1NVM
Crystal structure of a bifunctional aldolase-dehydrogenase : sequestering a reactive and volatile intermediate
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 | HMGL-like | 8021269 | 4000416 | SCOP2 (2022-06-29) |
A | SCOP2 Family | DmpG/LeuA communication domain-like | 8021270 | 4003687 | SCOP2 (2022-06-29) |
A | SCOP2 Superfamily | Aldolase | 8033649 | 3000445 | SCOP2 (2022-06-29) |
A | SCOP2 Superfamily | post-HMGL domain-like | 8033650 | 3001285 | SCOP2 (2022-06-29) |
C | SCOP2B Superfamily | post-HMGL domain-like | 8033650 | 3001285 | SCOP2B (2022-06-29) |
C | SCOP2B Superfamily | Aldolase | 8033649 | 3000445 | SCOP2B (2022-06-29) |
E | SCOP2B Superfamily | Aldolase | 8033649 | 3000445 | SCOP2B (2022-06-29) |
E | SCOP2B Superfamily | post-HMGL domain-like | 8033650 | 3001285 | SCOP2B (2022-06-29) |
G | SCOP2B Superfamily | post-HMGL domain-like | 8033650 | 3001285 | SCOP2B (2022-06-29) |
G | SCOP2B Superfamily | Aldolase | 8033649 | 3000445 | SCOP2B (2022-06-29) |
B | SCOP2 Family | Glyceraldehyde-3-phosphate dehydrogenase (GAPDH)-like | 8056097 | 4000077 | SCOP2 (2022-06-29) |
B | SCOP2 Superfamily | GAPDH-like | 8056098 | 3000043 | SCOP2 (2022-06-29) |
D | SCOP2B Superfamily | GAPDH-like | 8056098 | 3000043 | SCOP2B (2022-06-29) |
F | SCOP2B Superfamily | GAPDH-like | 8056098 | 3000043 | SCOP2B (2022-06-29) |
H | SCOP2B Superfamily | GAPDH-like | 8056098 | 3000043 | 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 | DmpG_comm | e1nvmA1 | A: alpha arrays | X: RuvA-C | H: post-HMGL domain-like (From Topology) | T: post-HMGL domain-like | F: DmpG_comm | ECOD (1.6) |
A | HMGL-like_1 | e1nvmA2 | A: a/b barrels | X: TIM beta/alpha-barrel | H: TIM barrels (From Topology) | T: TIM barrels | F: HMGL-like_1 | ECOD (1.6) |
C | DmpG_comm | e1nvmC1 | A: alpha arrays | X: RuvA-C | H: post-HMGL domain-like (From Topology) | T: post-HMGL domain-like | F: DmpG_comm | ECOD (1.6) |
C | HMGL-like_1 | e1nvmC2 | A: a/b barrels | X: TIM beta/alpha-barrel | H: TIM barrels (From Topology) | T: TIM barrels | F: HMGL-like_1 | ECOD (1.6) |
E | DmpG_comm | e1nvmE1 | A: alpha arrays | X: RuvA-C | H: post-HMGL domain-like (From Topology) | T: post-HMGL domain-like | F: DmpG_comm | ECOD (1.6) |
E | HMGL-like_1 | e1nvmE2 | A: a/b barrels | X: TIM beta/alpha-barrel | H: TIM barrels (From Topology) | T: TIM barrels | F: HMGL-like_1 | ECOD (1.6) |
G | DmpG_comm | e1nvmG1 | A: alpha arrays | X: RuvA-C | H: post-HMGL domain-like (From Topology) | T: post-HMGL domain-like | F: DmpG_comm | ECOD (1.6) |
G | HMGL-like_1 | e1nvmG2 | A: a/b barrels | X: TIM beta/alpha-barrel | H: TIM barrels (From Topology) | T: TIM barrels | F: HMGL-like_1 | ECOD (1.6) |
B | AcetDehyd-dimer | e1nvmB1 | A: a+b two layers | X: FwdE/GAPDH domain-like | H: Glyceraldehyde-3-phosphate dehydrogenase-like, C-terminal domain (From Topology) | T: Glyceraldehyde-3-phosphate dehydrogenase-like, C-terminal domain | F: AcetDehyd-dimer | ECOD (1.6) |
B | Semialdhyde_dh | e1nvmB2 | A: a/b three-layered sandwiches | X: Rossmann-like | H: Rossmann-related | T: NAD(P)-binding Rossmann-fold domains | F: Semialdhyde_dh | ECOD (1.6) |
D | AcetDehyd-dimer | e1nvmD1 | A: a+b two layers | X: FwdE/GAPDH domain-like | H: Glyceraldehyde-3-phosphate dehydrogenase-like, C-terminal domain (From Topology) | T: Glyceraldehyde-3-phosphate dehydrogenase-like, C-terminal domain | F: AcetDehyd-dimer | ECOD (1.6) |
D | Semialdhyde_dh | e1nvmD2 | A: a/b three-layered sandwiches | X: Rossmann-like | H: Rossmann-related | T: NAD(P)-binding Rossmann-fold domains | F: Semialdhyde_dh | ECOD (1.6) |
F | AcetDehyd-dimer | e1nvmF1 | A: a+b two layers | X: FwdE/GAPDH domain-like | H: Glyceraldehyde-3-phosphate dehydrogenase-like, C-terminal domain (From Topology) | T: Glyceraldehyde-3-phosphate dehydrogenase-like, C-terminal domain | F: AcetDehyd-dimer | ECOD (1.6) |
