5I8I | pdb_00005i8i

Crystal Structure of the K. lactis Urea Amidolyase

External Resource: Annotation

Domain Annotation: ECOD Classification
Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
D	CT_C_D_C	e5i8iD2	A: beta barrels	X: Cyclophilin-like (From Topology)	H: Cyclophilin-like (From Topology)	T: Cyclophilin-like	F: CT_C_D_C	ECOD (1.6)
D	CT_A_B_C	e5i8iD4	A: beta barrels	X: Cyclophilin-like (From Topology)	H: Cyclophilin-like (From Topology)	T: Cyclophilin-like	F: CT_A_B_C	ECOD (1.6)
D	CT_A_B_N	e5i8iD3	A: beta sandwiches	X: jelly-roll	H: Double-stranded beta-helix (From Topology)	T: Double-stranded beta-helix	F: CT_A_B_N	ECOD (1.6)
D	CT_C_D_N	e5i8iD9	A: a+b two layers	X: Glucose permease domain IIB-like	H: PH0987 N-terminal domain-like (From Topology)	T: PH0987 N-terminal domain-like	F: CT_C_D_N	ECOD (1.6)
D	GGACT_1	e5i8iD5	A: a+b two layers	X: BtrG-like (Pfam 03674) (From Topology)	H: BtrG-like (Pfam 03674) (From Topology)	T: BtrG-like (Pfam 03674)	F: GGACT_1	ECOD (1.6)
D	ATP-grasp	e5i8iD7	A: a+b complex topology	X: Protein kinase/SAICAR synthase/ATP-grasp (From Homology)	H: Protein kinase/SAICAR synthase/ATP-grasp	T: ATP-grasp	F: ATP-grasp	ECOD (1.6)
D	Biotin_carb_C	e5i8iD8	A: a+b complex topology	X: alpha/beta-Hammerhead/Barrel-sandwich hybrid	H: alpha/beta-Hammerhead/Barrel-sandwich hybrid	T: CO dehydrogenase molybdoprotein N-domain-like	F: Biotin_carb_C	ECOD (1.6)
D	Biotin_carb_N	e5i8iD6	A: a/b three-layered sandwiches	X: Rossmann-like	H: Rossmann-related	T: PreATP-grasp domain	F: Biotin_carb_N	ECOD (1.6)
D	Amidase	e5i8iD1	A: a/b three-layered sandwiches	X: Amidase signature (AS) enzymes (From Topology)	H: Amidase signature (AS) enzymes (From Topology)	T: Amidase signature (AS) enzymes	F: Amidase	ECOD (1.6)
C	CT_C_D_C	e5i8iC2	A: beta barrels	X: Cyclophilin-like (From Topology)	H: Cyclophilin-like (From Topology)	T: Cyclophilin-like	F: CT_C_D_C	ECOD (1.6)
C	CT_A_B_C	e5i8iC4	A: beta barrels	X: Cyclophilin-like (From Topology)	H: Cyclophilin-like (From Topology)	T: Cyclophilin-like	F: CT_A_B_C	ECOD (1.6)
C	CT_A_B_N	e5i8iC3	A: beta sandwiches	X: jelly-roll	H: Double-stranded beta-helix (From Topology)	T: Double-stranded beta-helix	F: CT_A_B_N	ECOD (1.6)
C	CT_C_D_N	e5i8iC9	A: a+b two layers	X: Glucose permease domain IIB-like	H: PH0987 N-terminal domain-like (From Topology)	T: PH0987 N-terminal domain-like	F: CT_C_D_N	ECOD (1.6)
C	GGACT_1	e5i8iC5	A: a+b two layers	X: BtrG-like (Pfam 03674) (From Topology)	H: BtrG-like (Pfam 03674) (From Topology)	T: BtrG-like (Pfam 03674)	F: GGACT_1	ECOD (1.6)
C	ATP-grasp	e5i8iC7	A: a+b complex topology	X: Protein kinase/SAICAR synthase/ATP-grasp (From Homology)	H: Protein kinase/SAICAR synthase/ATP-grasp	T: ATP-grasp	F: ATP-grasp	ECOD (1.6)
C	Biotin_carb_C	e5i8iC8	A: a+b complex topology	X: alpha/beta-Hammerhead/Barrel-sandwich hybrid	H: alpha/beta-Hammerhead/Barrel-sandwich hybrid	T: CO dehydrogenase molybdoprotein N-domain-like	F: Biotin_carb_C	ECOD (1.6)
C	Biotin_carb_N	e5i8iC6	A: a/b three-layered sandwiches	X: Rossmann-like	H: Rossmann-related	T: PreATP-grasp domain	F: Biotin_carb_N	ECOD (1.6)
