6YSA | pdb_00006ysa

Crystal structure of Arabidopsis thaliana legumain isoform beta in zymogen state

External Resource: Annotation

Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
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)
L	SCOP2B Superfamily	Caspase-like	8104319	3001096	SCOP2B (2022-06-29)
K	SCOP2B Superfamily	Caspase-like	8104319	3001096	SCOP2B (2022-06-29)
J	SCOP2B Superfamily	Caspase-like	8104319	3001096	SCOP2B (2022-06-29)
I	SCOP2B Superfamily	Caspase-like	8104319	3001096	SCOP2B (2022-06-29)
H	SCOP2B Superfamily	Caspase-like	8104319	3001096	SCOP2B (2022-06-29)
G	SCOP2B Superfamily	Caspase-like	8104319	3001096	SCOP2B (2022-06-29)
F	SCOP2B Superfamily	Caspase-like	8104319	3001096	SCOP2B (2022-06-29)
E	SCOP2B Superfamily	Caspase-like	8104319	3001096	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	Caspase-like	8104319	3001096	SCOP2B (2022-06-29)
C	SCOP2 Family	Legumain-like	8104318	4006439	SCOP2 (2022-06-29)
C	SCOP2 Superfamily	Caspase-like	8104319	3001096	SCOP2 (2022-06-29)
B	SCOP2B Superfamily	Caspase-like	8104319	3001096	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	Caspase-like	8104319	3001096	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)
L		e6ysaL1	A: alpha arrays	X: putative RnfG subunit of electron transport complex	H: putative RnfG subunit of electron transport complex	T: Aspartate/ornithine carbamoyltransferase	F:	ECOD (v295.2)
K		e6ysaK1	A: alpha arrays	X: putative RnfG subunit of electron transport complex	H: putative RnfG subunit of electron transport complex	T: Aspartate/ornithine carbamoyltransferase	F:	ECOD (v295.2)
J		e6ysaJ1	A: alpha arrays	X: putative RnfG subunit of electron transport complex	H: putative RnfG subunit of electron transport complex	T: Aspartate/ornithine carbamoyltransferase	F:	ECOD (v295.2)
I		e6ysaI1	A: alpha arrays	X: putative RnfG subunit of electron transport complex	H: putative RnfG subunit of electron transport complex	T: Aspartate/ornithine carbamoyltransferase	F:	ECOD (v295.2)
H		e6ysaH1	A: alpha arrays	X: putative RnfG subunit of electron transport complex	H: putative RnfG subunit of electron transport complex	T: Aspartate/ornithine carbamoyltransferase	F:	ECOD (v295.2)
G		e6ysaG1	A: alpha arrays	X: putative RnfG subunit of electron transport complex	H: putative RnfG subunit of electron transport complex	T: Aspartate/ornithine carbamoyltransferase	F:	ECOD (v295.2)
F		e6ysaF1	A: alpha arrays	X: putative RnfG subunit of electron transport complex	H: putative RnfG subunit of electron transport complex	T: Aspartate/ornithine carbamoyltransferase	F:	ECOD (v295.2)
E		e6ysaE1	A: alpha arrays	X: putative RnfG subunit of electron transport complex	H: putative RnfG subunit of electron transport complex	T: Aspartate/ornithine carbamoyltransferase	F:	ECOD (v295.2)
D		e6ysaD1	A: alpha arrays	X: putative RnfG subunit of electron transport complex	H: putative RnfG subunit of electron transport complex	T: Aspartate/ornithine carbamoyltransferase	F:	ECOD (v295.2)
C	WD40, Beta-prop_WDR3_2nd	e6ysaC1	A: alpha arrays	X: putative RnfG subunit of electron transport complex	H: putative RnfG subunit of electron transport complex	T: Aspartate/ornithine carbamoyltransferase	F: WD40, Beta-prop_WDR3_2nd	ECOD (v295.2)
B		e6ysaB1	A: alpha arrays	X: putative RnfG subunit of electron transport complex	H: putative RnfG subunit of electron transport complex	T: Aspartate/ornithine carbamoyltransferase	F:	ECOD (v295.2)
A		e6ysaA1	A: alpha arrays	X: putative RnfG subunit of electron transport complex	H: putative RnfG subunit of electron transport complex	T: Aspartate/ornithine carbamoyltransferase	F:	ECOD (v295.2)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B, C, D, E A, B, C, D, E, F, G, H, I, J, K, L	PF01650	Peptidase C13 family (Peptidase_C13)	Peptidase C13 family	Members of this family are asparaginyl peptidases [1]. The blood fluke parasite Schistosoma mansoni has at least five Clan CA cysteine peptidases in its digestive tract including cathepsins B (2 isoforms), C, F and L. All have been recombinantly expr ...	Members of this family are asparaginyl peptidases [1]. The blood fluke parasite Schistosoma mansoni has at least five Clan CA cysteine peptidases in its digestive tract including cathepsins B (2 isoforms), C, F and L. All have been recombinantly expressed as active enzymes, albeit in various stages of activation [2]. In addition, a Clan CD peptidase, termed asparaginyl endopeptidase or 'legumain' has been identified. This has formerly been characterised as a 'haemoglobinase', but this term is probably incorrect [2]. Two cDNAs have been described for Schistosoma mansoni legumain; one encodes an active enzyme whereas the active site cysteine residue encoded by the second cDNA is substituted by an asparagine residue. Both forms have been recombinantly expressed [3].	Domain
A, B, C, D, E A, B, C, D, E, F, G, H, I, J, K, L	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, E A, B, C, D, E, F, G, H, I, J, K, L	Vacuolar-processing enzyme beta-isozyme	cysteine-type peptidase activity peptidase activity catalytic activity, acting on a protein cysteine-type endopeptidase activity hydrolase activity catalytic activity endopeptidase activity	catabolic process metabolic process cellular process primary metabolic process protein catabolic process protein metabolic process macromolecule metabolic process macromolecule catabolic process gene expression macromolecule biosynthetic process protein maturation biosynthetic process proteolysis protein processing catabolic process metabolic process cellular process primary metabolic process protein catabolic process protein metabolic process macromolecule metabolic process macromolecule catabolic process gene expression macromolecule biosynthetic process protein maturation biosynthetic process proteolysis protein processing vacuolar protein processing	membrane-bounded organelle storage vacuole intracellular anatomical structure vacuole intracellular membrane-bounded organelle protein storage vacuole intracellular organelle cellular anatomical structure organelle plant-type vacuole cytoplasm

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B, C, D, E A, B, C, D, E, F, G, H, I, J, K, L	IPR046427	Legumain prodomain superfamily	Homologous Superfamily
A, B, C, D, E A, B, C, D, E, F, G, H, I, J, K, L	IPR048501	Legumain, prodomain	Domain
A, B, C, D, E A, B, C, D, E, F, G, H, I, J, K, L	IPR001096	Peptidase C13, legumain	Family
A, B, C, D, E A, B, C, D, E, F, G, H, I, J, K, L	IPR043577	Asparaginyl endopeptidase	Family

Protein Modification Annotation

Modified Residue(s)
Chain	Residue(s)	Description
A, B, C, D, E A, B, C, D, E, F, G, H, I, J, K, L	SNN	Parent Component: ASN : AA0302 , AA0593 : L-aspartimide MOD:00307 , 2-(2-aminosuccinimidyl)pentanedioic acid (Asn) MOD:01940 , 2-(2-aminosuccinimidyl)pentanedioic acid (Asp) MOD:01941