5M52

Crystal structure of yeast Brr2 full-lenght in complex with Prp8 Jab1 domain

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 [auth C]	SCOP2B Superfamily	JAB1/MPN domain-like	8053281	3001105	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	JAB1/MPN domain-like	8053281	3001105	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)
A	PF02889	e5m52A15	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: PF02889	ECOD (1.6)
A	F_UNCLASSIFIED	e5m52A8	A: alpha arrays	X: HTH	H: HTH	T: winged	F: F_UNCLASSIFIED	ECOD (1.6)
A	F_UNCLASSIFIED	e5m52A10	A: alpha arrays	X: HhH/H2TH	H: SAM-like subdomain in Sec63-like proteins (From Topology)	T: SAM-like subdomain in Sec63-like proteins	F: F_UNCLASSIFIED	ECOD (1.6)
A	PF02889	e5m52A6	A: alpha arrays	X: Sec63 N-terminal subdomain-like (From Topology)	H: Sec63 N-terminal subdomain-like (From Topology)	T: Sec63 N-terminal subdomain-like	F: PF02889	ECOD (1.6)
A	PF18149	e5m52A9	A: alpha arrays	X: PWI domain-like	H: PWI domain (From Topology)	T: PWI domain	F: PF18149	ECOD (1.6)
A	PF21188	e5m52A4	A: alpha arrays	X: PWI domain-like	H: Pre-mRNA-splicing helicase BRR2 plug domain (From Topology)	T: Pre-mRNA-splicing helicase BRR2 plug domain	F: PF21188	ECOD (1.6)
A	F_UNCLASSIFIED	e5m52A12	A: a/b three-layered sandwiches	X: P-loop domains-like	H: P-loop domains-related	T: P-loop containing nucleoside triphosphate hydrolases	F: F_UNCLASSIFIED	ECOD (1.6)
A	PF00270	e5m52A1	A: a/b three-layered sandwiches	X: P-loop domains-like	H: P-loop domains-related	T: P-loop containing nucleoside triphosphate hydrolases	F: PF00270	ECOD (1.6)
A	PF00271	e5m52A2	A: a/b three-layered sandwiches	X: P-loop domains-like	H: P-loop domains-related	T: P-loop containing nucleoside triphosphate hydrolases	F: PF00271	ECOD (1.6)
A	F_UNCLASSIFIED	e5m52A5	A: extended segments	X: Pre-mRNA-splicing helicase BRR2 NC-clamp (From Topology)	H: Pre-mRNA-splicing helicase BRR2 NC-clamp (From Topology)	T: Pre-mRNA-splicing helicase BRR2 NC-clamp	F: F_UNCLASSIFIED	ECOD (1.6)
C [auth B]	PF02889	e5m52B8	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: PF02889	ECOD (1.6)
C [auth B]	F_UNCLASSIFIED	e5m52B9	A: alpha arrays	X: HTH	H: HTH	T: winged	F: F_UNCLASSIFIED	ECOD (1.6)
C [auth B]	F_UNCLASSIFIED	e5m52B13	A: alpha arrays	X: HhH/H2TH	H: SAM-like subdomain in Sec63-like proteins (From Topology)	T: SAM-like subdomain in Sec63-like proteins	F: F_UNCLASSIFIED	ECOD (1.6)
C [auth B]	PF02889	e5m52B5	A: alpha arrays	X: Sec63 N-terminal subdomain-like (From Topology)	H: Sec63 N-terminal subdomain-like (From Topology)	T: Sec63 N-terminal subdomain-like	F: PF02889	ECOD (1.6)
C [auth B]	PF18149	e5m52B11	A: alpha arrays	X: PWI domain-like	H: PWI domain (From Topology)	T: PWI domain	F: PF18149	ECOD (1.6)
C [auth B]	PF21188	e5m52B15	A: alpha arrays	X: PWI domain-like	H: Pre-mRNA-splicing helicase BRR2 plug domain (From Topology)	T: Pre-mRNA-splicing helicase BRR2 plug domain	F: PF21188	ECOD (1.6)
C [auth B]	F_UNCLASSIFIED	e5m52B4	A: a/b three-layered sandwiches	X: P-loop domains-like	H: P-loop domains-related	T: P-loop containing nucleoside triphosphate hydrolases	F: F_UNCLASSIFIED	ECOD (1.6)
C [auth B]	PF00270	e5m52B1	A: a/b three-layered sandwiches	X: P-loop domains-like	H: P-loop domains-related	T: P-loop containing nucleoside triphosphate hydrolases	F: PF00270	ECOD (1.6)
C [auth B]	PF00271	e5m52B3	A: a/b three-layered sandwiches	X: P-loop domains-like	H: P-loop domains-related	T: P-loop containing nucleoside triphosphate hydrolases	F: PF00271	ECOD (1.6)
C [auth B]	F_UNCLASSIFIED	e5m52B14	A: extended segments	X: Pre-mRNA-splicing helicase BRR2 NC-clamp (From Topology)	H: Pre-mRNA-splicing helicase BRR2 NC-clamp (From Topology)	T: Pre-mRNA-splicing helicase BRR2 NC-clamp	F: F_UNCLASSIFIED	ECOD (1.6)