C	Amidase	e5i8iC1	A: a/b three-layered sandwiches	X: Amidase signature (AS) enzymes (From Topology)	H: Amidase signature (AS) enzymes (From Topology)	T: Amidase signature (AS) enzymes	F: Amidase	ECOD (1.6)
B	CT_C_D_C	e5i8iB2	A: beta barrels	X: Cyclophilin-like (From Topology)	H: Cyclophilin-like (From Topology)	T: Cyclophilin-like	F: CT_C_D_C	ECOD (1.6)
B	CT_A_B_C	e5i8iB4	A: beta barrels	X: Cyclophilin-like (From Topology)	H: Cyclophilin-like (From Topology)	T: Cyclophilin-like	F: CT_A_B_C	ECOD (1.6)
B	CT_A_B_N	e5i8iB3	A: beta sandwiches	X: jelly-roll	H: Double-stranded beta-helix (From Topology)	T: Double-stranded beta-helix	F: CT_A_B_N	ECOD (1.6)
B	CT_C_D_N	e5i8iB9	A: a+b two layers	X: Glucose permease domain IIB-like	H: PH0987 N-terminal domain-like (From Topology)	T: PH0987 N-terminal domain-like	F: CT_C_D_N	ECOD (1.6)
B	GGACT_1	e5i8iB5	A: a+b two layers	X: BtrG-like (Pfam 03674) (From Topology)	H: BtrG-like (Pfam 03674) (From Topology)	T: BtrG-like (Pfam 03674)	F: GGACT_1	ECOD (1.6)
B	ATP-grasp	e5i8iB7	A: a+b complex topology	X: Protein kinase/SAICAR synthase/ATP-grasp (From Homology)	H: Protein kinase/SAICAR synthase/ATP-grasp	T: ATP-grasp	F: ATP-grasp	ECOD (1.6)
B	Biotin_carb_C	e5i8iB8	A: a+b complex topology	X: alpha/beta-Hammerhead/Barrel-sandwich hybrid	H: alpha/beta-Hammerhead/Barrel-sandwich hybrid	T: CO dehydrogenase molybdoprotein N-domain-like	F: Biotin_carb_C	ECOD (1.6)
B	Biotin_carb_N	e5i8iB6	A: a/b three-layered sandwiches	X: Rossmann-like	H: Rossmann-related	T: PreATP-grasp domain	F: Biotin_carb_N	ECOD (1.6)
B	Amidase	e5i8iB1	A: a/b three-layered sandwiches	X: Amidase signature (AS) enzymes (From Topology)	H: Amidase signature (AS) enzymes (From Topology)	T: Amidase signature (AS) enzymes	F: Amidase	ECOD (1.6)
A	CT_C_D_C	e5i8iA2	A: beta barrels	X: Cyclophilin-like (From Topology)	H: Cyclophilin-like (From Topology)	T: Cyclophilin-like	F: CT_C_D_C	ECOD (1.6)
A	CT_A_B_C	e5i8iA4	A: beta barrels	X: Cyclophilin-like (From Topology)	H: Cyclophilin-like (From Topology)	T: Cyclophilin-like	F: CT_A_B_C	ECOD (1.6)
A	CT_A_B_N	e5i8iA3	A: beta sandwiches	X: jelly-roll	H: Double-stranded beta-helix (From Topology)	T: Double-stranded beta-helix	F: CT_A_B_N	ECOD (1.6)
A	CT_C_D_N	e5i8iA9	A: a+b two layers	X: Glucose permease domain IIB-like	H: PH0987 N-terminal domain-like (From Topology)	T: PH0987 N-terminal domain-like	F: CT_C_D_N	ECOD (1.6)
A	GGACT_1	e5i8iA5	A: a+b two layers	X: BtrG-like (Pfam 03674) (From Topology)	H: BtrG-like (Pfam 03674) (From Topology)	T: BtrG-like (Pfam 03674)	F: GGACT_1	ECOD (1.6)
A	ATP-grasp	e5i8iA7	A: a+b complex topology	X: Protein kinase/SAICAR synthase/ATP-grasp (From Homology)	H: Protein kinase/SAICAR synthase/ATP-grasp	T: ATP-grasp	F: ATP-grasp	ECOD (1.6)
A	Biotin_carb_C	e5i8iA8	A: a+b complex topology	X: alpha/beta-Hammerhead/Barrel-sandwich hybrid	H: alpha/beta-Hammerhead/Barrel-sandwich hybrid	T: CO dehydrogenase molybdoprotein N-domain-like	F: Biotin_carb_C	ECOD (1.6)
A	Biotin_carb_N	e5i8iA6	A: a/b three-layered sandwiches	X: Rossmann-like	H: Rossmann-related	T: PreATP-grasp domain	F: Biotin_carb_N	ECOD (1.6)
