4BGD | pdb_00004bgd

Crystal structure of Brr2 in complex with the Jab1/MPN domain of Prp8

External Resource: Annotation

Domain Annotation: SCOP/SCOPe Classification
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: SCOP/SCOPe Classification SCOP-e Database Homepage

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
B [auth C]	d4bgdc_	Alpha and beta proteins (a/b)	Cytidine deaminase-like	JAB1/MPN domain	automated matches	automated matches	BAKER'S YEAST (Saccharomyces cerevisiae ) [TaxId: 4932 ],	SCOPe (2.08)

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)

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
B [auth C]	Globin	e4bgdC1	A: alpha bundles	X: all-alpha NTP pyrophosphatases	H: all-alpha NTP pyrophosphatases	T: MazG-related	F: Globin	ECOD (develop294)
A	PGDH_C	e4bgdA1	A: alpha bundles	X: Thioredoxin-like	H: ClpP/crotonase	T: ClpP/crotonase	F: PGDH_C	ECOD (develop294)

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)
A	3.40.50.300	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	P-loop containing nucleotide triphosphate hydrolases	CATH (4.3.0)
A	1.10.10.10	Mainly Alpha	Orthogonal Bundle	Arc Repressor Mutant, subunit A	Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain	CATH (4.3.0)
A	1.10.3380.10	Mainly Alpha	Orthogonal Bundle	Sec63 N-terminal domain-like fold	Sec63 N-terminal domain-like domain	CATH (4.3.0)
A	1.10.150.20	Mainly Alpha	Orthogonal Bundle	DNA polymerase	domain 1	CATH (4.3.0)
A	2.60.40.150	Mainly Beta	Sandwich	Immunoglobulin-like	C2 domain	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
B [auth C]	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
A	PF23445	Winged Helix-turn-helix domain (WHD_SNRNP200)	Winged Helix-turn-helix domain	This entry represents a winged Helix-Turn-Helix domain found in a variety of helicase enzymes.	Domain
A	PF02889	Sec63 Brl domain (Sec63)	Sec63 Brl domain	-	Family
A	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	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

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
B [auth C]	PRE-MRNA-SPLICING FACTOR 8	peptidase activity catalytic activity, acting on a protein metallopeptidase activity hydrolase activity catalytic activity RNA binding snRNA binding binding nucleic acid binding U1 snRNA binding U6 snRNA binding mRNA binding U5 snRNA binding U2 snRNA binding peptidase activity catalytic activity, acting on a protein metallopeptidase activity hydrolase activity catalytic activity RNA binding snRNA binding 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 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 RNA biosynthetic process nucleic acid biosynthetic process protein-RNA complex organization cellular component assembly protein-containing complex assembly cellular component organization or biogenesis ribonucleoprotein complex biogenesis 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 RNA biosynthetic process nucleic acid biosynthetic process protein-RNA complex organization cellular component assembly protein-containing complex assembly cellular component organization or biogenesis RNA processing RNA splicing protein-containing complex organization spliceosomal snRNP assembly primary metabolic process gene expression nucleobase-containing compound biosynthetic process mRNA metabolic process macromolecule biosynthetic process nucleic acid 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 intracellular organelle cellular anatomical structure spliceosomal complex organelle ribonucleoprotein complex Prp19 complex membrane-bounded organelle catalytic step 2 spliceosome protein-containing complex intracellular anatomical structure catalytic complex nucleus nuclear protein-containing complex intracellular membrane-bounded organelle intracellular organelle cellular anatomical structure spliceosomal complex organelle ribonucleoprotein complex Prp19 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
A	PRE-MRNA-SPLICING HELICASE BRR2	binding nucleic acid binding adenyl ribonucleotide binding nucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding nucleoside phosphate binding ion binding purine nucleotide binding anion binding adenyl nucleotide binding ATP binding heterocyclic compound binding carbohydrate derivative binding binding nucleic acid binding adenyl ribonucleotide binding nucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding nucleoside phosphate binding ion binding purine nucleotide binding anion binding adenyl nucleotide binding ATP binding heterocyclic compound binding carbohydrate derivative binding ribonucleotide binding small molecule 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 nucleic acid conformation isomerase activity isomerase activity catalytic activity, acting on RNA catalytic activity, acting on a nucleic acid helicase activity RNA helicase activity ATP-dependent activity, acting on RNA macromolecular conformation isomerase activity identical protein binding protein binding	ribonucleoprotein complex biogenesis RNA metabolic process mRNA processing protein-RNA complex assembly cellular component organization cellular component biogenesis nucleobase-containing compound metabolic process RNA biosynthetic process nucleic acid biosynthetic process protein-RNA complex organization cellular component assembly protein-containing complex assembly cellular component organization or biogenesis RNA processing ribonucleoprotein complex biogenesis RNA metabolic process mRNA processing protein-RNA complex assembly cellular component organization cellular component biogenesis nucleobase-containing compound metabolic process RNA biosynthetic process nucleic acid biosynthetic process protein-RNA complex organization cellular component assembly protein-containing complex assembly cellular component organization or biogenesis RNA processing RNA splicing spliceosome conformational change to release U4 (or U4atac) and U1 (or U11) protein-containing complex organization spliceosomal conformational changes to generate catalytic conformation primary metabolic process gene expression nucleobase-containing compound biosynthetic process mRNA metabolic process macromolecule biosynthetic process nucleic acid 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	protein-containing complex Prp19 complex membrane-bounded organelle spliceosomal snRNP complex intracellular anatomical structure nucleus nuclear protein-containing complex Sm-like protein family complex intracellular membrane-bounded organelle intracellular organelle U4/U6 x U5 tri-snRNP complex cellular anatomical structure spliceosomal tri-snRNP complex small nuclear ribonucleoprotein complex protein-containing complex Prp19 complex membrane-bounded organelle spliceosomal snRNP complex intracellular anatomical structure nucleus nuclear protein-containing complex Sm-like protein family complex intracellular membrane-bounded organelle intracellular organelle U4/U6 x U5 tri-snRNP complex cellular anatomical structure spliceosomal tri-snRNP complex small nuclear ribonucleoprotein complex organelle ribonucleoprotein complex spliceosomal complex U5 snRNP

