2IHT
Carboxyethylarginine synthase from Streptomyces clavuligerus: SeMet structure
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 | SCOP2B Superfamily | Thiamin diphosphate-binding fold (THDP-binding) | 8034529 | 3001790 | SCOP2B (2022-06-29) |
A | SCOP2B Superfamily | DHS-like NAD/FAD-binding domain | 8034528 | 3001728 | SCOP2B (2022-06-29) |
A | SCOP2B Superfamily | Thiamin diphosphate-binding fold (THDP-binding) | 8034530 | 3001790 | SCOP2B (2022-06-29) |
B | SCOP2B Superfamily | Thiamin diphosphate-binding fold (THDP-binding) | 8034530 | 3001790 | SCOP2B (2022-06-29) |
B | SCOP2B Superfamily | DHS-like NAD/FAD-binding domain | 8034528 | 3001728 | SCOP2B (2022-06-29) |
B | SCOP2B Superfamily | Thiamin diphosphate-binding fold (THDP-binding) | 8034529 | 3001790 | SCOP2B (2022-06-29) |
C | SCOP2B Superfamily | DHS-like NAD/FAD-binding domain | 8034528 | 3001728 | SCOP2B (2022-06-29) |
C | SCOP2B Superfamily | Thiamin diphosphate-binding fold (THDP-binding) | 8034529 | 3001790 | SCOP2B (2022-06-29) |
C | SCOP2B Superfamily | Thiamin diphosphate-binding fold (THDP-binding) | 8034530 | 3001790 | SCOP2B (2022-06-29) |
D | SCOP2B Superfamily | Thiamin diphosphate-binding fold (THDP-binding) | 8034529 | 3001790 | SCOP2B (2022-06-29) |
D | SCOP2B Superfamily | DHS-like NAD/FAD-binding domain | 8034528 | 3001728 | SCOP2B (2022-06-29) |
D | SCOP2B Superfamily | Thiamin diphosphate-binding fold (THDP-binding) | 8034530 | 3001790 | 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 | TPP_enzyme_M | e2ihtA1 | A: a/b three-layered sandwiches | X: Rossmann-like | H: Rossmann-related | T: DHS-like NAD/FAD-binding domain | F: TPP_enzyme_M | ECOD (1.6) |
A | TPP_enzyme_C | e2ihtA3 | A: a/b three-layered sandwiches | X: Thiamin diphosphate-binding fold (THDP-binding) (From Topology) | H: Thiamin diphosphate-binding fold (THDP-binding) (From Topology) | T: Thiamin diphosphate-binding fold (THDP-binding) | F: TPP_enzyme_C | ECOD (1.6) |
A | TPP_enzyme_N | e2ihtA2 | A: a/b three-layered sandwiches | X: Thiamin diphosphate-binding fold (THDP-binding) (From Topology) | H: Thiamin diphosphate-binding fold (THDP-binding) (From Topology) | T: Thiamin diphosphate-binding fold (THDP-binding) | F: TPP_enzyme_N | ECOD (1.6) |
B | TPP_enzyme_M | e2ihtB1 | A: a/b three-layered sandwiches | X: Rossmann-like | H: Rossmann-related | T: DHS-like NAD/FAD-binding domain | F: TPP_enzyme_M | ECOD (1.6) |
B | TPP_enzyme_C | e2ihtB3 | A: a/b three-layered sandwiches | X: Thiamin diphosphate-binding fold (THDP-binding) (From Topology) | H: Thiamin diphosphate-binding fold (THDP-binding) (From Topology) | T: Thiamin diphosphate-binding fold (THDP-binding) | F: TPP_enzyme_C | ECOD (1.6) |
B | TPP_enzyme_N | e2ihtB2 | A: a/b three-layered sandwiches | X: Thiamin diphosphate-binding fold (THDP-binding) (From Topology) | H: Thiamin diphosphate-binding fold (THDP-binding) (From Topology) | T: Thiamin diphosphate-binding fold (THDP-binding) | F: TPP_enzyme_N | ECOD (1.6) |
C | TPP_enzyme_M | e2ihtC1 | A: a/b three-layered sandwiches | X: Rossmann-like | H: Rossmann-related | T: DHS-like NAD/FAD-binding domain | F: TPP_enzyme_M | ECOD (1.6) |
C | TPP_enzyme_C | e2ihtC3 | A: a/b three-layered sandwiches | X: Thiamin diphosphate-binding fold (THDP-binding) (From Topology) | H: Thiamin diphosphate-binding fold (THDP-binding) (From Topology) | T: Thiamin diphosphate-binding fold (THDP-binding) | F: TPP_enzyme_C | ECOD (1.6) |
C | TPP_enzyme_N | e2ihtC2 | A: a/b three-layered sandwiches | X: Thiamin diphosphate-binding fold (THDP-binding) (From Topology) | H: Thiamin diphosphate-binding fold (THDP-binding) (From Topology) | T: Thiamin diphosphate-binding fold (THDP-binding) | F: TPP_enzyme_N | ECOD (1.6) |
D | TPP_enzyme_M | e2ihtD1 | A: a/b three-layered sandwiches | X: Rossmann-like | H: Rossmann-related | T: DHS-like NAD/FAD-binding domain | F: TPP_enzyme_M | ECOD (1.6) |
D | TPP_enzyme_C | e2ihtD3 | A: a/b three-layered sandwiches | X: Thiamin diphosphate-binding fold (THDP-binding) (From Topology) | H: Thiamin diphosphate-binding fold (THDP-binding) (From Topology) | T: Thiamin diphosphate-binding fold (THDP-binding) | F: TPP_enzyme_C | ECOD (1.6) |
D | TPP_enzyme_N | e2ihtD2 | A: a/b three-layered sandwiches | X: Thiamin diphosphate-binding fold (THDP-binding) (From Topology) | H: Thiamin diphosphate-binding fold (THDP-binding) (From Topology) | T: Thiamin diphosphate-binding fold (THDP-binding) | F: TPP_enzyme_N | ECOD (1.6) |
