4Z2Z | pdb_00004z2z

New crystal structure of yeast Ddi1 aspartyl protease reveals substrate engagement mode

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	Acid proteases	8090353	3001059	SCOP2B (2022-06-29)
A	SCOP2 Family	Dimeric aspartyl proteases	8049470	4004443	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	Acid proteases	8090353	3001059	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	Asp_Arg_Hydrox	e4z2zB1	A: a/b three-layered sandwiches	X: jelly-roll	H: Double-stranded beta-helix	T: Double-stranded beta-helix	F: Asp_Arg_Hydrox	ECOD (v294.1)
A	Asp_Arg_Hydrox	e4z2zA1	A: a/b three-layered sandwiches	X: jelly-roll	H: Double-stranded beta-helix	T: Double-stranded beta-helix	F: Asp_Arg_Hydrox	ECOD (v294.1)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
B	2.40.70.10	Mainly Beta	Beta Barrel	Cathepsin D, subunit A	domain 1	CATH (4.3.0)
A	2.40.70.10	Mainly Beta	Beta Barrel	Cathepsin D, subunit A	domain 1	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B	PF13975	gag-polyprotein putative aspartyl protease (gag-asp_proteas)	gag-polyprotein putative aspartyl protease	This family of putative aspartyl proteases is found pre-dominantly in retroviral proteins.	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B	DNA damage-inducible protein 1	aspartic-type peptidase activity peptidase activity catalytic activity, acting on a protein hydrolase activity aspartic-type endopeptidase activity catalytic activity endopeptidase activity protein binding binding SNARE binding proteasome regulatory particle binding protein-containing complex binding polyubiquitin modification-dependent protein binding modification-dependent protein binding aspartic-type peptidase activity peptidase activity catalytic activity, acting on a protein hydrolase activity aspartic-type endopeptidase activity catalytic activity endopeptidase activity protein binding binding SNARE binding proteasome regulatory particle binding protein-containing complex binding polyubiquitin modification-dependent protein binding modification-dependent protein binding ubiquitin binding ubiquitin-like protein binding protein-macromolecule adaptor activity molecular adaptor activity	catabolic process primary metabolic process protein catabolic process macromolecule catabolic process modification-dependent macromolecule catabolic process modification-dependent protein catabolic process ubiquitin-dependent protein catabolic process metabolic process cellular process protein metabolic process macromolecule metabolic process establishment of protein localization cellular localization transport catabolic process primary metabolic process protein catabolic process macromolecule catabolic process modification-dependent macromolecule catabolic process modification-dependent protein catabolic process ubiquitin-dependent protein catabolic process metabolic process cellular process protein metabolic process macromolecule metabolic process establishment of protein localization cellular localization transport establishment of protein localization to vacuole vesicle-mediated transport localization intercellular transport late endosome to vacuole transport late endosome to vacuole transport via multivesicular body sorting pathway establishment of localization in cell intracellular protein localization endosome transport via multivesicular body sorting pathway protein transport to vacuole involved in ubiquitin-dependent protein catabolic process via the multivesicular body sorting pathway protein localization to vacuole intracellular transport establishment of localization endosomal transport establishment of protein localization to organelle protein transport multivesicular body sorting pathway protein localization to organelle macromolecule localization ubiquitin-dependent protein catabolic process via the multivesicular body sorting pathway vacuolar transport intracellular protein transport secretion establishment of protein localization to extracellular region export from cell protein secretion protein localization to extracellular region secretion by cell regulation of cellular process positive regulation of DNA replication positive regulation of biological process regulation of primary metabolic process nucleobase-containing compound metabolic process positive regulation of metabolic process positive regulation of macromolecule metabolic process regulation of nucleobase-containing compound metabolic process positive regulation of cellular process regulation of biological process biological regulation DNA metabolic process regulation of macromolecule metabolic process nucleic acid metabolic process DNA replication positive regulation of DNA metabolic process regulation of metabolic process regulation of DNA metabolic process regulation of DNA replication	cell periphery cellular anatomical structure plasma membrane membrane intracellular anatomical structure cytoplasm

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B	IPR019103	Aspartic peptidase, DDI1-type	Domain
A, B	IPR001995	Peptidase A2A, retrovirus, catalytic	Domain
A, B	IPR033882	DNA damage inducible protein 1 ubiquitin-like domain	Domain
A, B	IPR021109	Aspartic peptidase domain superfamily	Homologous Superfamily
A, B	IPR009060	UBA-like superfamily	Homologous Superfamily
A, B	IPR015940	Ubiquitin-associated 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.