F | Semialdhyde_dh | e1nvmF2 | A: a/b three-layered sandwiches | X: Rossmann-like | H: Rossmann-related | T: NAD(P)-binding Rossmann-fold domains | F: Semialdhyde_dh | ECOD (1.6) |
H | AcetDehyd-dimer | e1nvmH1 | A: a+b two layers | X: FwdE/GAPDH domain-like | H: Glyceraldehyde-3-phosphate dehydrogenase-like, C-terminal domain (From Topology) | T: Glyceraldehyde-3-phosphate dehydrogenase-like, C-terminal domain | F: AcetDehyd-dimer | ECOD (1.6) |
H | Semialdhyde_dh | e1nvmH2 | A: a/b three-layered sandwiches | X: Rossmann-like | H: Rossmann-related | T: NAD(P)-binding Rossmann-fold domains | F: Semialdhyde_dh | ECOD (1.6) |
Domain Annotation: CATH CATH Database Homepage
Protein Family Annotation Pfam Database Homepage
Chains | Accession | Name | Description | Comments | Source |
---|---|---|---|---|---|
PF07836 | DmpG-like communication domain (DmpG_comm) | DmpG-like communication domain | This domain is found towards the C-terminal region of various aldolase enzymes. It consists of five alpha-helices, four of which form an antiparallel helical bundle that plugs the C-terminus of the N-terminal TIM barrel domain [1]. The communicatio ... | Domain | |
PF00682 | HMGL-like (HMGL-like) | HMGL-like | This family contains a diverse set of enzymes. These include various aldolases and a region of pyruvate carboxylase. | Domain | |
PF01118 | Semialdehyde dehydrogenase, NAD binding domain (Semialdhyde_dh) | Semialdehyde dehydrogenase, NAD binding domain | This Pfam entry contains the following members: N-acetyl-glutamine semialdehyde dehydrogenase (AgrC) Aspartate-semialdehyde dehydrogenase | Domain | |
PF09290 | Prokaryotic acetaldehyde dehydrogenase, dimerisation (AcetDehyd-dimer) | Prokaryotic acetaldehyde dehydrogenase, dimerisation | Members of this family are found in prokaryotic acetaldehyde dehydrogenase (acylating), and adopt a structure consisting of an alpha-beta-alpha-beta(3) core. They mediate dimerisation of the protein [1]. | Domain |
Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage
InterPro: Protein Family Classification InterPro Database Homepage
Chains | Accession | Name | Type |
---|---|---|---|
IPR012425 | DmpG-like communication | Domain | |
IPR035685 | 4-hydroxy-2-oxovalerate aldolase, N-terminal catalytic TIM barrel domain | Domain | |
IPR013785 | Aldolase-type TIM barrel | Homologous Superfamily | |
IPR050073 | Alpha-IPM synthase/homocitrate synthase | Family | |
IPR017629 | 4-hydroxy-2-oxovalerate aldolase | Family | |
IPR000891 | Pyruvate carboxyltransferase | Domain | |
IPR036291 | NAD(P)-binding domain superfamily | Homologous Superfamily | |
IPR015426 | Acetaldehyde dehydrogenase, C-terminal | Domain | |
IPR003361 | Acetaldehyde dehydrogenase | Family | |
IPR000534 | Semialdehyde dehydrogenase, NAD-binding | Domain |
Structure Motif Annotation: Mechanism and Catalytic Site Atlas M-CSA Database Homepage
Chains | Enzyme Name | Description | Catalytic Residues |
---|---|---|---|
4-hydroxy-2-oxovalerate aldolase M-CSA #652 | 4-hydroxy-2-ketovalerate aldolase catalyses the conversion of 4-hydroxy-2-ketovalerate to acetaldehyde and pyruvate. It associates tightly with acetaldehyde dehydrogenase and appears to be inactive when expressed without this dehydrogenase. The aldolase and dehydrogenase form a bifunctional enzyme, and there is evidence that the reactive acetaldehyde intermediate is passed between the two active sites via a channelling tunnel. the bifunctional enzyme catalyses the final two steps in the degradation of catechol, an intermediate in the degradation of aromatic compounds by many bacteria. | Defined by 5 residues: ASP:A-18HIS:A-21HIS:A-200HIS:A-202TYR:A-291 | EC: 4.1.3 (PDB Primary Data) |