A	Amidase	e5i8iA1	A: a/b three-layered sandwiches	X: Amidase signature (AS) enzymes (From Topology)	H: Amidase signature (AS) enzymes (From Topology)	T: Amidase signature (AS) enzymes	F: Amidase	ECOD (1.6)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B, C, D	PF01425	Amidase (Amidase)	Amidase	This entry represents the amidase signature domain that consists structurally of a core domain that is covered by alpha-helices. In most members, this is found as a standalone domain, while in others, such as Scytalone dehydratase-like protein Arp1, ...	This entry represents the amidase signature domain that consists structurally of a core domain that is covered by alpha-helices. In most members, this is found as a standalone domain, while in others, such as Scytalone dehydratase-like protein Arp1, it is found in association with other domains.	Domain
A, B, C, D	PF02626	Carboxyltransferase domain, subdomain A and B (CT_A_B)	Carboxyltransferase domain, subdomain A and B	-	Family
A, B, C, D	PF02682	Carboxyltransferase domain, subdomain C and D (CT_C_D)	Carboxyltransferase domain, subdomain C and D	-	Family
A, B, C, D	PF02786	Carbamoyl-phosphate synthase L chain, ATP binding domain (CPSase_L_D2)	Carbamoyl-phosphate synthase L chain, ATP binding domain	Carbamoyl-phosphate synthase catalyses the ATP-dependent synthesis of carbamyl-phosphate from glutamine or ammonia and bicarbonate. This important enzyme initiates both the urea cycle and the biosynthesis of arginine and/or pyrimidines [2]. The c ...	Carbamoyl-phosphate synthase catalyses the ATP-dependent synthesis of carbamyl-phosphate from glutamine or ammonia and bicarbonate. This important enzyme initiates both the urea cycle and the biosynthesis of arginine and/or pyrimidines [2]. The carbamoyl-phosphate synthase (CPS) enzyme in prokaryotes is a heterodimer of a small and large chain. The small chain promotes the hydrolysis of glutamine to ammonia, which is used by the large chain to synthesise carbamoyl phosphate. See Pfam:PF00988. The small chain has a GATase domain in the carboxyl terminus. See Pfam:PF00117. The ATP binding domain (this one) has an ATP-grasp fold.	Domain
A, B, C, D	PF02785	Biotin carboxylase C-terminal domain (Biotin_carb_C)	Biotin carboxylase C-terminal domain	Biotin carboxylase is a component of the acetyl-CoA carboxylase multi-component enzyme which catalyses the first committed step in fatty acid synthesis in animals, plants and bacteria. Most of the active site residues reported in reference [1] are in ...	Biotin carboxylase is a component of the acetyl-CoA carboxylase multi-component enzyme which catalyses the first committed step in fatty acid synthesis in animals, plants and bacteria. Most of the active site residues reported in reference [1] are in this C-terminal domain.	Domain
A, B, C, D	PF00289	Biotin carboxylase, N-terminal domain (Biotin_carb_N)	Biotin carboxylase, N-terminal domain	This domain is structurally related to the PreATP-grasp domain. The family contains the N-terminus of biotin carboxylase enzymes [1,3], and propionyl-CoA carboxylase A chain [2].	Domain
