5NIJ | pdb_00005nij

Crystal structure of arabidopsis thaliana legumain isoform gamma in two-chain activation state

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
Protein Modification Annotation

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
D	SCOP2B Superfamily	Caspase-like	8104082	3001096	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	Caspase-like	8104082	3001096	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Caspase-like	8104082	3001096	SCOP2B (2022-06-29)
A	SCOP2 Family	Legumain-like	8061319	4006439	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	Caspase-like	8104082	3001096	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)
D	Glyco_transf_4	e5nijD1	A: a/b three-layered sandwiches	X: Periplasmic binding protein-like II	H: Rubredoxin-related	T: Tetrapyrrole methylase C-terminal domain	F: Glyco_transf_4	ECOD (v294.1)
C	Glyco_transf_4	e5nijC1	A: a/b three-layered sandwiches	X: Periplasmic binding protein-like II	H: Rubredoxin-related	T: Tetrapyrrole methylase C-terminal domain	F: Glyco_transf_4	ECOD (v294.1)
B	V-set	e5nijB1	A: a/b three-layered sandwiches	X: Periplasmic binding protein-like II	H: Rubredoxin-related	T: Tetrapyrrole methylase C-terminal domain	F: V-set	ECOD (v294.1)
A	Glyco_transf_4	e5nijA1	A: a/b three-layered sandwiches	X: Periplasmic binding protein-like II	H: Rubredoxin-related	T: Tetrapyrrole methylase C-terminal domain	F: Glyco_transf_4	ECOD (v294.1)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
D	3.40.50.1460	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold		CATH (utative)
C	3.40.50.1460	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold		CATH (utative)
B	3.40.50.1460	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold		CATH (utative)
A	3.40.50.1460	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold		CATH (utative)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B, C, D	PF01650	Peptidase C13 family (Peptidase_C13)	Peptidase C13 family	-	Family
A, B, C, D	PF20985	Legumain, prodomain (Legum_prodom)	Legumain, prodomain	This domain is found in the proenzyme form of Vacuolar-processing enzyme (VPE), known as legumain. VPE is an asparagine-specific endopeptidase that plays important roles in many physiological processes, including the maturation of toll-like receptors ...	This domain is found in the proenzyme form of Vacuolar-processing enzyme (VPE), known as legumain. VPE is an asparagine-specific endopeptidase that plays important roles in many physiological processes, including the maturation of toll-like receptors 3/7/9. The mature active form of VPE is generated by autoproteolytic maturation at acidic pH. In the three-dimensional structure of the proenzyme, this prodomain is located on top of the protease domain, blocking access to the active site. It shows an entirely alpha-helical fold, with an activation peptide and a region that assemblies into a death domain-like fold at its C-terminal end [1-5].	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B, C, D	Vacuolar-processing enzyme gamma-isozyme	peptidase activity catalytic activity, acting on a protein hydrolase activity catalytic activity endopeptidase activity cysteine-type peptidase activity cysteine-type endopeptidase activity	response to stimulus response to stress response to wounding primary metabolic process gene expression macromolecule biosynthetic process protein maturation biosynthetic process proteolysis protein processing metabolic process cellular process protein metabolic process macromolecule metabolic process response to stimulus response to stress response to wounding primary metabolic process gene expression macromolecule biosynthetic process protein maturation biosynthetic process proteolysis protein processing metabolic process cellular process protein metabolic process macromolecule metabolic process vacuolar protein processing response to lipid response to jasmonic acid response to hormone response to fatty acid response to chemical response to endogenous stimulus response to oxygen-containing compound response to ethylene developmental process multicellular organismal process plant organ development plant organ senescence multicellular organism development anatomical structure development leaf development leaf senescence shoot system development phyllome development system development response to salicylic acid	membrane-bounded organelle intracellular organelle cellular anatomical structure intracellular anatomical structure organelle lytic vacuole vacuole cytoplasm intracellular membrane-bounded organelle storage vacuole protein storage vacuole plant-type vacuole

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B, C, D	IPR048501	Legumain, prodomain	Domain
A, B, C, D	IPR046427	Legumain prodomain superfamily	Homologous Superfamily
A, B, C, D	IPR001096	Peptidase C13, legumain	Family
A, B, C, D	IPR043577	Asparaginyl endopeptidase	Family

Protein Modification Annotation

Modified Residue(s)
Chain	Residue(s)	Description
A, B, C, D	SCH	Parent Component: CYS RESID: AA0101 PSI-MOD : L-cysteine methyl disulfide MOD:00110
A, B, C, D	SNN	Parent Component: ASN RESID: AA0101 , AA0302 , AA0593 PSI-MOD : L-cysteine methyl disulfide MOD:00110 , L-aspartimide MOD:00307 , 2-(2-aminosuccinimidyl)pentanedioic acid (Asn) MOD:01940 , 2-(2-aminosuccinimidyl)pentanedioic acid (Asp) MOD:01941

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.