Domain Annotation: CATH CATH Database Homepage
Chain | Domain | Class | Architecture | Topology | Homology | Provenance Source (Version) |
---|---|---|---|---|---|---|
A | 3.40.50.970 | Alpha Beta | 3-Layer(aba) Sandwich | Rossmann fold | Thiamin diphosphate (ThDP)-binding fold, Pyr/PP domains | CATH (4.3.0) |
A | 3.40.50.1220 | Alpha Beta | 3-Layer(aba) Sandwich | Rossmann fold | TPP-binding domain | CATH (4.3.0) |
B | 3.40.50.970 | Alpha Beta | 3-Layer(aba) Sandwich | Rossmann fold | Thiamin diphosphate (ThDP)-binding fold, Pyr/PP domains | CATH (4.3.0) |
B | 3.40.50.1220 | Alpha Beta | 3-Layer(aba) Sandwich | Rossmann fold | TPP-binding domain | CATH (4.3.0) |
C | 3.40.50.970 | Alpha Beta | 3-Layer(aba) Sandwich | Rossmann fold | Thiamin diphosphate (ThDP)-binding fold, Pyr/PP domains | CATH (4.3.0) |
C | 3.40.50.1220 | Alpha Beta | 3-Layer(aba) Sandwich | Rossmann fold | TPP-binding domain | CATH (4.3.0) |
D | 3.40.50.970 | Alpha Beta | 3-Layer(aba) Sandwich | Rossmann fold | Thiamin diphosphate (ThDP)-binding fold, Pyr/PP domains | CATH (4.3.0) |
D | 3.40.50.1220 | Alpha Beta | 3-Layer(aba) Sandwich | Rossmann fold | TPP-binding domain | CATH (4.3.0) |
Protein Family Annotation Pfam Database Homepage
Chains | Accession | Name | Description | Comments | Source |
---|---|---|---|---|---|
PF00205 | Thiamine pyrophosphate enzyme, central domain (TPP_enzyme_M) | Thiamine pyrophosphate enzyme, central domain | The central domain of TPP enzymes contains a 2-fold Rossman fold. | Domain | |
PF02775 | Thiamine pyrophosphate enzyme, C-terminal TPP binding domain (TPP_enzyme_C) | Thiamine pyrophosphate enzyme, C-terminal TPP binding domain | - | Domain | |
PF02776 | Thiamine pyrophosphate enzyme, N-terminal TPP binding domain (TPP_enzyme_N) | Thiamine pyrophosphate enzyme, N-terminal TPP binding domain | - | Domain |
Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage
InterPro: Protein Family Classification InterPro Database Homepage
Chains | Accession | Name | Type |
---|---|---|---|
IPR045229 | Thiamine pyrophosphate enzyme | Family | |
IPR012001 | Thiamine pyrophosphate enzyme, N-terminal TPP-binding domain | Domain | |
IPR000399 | TPP-binding enzyme, conserved site | Conserved Site | |
IPR012000 | Thiamine pyrophosphate enzyme, central domain | Domain | |
IPR029061 | Thiamin diphosphate-binding fold | Homologous Superfamily | |
IPR029035 | DHS-like NAD/FAD-binding domain superfamily | Homologous Superfamily | |
IPR011766 | Thiamine pyrophosphate enzyme, TPP-binding | Domain |
Structure Motif Annotation: Mechanism and Catalytic Site Atlas M-CSA Database Homepage
Chains | Enzyme Name | Description | Catalytic Residues |
---|---|---|---|
N(2)-(2-carboxyethyl)arginine synthase M-CSA #367 | Thiamine-pyrophosphate dependent N(2)-(2-carboxyethyl)arginine synthase catalyses the initial step in the biosynthesis of the clinically relevant beta-lactamase inhibitor, clavulanic acid. The reaction involves the condensation of two primary metabolites, D-glyceraldehyde-3-phosphate and l-arginine to form N(2)-(2-carboxyethyl)arginine and phosphate. This C-N bond forming reaction forms an unusual alpha, beta-unsaturated acyl-thiamine-pyrophosphate intermediate. This enzyme is the first gene in the clavulanic acid cluster of the organism Streptomyces clavuligerus, with 18 other genes of the genome known to take part in this biosynthetic pathway. Besides this enzyme’s biosynthetic importance, it is also of mechanistic interest because of its unusual mechanism for a thiamine-pyrophosphate dependent enzyme. As expected of a thiamine-pyrophosphate dependent enzyme, sequence analysis indicates the presence of a thiamine binding mode – a motif well conserved between enzymes which use this cofactor. The mechanism can require thiamine as a cofactor in two ways: i) to effect the nucleophilic attack at a carbonyl group, and ii) to stabilise the carbanion formed after proton transfer (or decarboxylation, as catalysed by some thiamine-pyrophosphate utilising enzymes). The enzyme is tetrameric, both physiologically and in crystallography data. | Defined by 6 residues: PHE:A-438ASP:A-463ASN:A-490THR:A-492TYR:A-561GLU:B-57 | EC: 2.5.1.66 (PDB Primary Data) |