5K4A | pdb_00005k4a

Structure of the amidase mutant E79A at 2.3 Angstrom resolution

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 [auth E]	SCOP2B Superfamily	Class I glutamine amidotransferase-like	8079930	3001405	SCOP2B (2022-06-29)
E [auth D]	SCOP2B Superfamily	Class I glutamine amidotransferase-like	8079930	3001405	SCOP2B (2022-06-29)
D [auth B]	SCOP2B Superfamily	Class I glutamine amidotransferase-like	8079930	3001405	SCOP2B (2022-06-29)
C [auth A]	SCOP2B Superfamily	Class I glutamine amidotransferase-like	8079930	3001405	SCOP2B (2022-06-29)
B [auth F]	SCOP2B Superfamily	Class I glutamine amidotransferase-like	8079930	3001405	SCOP2B (2022-06-29)
A [auth C]	SCOP2B Superfamily	Class I glutamine amidotransferase-like	8079930	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)
F [auth E]	DJ-1_PfpI	e5k4aE1	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)
E [auth D]	DJ-1_PfpI	e5k4aD1	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)
D [auth B]	DJ-1_PfpI	e5k4aB1	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 [auth A]	DJ-1_PfpI	e5k4aA1	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 [auth F]	DJ-1_PfpI	e5k4aF1	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)
A [auth C]	DJ-1_PfpI	e5k4aC1	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)
F [auth E]	3.40.50.880	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	Class I glutamine amidotransferase (GATase) domain	CATH (4.3.0)
E [auth D]	3.40.50.880	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	Class I glutamine amidotransferase (GATase) domain	CATH (4.3.0)
D [auth B]	3.40.50.880	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	Class I glutamine amidotransferase (GATase) domain	CATH (4.3.0)
C [auth A]	3.40.50.880	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	Class I glutamine amidotransferase (GATase) domain	CATH (4.3.0)
B [auth F]	3.40.50.880	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	Class I glutamine amidotransferase (GATase) domain	CATH (4.3.0)
A [auth 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 [auth C], B [auth F], C [auth A], D [auth B], E [auth D], A [auth C], B [auth F], C [auth A], D [auth B], E [auth D], F [auth E]	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 [auth C], B [auth F], C [auth A], D [auth B], E [auth D], A [auth C], B [auth F], C [auth A], D [auth B], E [auth D], F [auth E]	Intracellular protease/amidase	hydro-lyase activity lyase activity catalytic activity glyoxalase III activity carbon-oxygen lyase activity catalytic activity, acting on a protein protein deglycase activity hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds, in linear amides hydrolase activity hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds	cellular response to stimulus response to stimulus primary metabolic process DNA metabolic process nucleic acid metabolic process nucleobase-containing compound metabolic process cellular response to stress DNA damage response response to stress metabolic process cellular process macromolecule metabolic process DNA repair response to ketone cellular response to stimulus response to stimulus primary metabolic process DNA metabolic process nucleic acid metabolic process nucleobase-containing compound metabolic process cellular response to stress DNA damage response response to stress metabolic process cellular process macromolecule metabolic process DNA repair response to ketone catabolic process oxoacid metabolic process ketone metabolic process detoxification methylglyoxal catabolic process organic acid metabolic process methylglyoxal catabolic process to lactate lactate metabolic process cellular detoxification of aldehyde cellular response to methylglyoxal cellular response to aldehyde cellular detoxification of methylglyoxal ketone catabolic process small molecule metabolic process cellular response to ketone methylglyoxal catabolic process to D-lactate via S-lactoyl-glutathione cellular detoxification response to oxygen-containing compound carboxylic acid metabolic process response to methylglyoxal cellular response to oxygen-containing compound aldehyde metabolic process response to toxic substance cellular response to chemical stimulus response to chemical monocarboxylic acid metabolic process aldehyde catabolic process small molecule catabolic process cellular response to toxic substance methylglyoxal metabolic process	cellular anatomical structure intracellular anatomical structure cytoplasm

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A [auth C], B [auth F], C [auth A], D [auth B], E [auth D], A [auth C], B [auth F], C [auth A], D [auth B], E [auth D], F [auth E]	IPR029062	Class I glutamine amidotransferase-like	Homologous Superfamily
A [auth C], B [auth F], C [auth A], D [auth B], E [auth D], A [auth C], B [auth F], C [auth A], D [auth B], E [auth D], F [auth E]	IPR002818	DJ-1/PfpI	Domain
A [auth C], B [auth F], C [auth A], D [auth B], E [auth D], A [auth C], B [auth F], C [auth A], D [auth B], E [auth D], F [auth E]	IPR017283	Protein/nucleic acid deglycase HchA	Family
A [auth C], B [auth F], C [auth A], D [auth B], E [auth D], A [auth C], B [auth F], C [auth A], D [auth B], E [auth D], F [auth E]	IPR050325	Protein/nucleic acid deglycase	Family

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.