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
B [auth C]	IPR012984	PROCT domain	Domain
B [auth C]	IPR012591	PRO8NT domain	Domain
B [auth C]	IPR019580	Pre-mRNA-processing-splicing factor 8, U6-snRNA-binding	Domain
B [auth C]	IPR027652	Pre-mRNA-processing-splicing factor 8	Family
B [auth C]	IPR043172	Prp8 RNase domain IV, palm region	Homologous Superfamily
B [auth C]	IPR012592	PROCN domain	Domain
B [auth C]	IPR012337	Ribonuclease H-like superfamily	Homologous Superfamily
B [auth C]	IPR043173	Prp8 RNase domain IV, fingers region	Homologous Superfamily
B [auth C]	IPR021983	PRP8 domain IV core	Domain
B [auth C]	IPR019581	Pre-mRNA-processing-splicing factor 8, U5-snRNA-binding	Domain
B [auth C]	IPR037518	MPN domain	Domain
B [auth C]	IPR019582	RNA recognition motif, spliceosomal PrP8	Domain
B [auth C]	IPR042516	Pre-mRNA-processing-splicing factor 8, U5-snRNA-binding domain superfamily	Homologous Superfamily
B [auth C]	IPR000555	JAB1/MPN/MOV34 metalloenzyme domain	Domain
A	IPR048863	Pre-mRNA-splicing helicase BRR2-like, plug domain	Domain
A	IPR041094	Brr2, N-terminal helicase PWI domain	Domain
A	IPR004179	Sec63 domain	Domain
A	IPR014756	Immunoglobulin E-set	Homologous Superfamily
A	IPR011545	DEAD/DEAH-box helicase domain	Domain
A	IPR057842	MER3 helicase-like, winged helix domain	Domain
A	IPR027417	P-loop containing nucleoside triphosphate hydrolase	Homologous Superfamily
A	IPR050474	Helicase Hel308/SKI2-like	Family
A	IPR001650	Helicase, C-terminal domain-like	Domain
A	IPR036388	Winged helix-like DNA-binding domain superfamily	Homologous Superfamily
A	IPR014001	Helicase superfamily 1/2, ATP-binding domain	Domain
A	IPR036390	Winged helix DNA-binding domain superfamily	Homologous Superfamily
A	IPR035892	C2 domain superfamily	Homologous Superfamily