1G2I

CRYSTAL STRUCTURE OF A NOVEL INTRACELLULAR PROTEASE FROM PYROCOCCUS HORIKOSHII AT 2 A RESOLUTION

External Resource: Annotation

Domain Annotation: SCOP/SCOPe Classification
Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
Domain Annotation: CATH
Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification
Structure Motif: Primary M-CSA Annotation

Domain Annotation: SCOP/SCOPe Classification SCOP-e Database Homepage

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
A	d1g2ia_	Alpha and beta proteins (a/b)	Flavodoxin-like	Class I glutamine amidotransferase-like	DJ-1/PfpI	Intracellular protease	(Pyrococcus horikoshii ) [TaxId: 53953 ],	SCOPe (2.08)
B	d1g2ib_	Alpha and beta proteins (a/b)	Flavodoxin-like	Class I glutamine amidotransferase-like	DJ-1/PfpI	Intracellular protease	(Pyrococcus horikoshii ) [TaxId: 53953 ],	SCOPe (2.08)
C	d1g2ic_	Alpha and beta proteins (a/b)	Flavodoxin-like	Class I glutamine amidotransferase-like	DJ-1/PfpI	Intracellular protease	(Pyrococcus horikoshii ) [TaxId: 53953 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A	SCOP2 Family	DJ-1/PfpI	8031781	4003749	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	Class I glutamine amidotransferase-like	8044159	3001405	SCOP2 (2022-06-29)
B	SCOP2B Superfamily	Class I glutamine amidotransferase-like	8044159	3001405	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	Class I glutamine amidotransferase-like	8044159	3001405	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)
A	DJ-1_PfpI	e1g2iA1	A: a/b three-layered sandwiches	X: Flavodoxin-like	H: Class I glutamine amidotransferase-like	T: Class I glutamine amidotransferase-like	F: DJ-1_PfpI	ECOD (1.6)
B	DJ-1_PfpI	e1g2iB1	A: a/b three-layered sandwiches	X: Flavodoxin-like	H: Class I glutamine amidotransferase-like	T: Class I glutamine amidotransferase-like	F: DJ-1_PfpI	ECOD (1.6)
C	DJ-1_PfpI	e1g2iC1	A: a/b three-layered sandwiches	X: Flavodoxin-like	H: Class I glutamine amidotransferase-like	T: Class I glutamine amidotransferase-like	F: DJ-1_PfpI	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	3.40.50.880	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	Class I glutamine amidotransferase (GATase) domain	CATH (4.3.0)
B	3.40.50.880	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	Class I glutamine amidotransferase (GATase) domain	CATH (4.3.0)
C	3.40.50.880	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	Class I glutamine amidotransferase (GATase) domain	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B, C	PF01965	DJ-1/PfpI family (DJ-1_PfpI)	DJ-1/PfpI family	The family includes the protease PfpI Swiss:Q51732 [1]. This domain is also found in transcriptional regulators such as Swiss:Q9RJG8.	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B, C	PROTEASE I	catalytic activity, acting on a protein protein deglycase activity hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds, in linear amides hydrolase activity catalytic activity hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds peptidase 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	IPR029062	Class I glutamine amidotransferase-like	Homologous Superfamily
A, B, C	IPR002818	DJ-1/PfpI	Domain
A, B, C	IPR053435	Peptidase C56 Deglycase	Family
A, B, C	IPR006286	Deglycase PfpI-like	Family

Structure Motif Annotation: Mechanism and Catalytic Site Atlas M-CSA Database Homepage

Chains	Enzyme Name	Description	Catalytic Residues
A, C	intracellular protease M-CSA #964	The intracellular protease from Pyrococcus horikoshii (PH1704) and PfpI from Pyrococcus furiosus are members of a class of intracellular proteases that have no sequence homology to any other known protease family. They have significant similarity with deglycases that catalyse the deglycation of the Maillard adducts formed between amino groups of proteins and reactive carbonyl groups of glyoxals. The protein is a member of the DJ-1 family, mutations of which appear to have a significant role in the cause of recessively transmitted early-onset Parkinson disease (PD), and oxidative damage to DJ-1 has been associated with the pathogenesis of late-onset sporadic PD. However, the precise role of DJ-1 proteins have yet to be fully elucidated.	Defined by 6 residues: GLY:A-70ARG:A-71CYS:A-100HIS:A-101TYR:A-120GLU:C-74 [auth C-474] \| Explore in 3D: M-CSA Motif Definition Search M-CSA Motif EC: 3.2 (PDB Primary Data) Search M-CSA Motif + EC 3.2 EC: 3.4.22 (UniProt) Search M-CSA Motif + EC 3.4.22 EC: 3.5.1.124 (UniProt) Search M-CSA Motif + EC 3.5.1.124

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.