1BXR
STRUCTURE OF CARBAMOYL PHOSPHATE SYNTHETASE COMPLEXED WITH THE ATP ANALOG AMPPNP
External Resource: Annotation
Domain Annotation: SCOP/SCOPe Classification SCOP-e Database Homepage
Domain Annotation: SCOP2 Classification SCOP2 Database Homepage
Chains | Type | Family Name | Domain Identifier | Family Identifier | Provenance Source (Version) |
---|---|---|---|---|---|
A | SCOP2 Family | BC ATP-binding domain-like | 8024182 | 4002053 | SCOP2 (2022-06-29) |
A | SCOP2 Family | BC ATP-binding domain-like | 8024184 | 4002053 | SCOP2 (2022-06-29) |
A | SCOP2 Family | Carbamoyl phosphate synthetase, large subunit connection domain | 8025752 | 4001126 | SCOP2 (2022-06-29) |
A | SCOP2 Family | Carbamoyl phosphate synthetase, large subunit allosteric, C-terminal domain | 8031796 | 4003761 | SCOP2 (2022-06-29) |
A | SCOP2 Family | BC N-terminal domain-like | 8031852 | 4003858 | SCOP2 (2022-06-29) |
A | SCOP2 Family | BC N-terminal domain-like | 8031854 | 4003858 | SCOP2 (2022-06-29) |
A | SCOP2 Superfamily | Glutathione synthetase ATP-binding domain-like | 8036561 | 3000094 | SCOP2 (2022-06-29) |
A | SCOP2 Superfamily | Glutathione synthetase ATP-binding domain-like | 8036563 | 3000094 | SCOP2 (2022-06-29) |
A | SCOP2 Superfamily | Carbamoyl phosphate synthetase, large subunit connection domain | 8038131 | 3000839 | SCOP2 (2022-06-29) |
A | SCOP2 Superfamily | Methylglyoxal synthase-like | 8044174 | 3001443 | SCOP2 (2022-06-29) |
A | SCOP2 Superfamily | PreATP-grasp domain | 8044230 | 3001680 | SCOP2 (2022-06-29) |
A | SCOP2 Superfamily | PreATP-grasp domain | 8044232 | 3001680 | SCOP2 (2022-06-29) |
E | SCOP2B Superfamily | Carbamoyl phosphate synthetase, large subunit connection domain | 8038131 | 3000839 | SCOP2B (2022-06-29) |
E | SCOP2B Superfamily | PreATP-grasp domain | 8044230 | 3001680 | SCOP2B (2022-06-29) |
E | SCOP2B Superfamily | Methylglyoxal synthase-like | 8044174 | 3001443 | SCOP2B (2022-06-29) |
E | SCOP2B Superfamily | Glutathione synthetase ATP-binding domain-like | 8036561 | 3000094 | SCOP2B (2022-06-29) |
E | SCOP2B Superfamily | PreATP-grasp domain | 8044232 | 3001680 | SCOP2B (2022-06-29) |
E | SCOP2B Superfamily | Glutathione synthetase ATP-binding domain-like | 8036563 | 3000094 | SCOP2B (2022-06-29) |
C | SCOP2B Superfamily | Carbamoyl phosphate synthetase, large subunit connection domain | 8038131 | 3000839 | SCOP2B (2022-06-29) |
C | SCOP2B Superfamily | PreATP-grasp domain | 8044230 | 3001680 | SCOP2B (2022-06-29) |
C | SCOP2B Superfamily | Methylglyoxal synthase-like | 8044174 | 3001443 | SCOP2B (2022-06-29) |
C | SCOP2B Superfamily | Glutathione synthetase ATP-binding domain-like | 8036561 | 3000094 | SCOP2B (2022-06-29) |
C | SCOP2B Superfamily | PreATP-grasp domain | 8044232 | 3001680 | SCOP2B (2022-06-29) |
C | SCOP2B Superfamily | Glutathione synthetase ATP-binding domain-like | 8036563 | 3000094 | SCOP2B (2022-06-29) |
G | SCOP2B Superfamily | Glutathione synthetase ATP-binding domain-like | 8036561 | 3000094 | SCOP2B (2022-06-29) |
G | SCOP2B Superfamily | Carbamoyl phosphate synthetase, large subunit connection domain | 8038131 | 3000839 | SCOP2B (2022-06-29) |
G | SCOP2B Superfamily | PreATP-grasp domain | 8044230 | 3001680 | SCOP2B (2022-06-29) |
G | SCOP2B Superfamily | PreATP-grasp domain | 8044232 | 3001680 | SCOP2B (2022-06-29) |
G | SCOP2B Superfamily | Methylglyoxal synthase-like | 8044174 | 3001443 | SCOP2B (2022-06-29) |
G | SCOP2B Superfamily | Glutathione synthetase ATP-binding domain-like | 8036563 | 3000094 | SCOP2B (2022-06-29) |
D | SCOP2B Superfamily | Class I glutamine amidotransferase-like | 8044144 | 3001405 | SCOP2B (2022-06-29) |
D | SCOP2B Superfamily | Carbamoyl phosphate synthetase, small subunit N-terminal domain | 8043909 | 3000949 | SCOP2B (2022-06-29) |
