1NVM

Crystal structure of a bifunctional aldolase-dehydrogenase : sequestering a reactive and volatile intermediate

External Resource: Annotation

Domain Annotation: SCOP/SCOPe Classification
Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
Domain Annotation: CATH
Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification
Structure Motif: Primary M-CSA Annotation

Domain Annotation: SCOP/SCOPe Classification SCOP-e Database Homepage

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
A	d1nvma1	All alpha proteins	RuvA C-terminal domain-like	post-HMGL domain-like	DmpG/LeuA communication domain-like	4-hydroxy-2-oxovalerate aldolase DmpG, communication domain	(Pseudomonas sp. CF600 ) [TaxId: 79676 ],	SCOPe (2.08)
A	d1nvma2	Alpha and beta proteins (a/b)	TIM beta/alpha-barrel	Aldolase	HMGL-like	4-hydroxy-2-oxovalerate aldolase DmpG, catalytic domain	(Pseudomonas sp. CF600 ) [TaxId: 79676 ],	SCOPe (2.08)
C	d1nvmc1	All alpha proteins	RuvA C-terminal domain-like	post-HMGL domain-like	DmpG/LeuA communication domain-like	4-hydroxy-2-oxovalerate aldolase DmpG, communication domain	(Pseudomonas sp. CF600 ) [TaxId: 79676 ],	SCOPe (2.08)
C	d1nvmc2	Alpha and beta proteins (a/b)	TIM beta/alpha-barrel	Aldolase	HMGL-like	4-hydroxy-2-oxovalerate aldolase DmpG, catalytic domain	(Pseudomonas sp. CF600 ) [TaxId: 79676 ],	SCOPe (2.08)
E	d1nvme1	All alpha proteins	RuvA C-terminal domain-like	post-HMGL domain-like	DmpG/LeuA communication domain-like	4-hydroxy-2-oxovalerate aldolase DmpG, communication domain	(Pseudomonas sp. CF600 ) [TaxId: 79676 ],	SCOPe (2.08)
E	d1nvme2	Alpha and beta proteins (a/b)	TIM beta/alpha-barrel	Aldolase	HMGL-like	4-hydroxy-2-oxovalerate aldolase DmpG, catalytic domain	(Pseudomonas sp. CF600 ) [TaxId: 79676 ],	SCOPe (2.08)
G	d1nvmg1	All alpha proteins	RuvA C-terminal domain-like	post-HMGL domain-like	DmpG/LeuA communication domain-like	4-hydroxy-2-oxovalerate aldolase DmpG, communication domain	(Pseudomonas sp. CF600 ) [TaxId: 79676 ],	SCOPe (2.08)
G	d1nvmg2	Alpha and beta proteins (a/b)	TIM beta/alpha-barrel	Aldolase	HMGL-like	4-hydroxy-2-oxovalerate aldolase DmpG, catalytic domain	(Pseudomonas sp. CF600 ) [TaxId: 79676 ],	SCOPe (2.08)
B	d1nvmb1	Alpha and beta proteins (a/b)	NAD(P)-binding Rossmann-fold domains	NAD(P)-binding Rossmann-fold domains	Glyceraldehyde-3-phosphate dehydrogenase-like, N-terminal domain	Acetaldehyde dehydrogenase (acylating)	(Pseudomonas sp. CF600 ) [TaxId: 79676 ],	SCOPe (2.08)
B	d1nvmb2	Alpha and beta proteins (a+b)	FwdE/GAPDH domain-like	Glyceraldehyde-3-phosphate dehydrogenase-like, C-terminal domain	GAPDH-like	Acetaldehyde dehydrogenase (acylating)	(Pseudomonas sp. CF600 ) [TaxId: 79676 ],	SCOPe (2.08)
D	d1nvmd1	Alpha and beta proteins (a/b)	NAD(P)-binding Rossmann-fold domains	NAD(P)-binding Rossmann-fold domains	Glyceraldehyde-3-phosphate dehydrogenase-like, N-terminal domain	Acetaldehyde dehydrogenase (acylating)	(Pseudomonas sp. CF600 ) [TaxId: 79676 ],	SCOPe (2.08)
D	d1nvmd2	Alpha and beta proteins (a+b)	FwdE/GAPDH domain-like	Glyceraldehyde-3-phosphate dehydrogenase-like, C-terminal domain	GAPDH-like	Acetaldehyde dehydrogenase (acylating)	(Pseudomonas sp. CF600 ) [TaxId: 79676 ],	SCOPe (2.08)
F	d1nvmf1	Alpha and beta proteins (a/b)	NAD(P)-binding Rossmann-fold domains	NAD(P)-binding Rossmann-fold domains	Glyceraldehyde-3-phosphate dehydrogenase-like, N-terminal domain	Acetaldehyde dehydrogenase (acylating)	(Pseudomonas sp. CF600 ) [TaxId: 79676 ],	SCOPe (2.08)
F	d1nvmf2	Alpha and beta proteins (a+b)	FwdE/GAPDH domain-like	Glyceraldehyde-3-phosphate dehydrogenase-like, C-terminal domain	GAPDH-like	Acetaldehyde dehydrogenase (acylating)	(Pseudomonas sp. CF600 ) [TaxId: 79676 ],	SCOPe (2.08)
H	d1nvmh1	Alpha and beta proteins (a/b)	NAD(P)-binding Rossmann-fold domains	NAD(P)-binding Rossmann-fold domains	Glyceraldehyde-3-phosphate dehydrogenase-like, N-terminal domain	Acetaldehyde dehydrogenase (acylating)	(Pseudomonas sp. CF600 ) [TaxId: 79676 ],	SCOPe (2.08)
H	d1nvmh2	Alpha and beta proteins (a+b)	FwdE/GAPDH domain-like	Glyceraldehyde-3-phosphate dehydrogenase-like, C-terminal domain	GAPDH-like	Acetaldehyde dehydrogenase (acylating)	(Pseudomonas sp. CF600 ) [TaxId: 79676 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A	SCOP2 Family	DmpG/LeuA communication domain-like	8021270	4003687	SCOP2 (2022-06-29)
A	SCOP2 Family	HMGL-like	8021269	4000416	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	post-HMGL domain-like	8033650	3001285	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	Aldolase	8033649	3000445	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