B [auth C]	PF08084	e5m52C1	A: a+b three layers	X: Cytidine deaminase-like (From Topology)	H: Cytidine deaminase-like (From Topology)	T: Cytidine deaminase-like	F: PF08084	ECOD (1.6)
D	PF08084	e5m52D1	A: a+b three layers	X: Cytidine deaminase-like (From Topology)	H: Cytidine deaminase-like (From Topology)	T: Cytidine deaminase-like	F: PF08084	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
B [auth C]	3.40.140.10	Alpha Beta	3-Layer(aba) Sandwich	Cytidine Deaminase	domain 2	CATH (4.3.0)
D	3.40.140.10	Alpha Beta	3-Layer(aba) Sandwich	Cytidine Deaminase	domain 2	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, C [auth B]	PF02889	Sec63 Brl domain (Sec63)	Sec63 Brl domain	-	Family
A, C [auth B]	PF21188	Pre-mRNA-splicing helicase BRR2 plug domain (BRR2_plug)	Pre-mRNA-splicing helicase BRR2 plug domain	This entry represents the Plug domain from the Brr2 RNA helicase protein. The Brr2 helicase provides the key remodelling activity for spliceosome catalytic activation, during which it disrupts the U4/U6 di-snRNP (small nuclear RNA protein) [2]. The p ...	This entry represents the Plug domain from the Brr2 RNA helicase protein. The Brr2 helicase provides the key remodelling activity for spliceosome catalytic activation, during which it disrupts the U4/U6 di-snRNP (small nuclear RNA protein) [2]. The plug domain is a small alpha helical bundle domain found near the N-terminus of the Brr2 protein [2].	Domain
A, C [auth B]	PF00270	DEAD/DEAH box helicase (DEAD)	DEAD/DEAH box helicase	Members of this family include the DEAD and DEAH box helicases. Helicases are involved in unwinding nucleic acids. The DEAD box helicases are involved in various aspects of RNA metabolism, including nuclear transcription, pre mRNA splicing, ribosome ...	Members of this family include the DEAD and DEAH box helicases. Helicases are involved in unwinding nucleic acids. The DEAD box helicases are involved in various aspects of RNA metabolism, including nuclear transcription, pre mRNA splicing, ribosome biogenesis, nucleocytoplasmic transport, translation, RNA decay and organellar gene expression.	Domain
A, C [auth B]	PF00271	Helicase conserved C-terminal domain (Helicase_C)	Helicase conserved C-terminal domain	The Prosite family is restricted to DEAD/H helicases, whereas this domain family is found in a wide variety of helicases and helicase related proteins. It may be that this is not an autonomously folding unit, but an integral part of the helicase.	Domain
B [auth C], D	PF08084	PROCT (NUC072) domain (PROCT)	PROCT (NUC072) domain	The PROCT domain is the C-terminal domain in pre-mRNA splicing factors of PRO8 family [1].	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, C [auth B]	Pre-mRNA-splicing helicase BRR2	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 nucleic acid binding pyrophosphatase activity ATP hydrolysis activity ribonucleoside triphosphate phosphatase activity hydrolase activity, acting on acid anhydrides, in phosphorus-containing anhydrides hydrolase activity hydrolase activity, acting on acid anhydrides catalytic activity ATP-dependent activity catalytic activity, acting on RNA catalytic activity, acting on a nucleic acid helicase activity RNA helicase activity ATP-dependent activity, acting on RNA identical protein binding protein binding	RNA splicing cellular biosynthetic process cellular metabolic process RNA metabolic process primary metabolic process gene expression mRNA processing mRNA metabolic process macromolecule biosynthetic process nucleic acid