H | SCOP2B Superfamily | Class I glutamine amidotransferase-like | 8044144 | 3001405 | SCOP2B (2022-06-29) |
H | SCOP2B Superfamily | Carbamoyl phosphate synthetase, small subunit N-terminal domain | 8043909 | 3000949 | SCOP2B (2022-06-29) |
B | SCOP2B Superfamily | Class I glutamine amidotransferase-like | 8044144 | 3001405 | SCOP2B (2022-06-29) |
B | SCOP2B Superfamily | Carbamoyl phosphate synthetase, small subunit N-terminal domain | 8043909 | 3000949 | SCOP2B (2022-06-29) |
F | SCOP2B Superfamily | Carbamoyl phosphate synthetase, small subunit N-terminal domain | 8043909 | 3000949 | SCOP2B (2022-06-29) |
F | SCOP2B Superfamily | Class I glutamine amidotransferase-like | 8044144 | 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 | CPSase_L_D3 | e1bxrA1 | A: alpha arrays | X: HTH | H: HTH | T: winged | F: CPSase_L_D3 | ECOD (1.6) |
A | ATP-grasp | e1bxrA2 | 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 | carB | e1bxrA4 | A: a/b three-layered sandwiches | X: Rossmann-like | H: Rossmann-related | T: PreATP-grasp domain | F: carB | ECOD (1.6) |
A | MGS | e1bxrA6 | A: a/b three-layered sandwiches | X: Methylglyoxal synthase-like (From Topology) | H: Methylglyoxal synthase-like (From Topology) | T: Methylglyoxal synthase-like | F: MGS | ECOD (1.6) |
E | CPSase_L_D3 | e1bxrE1 | A: alpha arrays | X: HTH | H: HTH | T: winged | F: CPSase_L_D3 | ECOD (1.6) |
E | ATP-grasp | e1bxrE2 | 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) |
E | carB | e1bxrE4 | A: a/b three-layered sandwiches | X: Rossmann-like | H: Rossmann-related | T: PreATP-grasp domain | F: carB | ECOD (1.6) |
E | MGS | e1bxrE6 | A: a/b three-layered sandwiches | X: Methylglyoxal synthase-like (From Topology) | H: Methylglyoxal synthase-like (From Topology) | T: Methylglyoxal synthase-like | F: MGS | ECOD (1.6) |
C | CPSase_L_D3 | e1bxrC1 | A: alpha arrays | X: HTH | H: HTH | T: winged | F: CPSase_L_D3 | ECOD (1.6) |
C | ATP-grasp | e1bxrC2 | 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 | carB | e1bxrC4 | A: a/b three-layered sandwiches | X: Rossmann-like | H: Rossmann-related | T: PreATP-grasp domain | F: carB | ECOD (1.6) |
C | MGS | e1bxrC6 | A: a/b three-layered sandwiches | X: Methylglyoxal synthase-like (From Topology) | H: Methylglyoxal synthase-like (From Topology) | T: Methylglyoxal synthase-like | F: MGS | ECOD (1.6) |
G | CPSase_L_D3 | e1bxrG1 | A: alpha arrays | X: HTH | H: HTH | T: winged | F: CPSase_L_D3 | ECOD (1.6) |
G | ATP-grasp | e1bxrG2 | 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) |
G | carB | e1bxrG4 | A: a/b three-layered sandwiches | X: Rossmann-like | H: Rossmann-related | T: PreATP-grasp domain | F: carB | ECOD (1.6) |
G | MGS | e1bxrG6 | A: a/b three-layered sandwiches | X: Methylglyoxal synthase-like (From Topology) | H: Methylglyoxal synthase-like (From Topology) | T: Methylglyoxal synthase-like | F: MGS | ECOD (1.6) |
D | GATase | e1bxrD1 | A: a/b three-layered sandwiches | X: Flavodoxin-like | H: Class I glutamine amidotransferase-like | T: Class I glutamine amidotransferase-like | F: GATase | ECOD (1.6) |
D | CPSase_sm_chain | e1bxrD2 | A: a/b three-layered sandwiches | X: The swivelling beta/beta/alpha domains | H: The swivelling beta/beta/alpha domain (From Topology) | T: The swivelling beta/beta/alpha domain | F: CPSase_sm_chain | ECOD (1.6) |
H | GATase | e1bxrH1 | A: a/b three-layered sandwiches | X: Flavodoxin-like | H: Class I glutamine amidotransferase-like | T: Class I glutamine amidotransferase-like | F: GATase | ECOD (1.6) |
H | CPSase_sm_chain | e1bxrH2 | A: a/b three-layered sandwiches | X: The swivelling beta/beta/alpha domains | H: The swivelling beta/beta/alpha domain (From Topology) | T: The swivelling beta/beta/alpha domain | F: CPSase_sm_chain | ECOD (1.6) |