A, B, C, D	PF21986	Allophanate hydrolase C-terminal domain (AH_C)	Allophanate hydrolase C-terminal domain	Allophanate hydrolase (AH) converts allophanate to ammonium and carbon dioxide. The AH structure is composed of N- and C-terminal domains. These domains catalyze sequential reactions: the N-terminal domain converts allophanate to N-carboxycarbamate, ...	Allophanate hydrolase (AH) converts allophanate to ammonium and carbon dioxide. The AH structure is composed of N- and C-terminal domains. These domains catalyze sequential reactions: the N-terminal domain converts allophanate to N-carboxycarbamate, whereas the C-terminal domain converts it to carbon dioxide and ammonium [2]. The C-terminal domain folds into alpha/beta structure in which some of the beta-strands form a barrel-like shape.	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B, C, D	Urea Amidolyase	binding adenyl ribonucleotide binding nucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding nucleoside phosphate binding ion binding purine nucleotide binding anion binding adenyl nucleotide binding ATP binding heterocyclic compound binding carbohydrate derivative binding ribonucleotide binding binding adenyl ribonucleotide binding nucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding nucleoside phosphate binding ion binding purine nucleotide binding anion binding adenyl nucleotide binding ATP binding heterocyclic compound binding carbohydrate derivative binding ribonucleotide binding small molecule binding hydrolase activity catalytic activity urea carboxylase activity ligase activity, forming carbon-nitrogen bonds ligase activity cation binding metal ion binding	small molecule metabolic process metabolic process cellular process	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B, C, D	IPR036928	Amidase signature (AS) superfamily	Homologous Superfamily
A, B, C, D	IPR005481	Biotin carboxylase-like, N-terminal domain	Domain
A, B, C, D	IPR014085	Allophanate hydrolase	Domain
A, B, C, D	IPR011761	ATP-grasp fold	Domain
A, B, C, D	IPR053844	Allophanate hydrolase, C-terminal domain	Domain
A, B, C, D	IPR003778	Carboxyltransferase domain, subdomain A and B	Domain
A, B, C, D	IPR029000	Cyclophilin-like domain superfamily	Homologous Superfamily
A, B, C, D	IPR011764	Biotin carboxylation domain	Domain
A, B, C, D	IPR023631	Amidase signature domain	Domain
A, B, C, D	IPR050856	Biotin-dependent Carboxylase Complex	Family
A, B, C, D	IPR005479	Carbamoyl phosphate synthase, ATP-binding domain	Domain
A, B, C, D	IPR014084	Urea carboxylase	Family
A, B, C, D	IPR005482	Biotin carboxylase, C-terminal	Domain
A, B, C, D	IPR003833	Carboxyltransferase domain, subdomain C and D	Domain
A, B, C, D	IPR016185	Pre-ATP-grasp domain superfamily	Homologous Superfamily
A, B, C, D	IPR011054	Rudiment single hybrid motif	Homologous Superfamily
A, B, C, D	IPR011053	Single hybrid motif	Homologous Superfamily
A, B, C, D	IPR001882	Biotin-binding site	Binding Site
A, B, C, D	IPR000089	Biotin/lipoyl attachment	Domain