4JN6 | pdb_00004jn6

Crystal Structure of the Aldolase-Dehydrogenase Complex from Mycobacterium tuberculosis HRv37

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

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

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
A	d4jn6a2	All alpha proteins	RuvA C-terminal domain-like	post-HMGL domain-like	automated matches	automated matches	(Mycobacterium tuberculosis ) [TaxId: 1773 ],	SCOPe (2.08)
A	d4jn6a1	Alpha and beta proteins (a/b)	TIM beta/alpha-barrel	Aldolase	automated matches	automated matches	(Mycobacterium tuberculosis ) [TaxId: 1773 ],	SCOPe (2.08)
C	d4jn6c2	All alpha proteins	RuvA C-terminal domain-like	post-HMGL domain-like	automated matches	automated matches	(Mycobacterium tuberculosis ) [TaxId: 1773 ],	SCOPe (2.08)
C	d4jn6c1	Alpha and beta proteins (a/b)	TIM beta/alpha-barrel	Aldolase	automated matches	automated matches	(Mycobacterium tuberculosis ) [TaxId: 1773 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A	SCOP2B Superfamily	post-HMGL domain-like	8101078	3001285	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	Aldolase	8099054	3000445	SCOP2B (2022-06-29)
C	SCOP2 Family	HMGL-like	8099053	4000416	SCOP2 (2022-06-29)
C	SCOP2 Family	DmpG/LeuA communication domain-like	8101076	4003687	SCOP2 (2022-06-29)
C	SCOP2 Superfamily	Aldolase	8099054	3000445	SCOP2 (2022-06-29)
C	SCOP2 Superfamily	post-HMGL domain-like	8101078	3001285	SCOP2 (2022-06-29)
B	SCOP2 Family	Glyceraldehyde-3-phosphate dehydrogenase (GAPDH)-like	8085562	4000077	SCOP2 (2022-06-29)
B	SCOP2 Superfamily	GAPDH-like	8085563	3000043	SCOP2 (2022-06-29)
D	SCOP2B Superfamily	GAPDH-like	8085563	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	e4jn6A1	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	e4jn6A2	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	e4jn6C2	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	e4jn6C1	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	e4jn6B1	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	e4jn6B2	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	e4jn6D1	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	e4jn6D2	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)
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)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, C	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	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	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	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	4-hydroxy-2-oxovalerate aldolase	cation binding manganese ion binding transition metal ion binding ion binding binding metal ion binding small molecule binding 2-isopropylmalate synthase activity acyltransferase activity acyltransferase activity, acyl groups converted into alkyl on transfer transferase activity catalytic activity 4-hydroxy-2-oxovalerate aldolase activity oxo-acid-lyase activity cation binding manganese ion binding transition metal ion binding ion binding binding metal ion binding small molecule binding 2-isopropylmalate synthase activity acyltransferase activity acyltransferase activity, acyl groups converted into alkyl on transfer transferase activity catalytic activity 4-hydroxy-2-oxovalerate aldolase activity oxo-acid-lyase activity lyase activity carbon-carbon lyase activity	catabolic process metabolic process cellular process oxoacid metabolic process pyruvate family amino acid biosynthetic process amino acid metabolic process organic acid metabolic process organic acid biosynthetic process alpha-amino acid metabolic process carboxylic acid biosynthetic process small molecule metabolic process branched-chain amino acid metabolic process L-leucine metabolic process L-leucine biosynthetic process catabolic process metabolic process cellular process oxoacid metabolic process pyruvate family amino acid biosynthetic process amino acid metabolic process organic acid metabolic process organic acid biosynthetic process alpha-amino acid metabolic process carboxylic acid biosynthetic process small molecule metabolic process branched-chain amino acid metabolic process L-leucine metabolic process L-leucine biosynthetic process small molecule biosynthetic process carboxylic acid metabolic process L-amino acid biosynthetic process primary metabolic process L-amino acid metabolic process proteinogenic amino acid metabolic process amino acid biosynthetic process biosynthetic process branched-chain amino acid biosynthetic process proteinogenic amino acid biosynthetic process alpha-amino acid biosynthetic process	cell periphery cellular anatomical structure external encapsulating structure cell wall peptidoglycan-based cell wall
B, D	Acetaldehyde dehydrogenase	NAD binding binding nucleoside phosphate binding purine nucleotide binding adenyl nucleotide binding nucleotide binding heterocyclic compound binding small molecule 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	catabolic process metabolic process cellular process	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, C	IPR012425	DmpG-like communication	Domain
A, C	IPR050073	2-IPM synthase/homocitrate synthase-like	Family
A, C	IPR035685	4-hydroxy-2-oxovalerate aldolase, N-terminal catalytic TIM barrel domain	Domain
A, C	IPR013785	Aldolase-type TIM barrel	Homologous Superfamily
A, C	IPR017629	4-hydroxy-2-oxovalerate aldolase	Family
A, C	IPR000891	Pyruvate carboxyltransferase	Domain
B, D	IPR036291	NAD(P)-binding domain superfamily	Homologous Superfamily
B, D	IPR015426	Acetaldehyde dehydrogenase, C-terminal	Domain
B, D	IPR003361	Acetaldehyde dehydrogenase	Family
B, D	IPR000534	Semialdehyde dehydrogenase, NAD-binding	Domain

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), 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 R01GM157729.