4ILJ | pdb_00004ilj

Crystal structure of an Prp8p RNaseH W1911A mutant protein

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	d4iljb1	Alpha and beta proteins (a/b)	Ribonuclease H-like motif	Ribonuclease H-like	Prp8 beta-finger domain-like	Pre-mRNA splicing factor 8, Prp8 / Spp42	Baker's yeast (Saccharomyces cerevisiae S288C ) [TaxId: 559292 ],	SCOPe (2.08)
B	d4iljb2	Artifacts	Tags	Tags	Tags	N-terminal Tags	Baker's yeast (Saccharomyces cerevisiae S288C ) [TaxId: 559292 ],	SCOPe (2.08)
A	d4ilja1	Alpha and beta proteins (a/b)	Ribonuclease H-like motif	Ribonuclease H-like	Prp8 beta-finger domain-like	Pre-mRNA splicing factor 8, Prp8 / Spp42	Baker's yeast (Saccharomyces cerevisiae S288C ) [TaxId: 559292 ],	SCOPe (2.08)
A	d4ilja2	Artifacts	Tags	Tags	Tags	N-terminal Tags	Baker's yeast (Saccharomyces cerevisiae S288C ) [TaxId: 559292 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
B	SCOP2B Superfamily	Ribonuclease H-like	8040983	3000143	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	Ribonuclease H-like	8040983	3000143	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	SmpA_OmlA	e4iljB1	A: a/b three-layered sandwiches	X: beta-Grasp	H: HTH	T: winged helix domain	F: SmpA_OmlA	ECOD (v294.1)
A	Pkinase	e4iljA1	A: a/b three-layered sandwiches	X: Rossmann-like	H: Rossmann-related	T: NagB/RpiA/CoA transferase-like	F: Pkinase	ECOD (v294.1)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
B	3.30.420.230	Alpha Beta	2-Layer Sandwich	Nucleotidyltransferase	domain 5	CATH (4.3.0)
B	1.20.80.40	Mainly Alpha	Up-down Bundle	Acyl-CoA Binding Protein	Prp8 RNase H domain, fingers region	CATH (4.3.0)
A	3.30.420.230	Alpha Beta	2-Layer Sandwich	Nucleotidyltransferase	domain 5	CATH (4.3.0)
A	1.20.80.40	Mainly Alpha	Up-down Bundle	Acyl-CoA Binding Protein	Prp8 RNase H domain, fingers region	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B	PF12134	PRP8 domain IV core (PRP8_domainIV)	PRP8 domain IV core	This domain is found in eukaryotes, and is about 20 amino acids in length. It is found associated with Pfam:PF10597, Pfam:PF10596, Pfam:PF10598, Pfam:PF08083, Pfam:PF08082, Pfam:PF01398, Pfam:PF08084. There is a conserved LILR sequence motif. The dom ...	This domain is found in eukaryotes, and is about 20 amino acids in length. It is found associated with Pfam:PF10597, Pfam:PF10596, Pfam:PF10598, Pfam:PF08083, Pfam:PF08082, Pfam:PF01398, Pfam:PF08084. There is a conserved LILR sequence motif. The domain is a selenomethionine domain in a subunit of the spliceosome. This domain adopts a RNase H like fold within its core structure but with little sequence similarity. The function of PRP8 domain IV is believed to be interaction with the splicosomal core [1].	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B	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

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B	IPR012984	PROCT domain	Domain
A, B	IPR012591	PRO8NT domain	Domain
A, B	IPR019580	Pre-mRNA-processing-splicing factor 8, U6-snRNA-binding	Domain
A, B	IPR027652	Pre-mRNA-processing-splicing factor 8	Family
A, B	IPR043172	Prp8 RNase domain IV, palm region	Homologous Superfamily
A, B	IPR012592	PROCN domain	Domain
A, B	IPR012337	Ribonuclease H-like superfamily	Homologous Superfamily
A, B	IPR043173	Prp8 RNase domain IV, fingers region	Homologous Superfamily
A, B	IPR021983	PRP8 domain IV core	Domain
A, B	IPR019581	Pre-mRNA-processing-splicing factor 8, U5-snRNA-binding	Domain
A, B	IPR037518	MPN domain	Domain
A, B	IPR019582	RNA recognition motif, spliceosomal PrP8	Domain
A, B	IPR042516	Pre-mRNA-processing-splicing factor 8, U5-snRNA-binding domain superfamily	Homologous Superfamily
A, B	IPR000555	JAB1/MPN/MOV34 metalloenzyme domain	Domain

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. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.