2MR9 | pdb_00002mr9

NMR structure of UBA domain of DNA-damage-inducible 1 protein (Ddi1)

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)
A	SCOP2 Family	UBA domain	8088648	4000749	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	UBA-like	8088649	3001235	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)
A	UBA	e2mr9A1	A: alpha arrays	X: RuvA-C	H: RuvA-C, UBA, CRAL/TRIO-N, HBS1 (From Topology)	T: RuvA-C, UBA, CRAL/TRIO-N, HBS1	F: UBA	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	1.10.8.10	Mainly Alpha	Orthogonal Bundle	Helicase, Ruva Protein	domain 3	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A	PF00627	UBA/TS-N domain (UBA)	UBA/TS-N domain	This small domain is composed of three alpha helices. This family includes the previously defined UBA and TS-N domains. The UBA-domain (ubiquitin associated domain) is a novel sequence motif found in several proteins having connections to ubiquitin a ...	This small domain is composed of three alpha helices. This family includes the previously defined UBA and TS-N domains. The UBA-domain (ubiquitin associated domain) is a novel sequence motif found in several proteins having connections to ubiquitin and the ubiquitination pathway. The structure of the UBA domain consists of a compact three helix bundle [1]. This domain is found at the N terminus of EF-TS hence the name TS-N. The structure of EF-TS is known and this domain is implicated in its interaction with EF-TU [2]. The domain has been found in non EF-TS proteins such as alpha-NAC Swiss:P70670 and MJ0280 Swiss:Q57728 [1].	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A	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 proteolysis involved in protein catabolic process primary metabolic process protein catabolic process macromolecule catabolic process modification-dependent macromolecule catabolic process modification-dependent protein catabolic process proteolysis ubiquitin-dependent protein catabolic process metabolic process cellular process macromolecule metabolic process protein metabolic process protein localization catabolic process proteolysis involved in protein catabolic process primary metabolic process protein catabolic process macromolecule catabolic process modification-dependent macromolecule catabolic process modification-dependent protein catabolic process proteolysis ubiquitin-dependent protein catabolic process metabolic process cellular process macromolecule metabolic process protein metabolic process protein localization establishment of protein localization cellular localization nitrogen compound transport transport establishment of protein localization to vacuole vesicle-mediated transport localization late endosome to vacuole transport late endosome to vacuole transport via multivesicular body sorting pathway cellular macromolecule localization establishment of localization in cell 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 macromolecule localization protein localization to organelle 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 positive regulation of nucleobase-containing compound metabolic 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	IPR019103	Aspartic peptidase, DDI1-type	Domain
A	IPR001995	Peptidase A2A, retrovirus, catalytic	Domain
A	IPR033882	DNA damage inducible protein 1 ubiquitin-like domain	Domain
A	IPR021109	Aspartic peptidase domain superfamily	Homologous Superfamily
A	IPR009060	UBA-like superfamily	Homologous Superfamily
A	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.