metabolic process nucleobase-containing compound metabolic process organic cyclic compound metabolic process organic substance metabolic process biosynthetic process RNA splicing, via transesterification reactions RNA splicing cellular biosynthetic process cellular metabolic process RNA metabolic process primary metabolic process gene expression mRNA processing mRNA metabolic process macromolecule biosynthetic process nucleic acid metabolic process nucleobase-containing compound metabolic process organic cyclic compound metabolic process organic substance metabolic process biosynthetic process RNA splicing, via transesterification reactions mRNA splicing, via spliceosome organic substance biosynthetic process metabolic process cellular process RNA splicing, via transesterification reactions with bulged adenosine as nucleophile macromolecule metabolic process RNA processing ribonucleoprotein complex biogenesis protein-RNA complex assembly cellular component organization cellular component biogenesis protein-RNA complex organization cellular component assembly protein-containing complex assembly cellular component organization or biogenesis spliceosome conformational change to release U4 (or U4atac) and U1 (or U11) protein-containing complex organization spliceosomal conformational changes to generate catalytic conformation	membrane-bounded organelle protein-containing complex intracellular anatomical structure nucleus nuclear protein-containing complex intracellular membrane-bounded organelle cellular anatomical entity intracellular organelle spliceosomal complex organelle ribonucleoprotein complex U5 snRNP spliceosomal snRNP complex Sm-like protein family complex membrane-bounded organelle protein-containing complex intracellular anatomical structure nucleus nuclear protein-containing complex intracellular membrane-bounded organelle cellular anatomical entity intracellular organelle spliceosomal complex organelle ribonucleoprotein complex U5 snRNP spliceosomal snRNP complex Sm-like protein family complex small nuclear ribonucleoprotein complex U4/U6 x U5 tri-snRNP complex spliceosomal tri-snRNP complex
B [auth C], D	Pre-mRNA-splicing factor 8	peptidase activity catalytic activity, acting on a protein metallopeptidase activity hydrolase activity catalytic activity RNA binding snRNA binding binding organic cyclic compound binding nucleic acid binding U1 snRNA binding U6 snRNA binding mRNA binding U5 snRNA binding peptidase activity catalytic activity, acting on a protein metallopeptidase activity hydrolase activity catalytic activity RNA binding snRNA binding binding organic cyclic compound binding nucleic acid binding U1 snRNA binding U6 snRNA binding mRNA binding U5 snRNA binding U2 snRNA binding pre-mRNA binding pre-mRNA intronic binding	ribonucleoprotein complex biogenesis cellular biosynthetic process RNA metabolic process mRNA processing spliceosomal tri-snRNP complex assembly protein-RNA complex assembly cellular component organization cellular component biogenesis nucleobase-containing compound metabolic process protein-RNA complex organization cellular component assembly organic substance metabolic process protein-containing complex assembly organic substance biosynthetic process ribonucleoprotein complex biogenesis cellular biosynthetic process RNA metabolic process mRNA processing spliceosomal tri-snRNP complex assembly protein-RNA complex assembly cellular component organization cellular component biogenesis nucleobase-containing compound metabolic process protein-RNA complex organization cellular component assembly organic substance metabolic process protein-containing