain
A, B	IPR036866	Ribonuclease Z/Hydroxyacylglutathione hydrolase-like	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.