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	3.20.20.70	Alpha Beta	Alpha-Beta Barrel	TIM Barrel	Aldolase class I	CATH (4.3.0)
A	1.10.8.60	Mainly Alpha	Orthogonal Bundle	Helicase, Ruva Protein	domain 3	CATH (4.3.0)
C	3.20.20.70	Alpha Beta	Alpha-Beta Barrel	TIM Barrel	Aldolase class I	CATH (4.3.0)
C	1.10.8.60	Mainly Alpha	Orthogonal Bundle	Helicase, Ruva Protein	domain 3	CATH (4.3.0)
E	3.20.20.70	Alpha Beta	Alpha-Beta Barrel	TIM Barrel	Aldolase class I	CATH (4.3.0)
E	1.10.8.60	Mainly Alpha	Orthogonal Bundle	Helicase, Ruva Protein	domain 3	CATH (4.3.0)
G	3.20.20.70	Alpha Beta	Alpha-Beta Barrel	TIM Barrel	Aldolase class I	CATH (4.3.0)
G	1.10.8.60	Mainly Alpha	Orthogonal Bundle	Helicase, Ruva Protein	domain 3	CATH (4.3.0)
B	3.40.50.720	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	NAD(P)-binding Rossmann-like Domain	CATH (4.3.0)
B	3.30.360.10	Alpha Beta	2-Layer Sandwich	Dihydrodipicolinate Reductase	domain 2	CATH (4.3.0)
D	3.40.50.720	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	NAD(P)-binding Rossmann-like Domain	CATH (4.3.0)
D	3.30.360.10	Alpha Beta	2-Layer Sandwich	Dihydrodipicolinate Reductase	domain 2	CATH (4.3.0)
F	3.40.50.720	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	NAD(P)-binding Rossmann-like Domain	CATH (4.3.0)
F	3.30.360.10	Alpha Beta	2-Layer Sandwich	Dihydrodipicolinate Reductase	domain 2	CATH (4.3.0)
H	3.40.50.720	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	NAD(P)-binding Rossmann-like Domain	CATH (4.3.0)
H	3.30.360.10	Alpha Beta	2-Layer Sandwich	Dihydrodipicolinate Reductase	domain 2	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, C, E, G	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 ...	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 communication domain is thought to play an important role in the heterodimerisation of the enzyme [1].	Domain
A, C, E, G	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
B, D, F, H	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
B, D, F, H	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

