2O1X
1-deoxy-D-xylulose 5-phosphate synthase (DXS) from Deinococcus radiodurans
Domain Annotation: ECOD Classification ECOD Database Homepage
Chains | Family Name | Domain Identifier | Architecture | Possible Homology | Homology | Topology | Family | Provenance Source (Version) |
---|---|---|---|---|---|---|---|---|
A | Transketolase_C | e2o1xA2 | A: a/b three-layered sandwiches | X: TK C-terminal domain-like (From Topology) | H: TK C-terminal domain-like (From Topology) | T: TK C-terminal domain-like | F: Transketolase_C | ECOD (1.6) |
A | Transketolase_N | e2o1xA5 | 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: Transketolase_N | ECOD (1.6) |
A | Transket_pyr | e2o1xA6 | 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: Transket_pyr | ECOD (1.6) |
B | Transketolase_C | e2o1xB1 | A: a/b three-layered sandwiches | X: TK C-terminal domain-like (From Topology) | H: TK C-terminal domain-like (From Topology) | T: TK C-terminal domain-like | F: Transketolase_C | ECOD (1.6) |
B | Transketolase_N | e2o1xB3 | 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: Transketolase_N | ECOD (1.6) |
B | Transket_pyr | e2o1xB4 | 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: Transket_pyr | ECOD (1.6) |
C | Transketolase_C | e2o1xC2 | A: a/b three-layered sandwiches | X: TK C-terminal domain-like (From Topology) | H: TK C-terminal domain-like (From Topology) | T: TK C-terminal domain-like | F: Transketolase_C | ECOD (1.6) |
C | Transketolase_N | e2o1xC3 | 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: Transketolase_N | ECOD (1.6) |
C | Transket_pyr | e2o1xC4 | 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: Transket_pyr | ECOD (1.6) |
D | Transketolase_C | e2o1xD1 | A: a/b three-layered sandwiches | X: TK C-terminal domain-like (From Topology) | H: TK C-terminal domain-like (From Topology) | T: TK C-terminal domain-like | F: Transketolase_C | ECOD (1.6) |
D | Transketolase_N | e2o1xD3 | 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: Transketolase_N | ECOD (1.6) |
D | Transket_pyr | e2o1xD4 | 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: Transket_pyr | 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 | 3.40.50.920 | Alpha Beta | 3-Layer(aba) Sandwich | Rossmann fold | 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 | 3.40.50.920 | Alpha Beta | 3-Layer(aba) Sandwich | Rossmann fold | 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 | 3.40.50.920 | Alpha Beta | 3-Layer(aba) Sandwich | Rossmann fold | 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 | 3.40.50.920 | Alpha Beta | 3-Layer(aba) Sandwich | Rossmann fold | CATH (4.3.0) |
Protein Family Annotation Pfam Database Homepage
Chains | Accession | Name | Description | Comments | Source |
---|---|---|---|---|---|
PF02779 | Transketolase, pyrimidine binding domain (Transket_pyr) | Transketolase, pyrimidine binding domain | This family includes transketolase enzymes, pyruvate dehydrogenases, and branched chain alpha-keto acid decarboxylases. | Domain | |
PF13292 | 1-deoxy-D-xylulose-5-phosphate synthase (DXP_synthase_N) | 1-deoxy-D-xylulose-5-phosphate synthase | - | Family | |
PF02780 | Transketolase, C-terminal domain (Transketolase_C) | Transketolase, C-terminal domain | The C-terminal domain of transketolase has been proposed as a regulatory molecule binding site [2]. | Domain |
Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage
InterPro: Protein Family Classification InterPro Database Homepage
Chains | Accession | Name | Type |
---|---|---|---|
IPR005477 | Deoxyxylulose-5-phosphate synthase | Family | |
IPR029061 | Thiamin diphosphate-binding fold | Homologous Superfamily | |
IPR009014 | Transketolase C-terminal/Pyruvate-ferredoxin oxidoreductase domain II | Homologous Superfamily | |
IPR005475 | Transketolase-like, pyrimidine-binding domain | Domain | |
IPR033248 | Transketolase, C-terminal domain | Domain | |
IPR020826 | Transketolase binding site | Binding Site |
Structure Motif Annotation: Mechanism and Catalytic Site Atlas M-CSA Database Homepage
Chains | Enzyme Name | Description | Catalytic Residues |
---|---|---|---|
1-deoxy-D-xylulose 5-phosphate synthase M-CSA #333 | 1-Deoxy-D-xylulose-5-phosphate synthase (DXS ) is a regulatory enzyme of the mevalonate-independent pathway involved in terpenoid biosynthesis. DXP synthase is a thiamine diphosphate-dependent enzyme related to transketolase and the pyruvate dehydrogenase E1-beta subunit. DXS is found in bacteria (gene:dxs) and plants (gene:CLA1) which catalyses the thiamine pyrophosphoate-dependent acyloin condensation reaction between carbon atoms 2 and 3 of pyruvate and glyceraldehyde 3-phosphate to yield 1-deoxy-D-xylulose-5-phosphate (DXP), a precursor in the biosynthetic pathway to isoprenoids, thiamine (vitamin B1), and pyridoxol (vitamin B6). DXS is evolutionary related to TK. This reaction is the first and rate limiting step of the mevalonate-independent pathway for the biosynthesis of isopentyl pyrophosphate, a process undertaken only in fungi, algae and bacteria. DXS differs from related thiamine diphosphate dependent enzymes by virtue of its domain arrangement: the active site is not situated on a chain interface, as seen in related enzymes, but instead resides between two domain faces within the same monomer of a homodimeric complex [PMID:17135236]. | EC: 2.2.1.7 (PDB Primary Data) |