complex assembly organic substance biosynthetic process cellular component organization or biogenesis RNA processing RNA splicing protein-containing complex organization spliceosomal snRNP assembly cellular metabolic process primary metabolic process gene expression mRNA metabolic process macromolecule biosynthetic process nucleic acid metabolic process organic cyclic compound metabolic process biosynthetic process RNA splicing, via transesterification reactions mRNA splicing, via spliceosome cellular process metabolic process RNA splicing, via transesterification reactions with bulged adenosine as nucleophile macromolecule metabolic process spliceosomal complex assembly mRNA splice site recognition mRNA 3'-splice site recognition mRNA 5'-splice site recognition mRNA cis splicing, via spliceosome generation of catalytic spliceosome for second transesterification step spliceosomal conformational changes to generate catalytic conformation	membrane-bounded organelle catalytic step 2 spliceosome protein-containing complex intracellular anatomical structure catalytic complex nucleus nuclear protein-containing complex intracellular membrane-bounded organelle cellular anatomical entity intracellular organelle spliceosomal complex organelle ribonucleoprotein complex cytoplasm membrane-bounded organelle catalytic step 2 spliceosome protein-containing complex intracellular anatomical structure catalytic complex nucleus nuclear protein-containing complex intracellular membrane-bounded organelle cellular anatomical entity intracellular organelle spliceosomal complex organelle ribonucleoprotein complex cytoplasm spliceosomal snRNP complex Sm-like protein family complex U4/U6 x U5 tri-snRNP complex spliceosomal tri-snRNP complex small nuclear ribonucleoprotein complex U5 snRNP

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, C [auth B]	IPR001650	Helicase, C-terminal domain-like	Domain
A, C [auth B]	IPR036388	Winged helix-like DNA-binding domain superfamily	Homologous Superfamily
A, C [auth B]	IPR014001	Helicase superfamily 1/2, ATP-binding domain	Domain
A, C [auth B]	IPR036390	Winged helix DNA-binding domain superfamily	Homologous Superfamily
A, C [auth B]	IPR048863	Pre-mRNA-splicing helicase BRR2-like, plug domain	Domain
A, C [auth B]	IPR041094	Brr2, N-terminal helicase PWI domain	Domain
A, C [auth B]	IPR004179	Sec63 domain	Domain
A, C [auth B]	IPR035892	C2 domain superfamily	Homologous Superfamily
A, C [auth B]	IPR014756	Immunoglobulin E-set	Homologous Superfamily
A, C [auth B]	IPR011545	DEAD/DEAH box helicase domain	Domain
A, C [auth B]	IPR027417	P-loop containing nucleoside triphosphate hydrolase	Homologous Superfamily
B [auth C], D	IPR012984	PROCT domain	Domain
B [auth C], D	IPR012591	PRO8NT domain	Domain
B [auth C], D	IPR019580	Pre-mRNA-processing-splicing factor 8, U6-snRNA-binding	Domain
B [auth C], D	IPR027652	Pre-mRNA-processing-splicing factor 8	Family
B [auth C], D	IPR043172	Prp8 RNase domain IV, palm region	Homologous Superfamily
B [auth C], D	IPR012592	PROCN domain	Domain
B [auth C], D	IPR012337	Ribonuclease H-like superfamily	Homologous Superfamily
B [auth C], D	IPR043173	Prp8 RNase domain IV, fingers region	Homologous Superfamily
B [auth C], D	IPR021983	PRP8 domain IV core	Domain
B [auth C], D	IPR019581	Pre-mRNA-processing-splicing factor 8, U5-snRNA-binding	Domain
B [auth C], D	IPR037518	MPN domain	Domain
B [auth C], D	IPR019582	RNA recognition motif, spliceosomal PrP8	Domain
B [auth C], D	IPR042516	Pre-mRNA-processing-splicing factor 8, U5-snRNA-binding domain superfamily	Homologous Superfamily
B [auth C], D	IPR000555	JAB1/MPN/MOV34 metalloenzyme domain	Domain