5YS4 | pdb_00005ys4

Crystal structure of retroviral protease-like domain of Ddi1 from Leishmania major

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)
F	SCOP2B Superfamily	Acid proteases	8086231	3001059	SCOP2B (2022-06-29)
E	SCOP2B Superfamily	Acid proteases	8086231	3001059	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	Acid proteases	8086231	3001059	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	Acid proteases	8086231	3001059	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Acid proteases	8086231	3001059	SCOP2B (2022-06-29)
A	SCOP2 Family	Dimeric aspartyl proteases	8080835	4004443	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	Acid proteases	8086231	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)
F	Asp_protease	e5ys4F1	A: beta barrels	X: cradle loop barrel	H: RIFT-related	T: acid protease	F: Asp_protease	ECOD (1.6)
E	Asp_protease	e5ys4E1	A: beta barrels	X: cradle loop barrel	H: RIFT-related	T: acid protease	F: Asp_protease	ECOD (1.6)
D	Asp_protease	e5ys4D1	A: beta barrels	X: cradle loop barrel	H: RIFT-related	T: acid protease	F: Asp_protease	ECOD (1.6)
C	Asp_protease	e5ys4C1	A: beta barrels	X: cradle loop barrel	H: RIFT-related	T: acid protease	F: Asp_protease	ECOD (1.6)
B	Asp_protease	e5ys4B1	A: beta barrels	X: cradle loop barrel	H: RIFT-related	T: acid protease	F: Asp_protease	ECOD (1.6)
A	Asp_protease	e5ys4A1	A: beta barrels	X: cradle loop barrel	H: RIFT-related	T: acid protease	F: Asp_protease	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
F	2.40.70.10	Mainly Beta	Beta Barrel	Cathepsin D, subunit A	domain 1	CATH (4.3.0)
E	2.40.70.10	Mainly Beta	Beta Barrel	Cathepsin D, subunit A	domain 1	CATH (4.3.0)
D	2.40.70.10	Mainly Beta	Beta Barrel	Cathepsin D, subunit A	domain 1	CATH (4.3.0)
C	2.40.70.10	Mainly Beta	Beta Barrel	Cathepsin D, subunit A	domain 1	CATH (4.3.0)
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, C, D, E A, B, C, D, E, F	PF09668	Aspartyl protease (Asp_protease)	Aspartyl protease	This domain is found in eukaryotic aspartyl protease DDI1 (DNA Damage Inducible protein 1; MEROPS identifier A28.001). The remarkable structural similarity between this central domain of DDI1 and the retroviral proteases suggests that DDI1 functions ...	This domain is found in eukaryotic aspartyl protease DDI1 (DNA Damage Inducible protein 1; MEROPS identifier A28.001). The remarkable structural similarity between this central domain of DDI1 and the retroviral proteases suggests that DDI1 functions proteolytically during regulated protein turnover [1, 2]. DDI1 has been shown to activate an endoplasmic-reticulum isoform of the transcription factor SKN-1 in Caenorhabditis elegans when the proteasome is dysfunctional [4]. DDI1 also has an amino-terminal ubiquitin-like domain and/or a UBA (ubiquitin-associated) domain [3].	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B, C, D, E A, B, C, D, E, F	DNA-damage inducible protein DDI1-like protein	aspartic-type peptidase activity peptidase activity catalytic activity, acting on a protein hydrolase activity aspartic-type endopeptidase activity catalytic activity endopeptidase activity	proteolysis metabolic process cellular process primary metabolic process protein metabolic process macromolecule metabolic process	cellular anatomical structure intracellular anatomical structure cytoplasm

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B, C, D, E A, B, C, D, E, F	IPR021109	Aspartic peptidase domain superfamily	Homologous Superfamily
A, B, C, D, E A, B, C, D, E, F	IPR019103	Aspartic peptidase, DDI1-type	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.