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, C, E, G	4-hydroxy-2-oxovalerate aldolase	cation binding manganese ion binding transition metal ion binding ion binding binding metal ion binding small molecule binding 4-hydroxy-2-oxovalerate aldolase activity oxo-acid-lyase activity lyase activity catalytic activity carbon-carbon lyase activity	catabolic process benzene-containing compound metabolic process oxoacid metabolic process benzoate metabolic process cellular metabolic process carboxylic acid metabolic process organic acid metabolic process organic acid catabolic process organic cyclic compound catabolic process cellular catabolic process benzoate catabolic process organic cyclic compound metabolic process organic substance metabolic process monocarboxylic acid catabolic process carboxylic acid catabolic process catabolic process benzene-containing compound metabolic process oxoacid metabolic process benzoate metabolic process cellular metabolic process carboxylic acid metabolic process organic acid metabolic process organic acid catabolic process organic cyclic compound catabolic process cellular catabolic process benzoate catabolic process organic cyclic compound metabolic process organic substance metabolic process monocarboxylic acid catabolic process carboxylic acid catabolic process metabolic process small molecule metabolic process cellular process benzoate catabolic process via hydroxylation monocarboxylic acid metabolic process small molecule catabolic process organic substance catabolic process phenol-containing compound catabolic process organic hydroxy compound catabolic process organic hydroxy compound metabolic process phenol-containing compound metabolic process	-
B, D, F, H	acetaldehyde dehydrogenase (acylating)	binding nucleoside phosphate binding purine nucleotide binding organic cyclic compound binding adenyl nucleotide binding nucleotide binding heterocyclic compound binding NADP binding small molecule binding NAD binding oxidoreductase activity oxidoreductase activity, acting on the aldehyde or oxo group of donors catalytic activity acetaldehyde dehydrogenase (acetylating) activity binding nucleoside phosphate binding purine nucleotide binding organic cyclic compound binding adenyl nucleotide binding nucleotide binding heterocyclic compound binding NADP binding small molecule binding NAD binding oxidoreductase activity oxidoreductase activity, acting on the aldehyde or oxo group of donors catalytic activity acetaldehyde dehydrogenase (acetylating) activity oxidoreductase activity, acting on the aldehyde or oxo group of donors, NAD or NADP as acceptor	phenol-containing compound catabolic process organic cyclic compound metabolic process catabolic process organic substance metabolic process organic hydroxy compound catabolic process organic hydroxy compound metabolic process phenol-containing compound metabolic process metabolic process organic substance catabolic process organic cyclic compound catabolic process	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, C, E, G	IPR012425	DmpG-like communication	Domain
A, C, E, G	IPR035685	4-hydroxy-2-oxovalerate aldolase, N-terminal catalytic TIM barrel domain	Domain
A, C, E, G	IPR013785	Aldolase-type TIM barrel	Homologous Superfamily
A, C, E, G	IPR017629	4-hydroxy-2-oxovalerate aldolase	Family
A, C, E, G	IPR000891	Pyruvate carboxyltransferase	Domain
B, D, F, H	IPR036291	NAD(P)-binding domain superfamily	Homologous Superfamily
B, D, F, H	IPR015426	Acetaldehyde dehydrogenase, C-terminal	Domain
B, D, F, H	IPR003361	Acetaldehyde dehydrogenase	Family
B, D, F, H	IPR000534	Semialdehyde dehydrogenase, NAD-binding	Domain

Structure Motif Annotation: Mechanism and Catalytic Site Atlas M-CSA Database Homepage

Chains	Enzyme Name	Description	Catalytic Residues
A	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 \| Explore in 3D: M-CSA Motif Definition Search M-CSA Motif EC: 4.1.3 (PDB Primary Data) Search M-CSA Motif + EC 4.1.3

RCSB PDB Core Operations are funded by the National Science Foundation (DBI-1832184), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM133198.