B | GATase | e1bxrB1 | A: a/b three-layered sandwiches | X: Flavodoxin-like | H: Class I glutamine amidotransferase-like | T: Class I glutamine amidotransferase-like | F: GATase | ECOD (1.6) |
B | CPSase_sm_chain | e1bxrB2 | A: a/b three-layered sandwiches | X: The swivelling beta/beta/alpha domains | H: The swivelling beta/beta/alpha domain (From Topology) | T: The swivelling beta/beta/alpha domain | F: CPSase_sm_chain | ECOD (1.6) |
F | GATase | e1bxrF1 | A: a/b three-layered sandwiches | X: Flavodoxin-like | H: Class I glutamine amidotransferase-like | T: Class I glutamine amidotransferase-like | F: GATase | ECOD (1.6) |
F | CPSase_sm_chain | e1bxrF2 | A: a/b three-layered sandwiches | X: The swivelling beta/beta/alpha domains | H: The swivelling beta/beta/alpha domain (From Topology) | T: The swivelling beta/beta/alpha domain | F: CPSase_sm_chain | ECOD (1.6) |
Domain Annotation: CATH CATH Database Homepage
Protein Family Annotation Pfam Database Homepage
Chains | Accession | Name | Description | Comments | Source |
---|---|---|---|---|---|
PF02142 | MGS-like domain (MGS) | MGS-like domain | This domain composes the whole protein of methylglyoxal synthetase and the domain is also found in Carbamoyl phosphate synthetase (CPS) where it forms a regulatory domain that binds to the allosteric effector ornithine. This family also includes ino ... | Domain | |
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 ... | Domain | |
PF02787 | Carbamoyl-phosphate synthetase large chain, oligomerisation domain (CPSase_L_D3) | Carbamoyl-phosphate synthetase large chain, oligomerisation domain | Carbamoyl-phosphate synthase catalyses the ATP-dependent synthesis of carbamyl-phosphate from glutamine or ammonia and bicarbonate. The carbamoyl-phosphate synthase (CPS) enzyme in prokaryotes is a heterodimer of a small and large chain. | Domain | |
PF00117 | Glutamine amidotransferase class-I (GATase) | Glutamine amidotransferase class-I | - | Domain | |
PF00988 | Carbamoyl-phosphate synthase small chain, CPSase domain (CPSase_sm_chain) | Carbamoyl-phosphate synthase small chain, CPSase domain | The carbamoyl-phosphate synthase domain is in the amino terminus of protein. Carbamoyl-phosphate synthase catalyses the ATP-dependent synthesis of carbamyl-phosphate from glutamine or ammonia and bicarbonate. This important enzyme initiates both ... | Domain | |
PF07722 | Peptidase C26 (Peptidase_C26) | Peptidase C26 | These peptidases have gamma-glutamyl hydrolase activity; that is they catalyse the cleavage of the gamma-glutamyl bond in poly-gamma-glutamyl substrates. They are structurally related to Pfam:PF00117, but contain extensions in four loops and at the C ... | Domain |
Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage
InterPro: Protein Family Classification InterPro Database Homepage
Structure Motif Annotation: Mechanism and Catalytic Site Atlas M-CSA Database Homepage
Chains | Enzyme Name | Description | Catalytic Residues |
---|---|---|---|
carbamoyl-phosphate synthase (glutamine-hydrolysing) M-CSA #435 | Carbamoyl phosphate synthetase (CPS) catalyses the formation of carbamoyl phosphate, an intermediate in the biosynthesis of pyrimidine nucleotides and arginine, from glutamine, bicarbonate, and two molecules of MgATP. The enzyme from Escherichia coli has three separate active sites, which are connected by a molecular tunnel that is almost 100 Angstroms in length and is a heterodimeric protein that is composed of two subunits of molecular weight ~40 and ~118 kD. | Defined by 21 residues: ARG:C-129ARG:C-169LYS:C-202GLU:C-215HIS:C-243ASN:C-283GLN:C-285GLU:C-299ASN:C-301ARG:C-303ARG:C-715GLY:C-721GLY:C-722GLU:C-761GLN:C-829GLU:C-841ASN:C-843ARG:C-848CYS:D-269HIS:D-353GLU:D-355 | EC: 6.3.5.5 (PDB Primary Data) |