1SMK | pdb_00001smk

Mature and translocatable forms of glyoxysomal malate dehydrogenase have different activities and stabilities but similar crystal structures

External Resource: Annotation

Domain Annotation: SCOP/SCOPe Classification
Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
Domain Annotation: CATH
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)
C	d1smkc1	Alpha and beta proteins (a/b)	NAD(P)-binding Rossmann-fold domains	NAD(P)-binding Rossmann-fold domains	automated matches	automated matches	(Citrullus lanatus ) [TaxId: 3654 ],	SCOPe (2.08)
C	d1smkc2	Alpha and beta proteins (a+b)	LDH C-terminal domain-like	LDH C-terminal domain-like	automated matches	automated matches	(Citrullus lanatus ) [TaxId: 3654 ],	SCOPe (2.08)
F	d1smkf1	Alpha and beta proteins (a/b)	NAD(P)-binding Rossmann-fold domains	NAD(P)-binding Rossmann-fold domains	automated matches	automated matches	(Citrullus lanatus ) [TaxId: 3654 ],	SCOPe (2.08)
F	d1smkf2	Alpha and beta proteins (a+b)	LDH C-terminal domain-like	LDH C-terminal domain-like	automated matches	automated matches	(Citrullus lanatus ) [TaxId: 3654 ],	SCOPe (2.08)
H	d1smkh1	Alpha and beta proteins (a/b)	NAD(P)-binding Rossmann-fold domains	NAD(P)-binding Rossmann-fold domains	automated matches	automated matches	(Citrullus lanatus ) [TaxId: 3654 ],	SCOPe (2.08)
H	d1smkh2	Alpha and beta proteins (a+b)	LDH C-terminal domain-like	LDH C-terminal domain-like	automated matches	automated matches	(Citrullus lanatus ) [TaxId: 3654 ],	SCOPe (2.08)
G	d1smkg1	Alpha and beta proteins (a/b)	NAD(P)-binding Rossmann-fold domains	NAD(P)-binding Rossmann-fold domains	automated matches	automated matches	(Citrullus lanatus ) [TaxId: 3654 ],	SCOPe (2.08)
G	d1smkg2	Alpha and beta proteins (a+b)	LDH C-terminal domain-like	LDH C-terminal domain-like	automated matches	automated matches	(Citrullus lanatus ) [TaxId: 3654 ],	SCOPe (2.08)
E	d1smke1	Alpha and beta proteins (a/b)	NAD(P)-binding Rossmann-fold domains	NAD(P)-binding Rossmann-fold domains	automated matches	automated matches	(Citrullus lanatus ) [TaxId: 3654 ],	SCOPe (2.08)
E	d1smke2	Alpha and beta proteins (a+b)	LDH C-terminal domain-like	LDH C-terminal domain-like	automated matches	automated matches	(Citrullus lanatus ) [TaxId: 3654 ],	SCOPe (2.08)
D	d1smkd1	Alpha and beta proteins (a/b)	NAD(P)-binding Rossmann-fold domains	NAD(P)-binding Rossmann-fold domains	automated matches	automated matches	(Citrullus lanatus ) [TaxId: 3654 ],	SCOPe (2.08)
D	d1smkd2	Alpha and beta proteins (a+b)	LDH C-terminal domain-like	LDH C-terminal domain-like	automated matches	automated matches	(Citrullus lanatus ) [TaxId: 3654 ],	SCOPe (2.08)
B	d1smkb1	Alpha and beta proteins (a/b)	NAD(P)-binding Rossmann-fold domains	NAD(P)-binding Rossmann-fold domains	automated matches	automated matches	(Citrullus lanatus ) [TaxId: 3654 ],	SCOPe (2.08)
B	d1smkb2	Alpha and beta proteins (a+b)	LDH C-terminal domain-like	LDH C-terminal domain-like	automated matches	automated matches	(Citrullus lanatus ) [TaxId: 3654 ],	SCOPe (2.08)
A	d1smka1	Alpha and beta proteins (a/b)	NAD(P)-binding Rossmann-fold domains	NAD(P)-binding Rossmann-fold domains	automated matches	automated matches	(Citrullus lanatus ) [TaxId: 3654 ],	SCOPe (2.08)
A	d1smka2	Alpha and beta proteins (a+b)	LDH C-terminal domain-like	LDH C-terminal domain-like	automated matches	automated matches	(Citrullus lanatus ) [TaxId: 3654 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
C	SCOP2B Superfamily	LDH/MDH/AglA-like	8068855	3000039	SCOP2B (2022-06-29)
F	SCOP2B Superfamily	LDH/MDH/AglA-like	8068855	3000039	SCOP2B (2022-06-29)
H	SCOP2B Superfamily	LDH/MDH/AglA-like	8068855	3000039	SCOP2B (2022-06-29)
G	SCOP2B Superfamily	LDH/MDH/AglA-like	8068855	3000039	SCOP2B (2022-06-29)
E	SCOP2B Superfamily	LDH/MDH/AglA-like	8068855	3000039	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	LDH/MDH/AglA-like	8068855	3000039	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	LDH/MDH/AglA-like	8068855	3000039	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	LDH/MDH/AglA-like	8068855	3000039	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)
C	tRNA-synt_1b	e1smkC2	A: a/b three-layered sandwiches	X: HTH	H: Nudix	T: winged helix domain	F: tRNA-synt_1b	ECOD (v294.1)
C	EPSP_synthase	e1smkC3	A: a/b three-layered sandwiches	X: P-loop domains-like	H: ARM repeat	T: ARM repeat	F: EPSP_synthase	ECOD (v294.1)
F	tRNA-synt_1b	e1smkF2	A: a/b three-layered sandwiches	X: HTH	H: Nudix	T: winged helix domain	F: tRNA-synt_1b	ECOD (v294.1)
F	EPSP_synthase	e1smkF3	A: a/b three-layered sandwiches	X: P-loop domains-like	H: ARM repeat	T: ARM repeat	F: EPSP_synthase	ECOD (v294.1)
H	tRNA-synt_1b	e1smkH2	A: a/b three-layered sandwiches	X: HTH	H: Nudix	T: winged helix domain	F: tRNA-synt_1b	ECOD (v294.1)
H	EPSP_synthase	e1smkH3	A: a/b three-layered sandwiches	X: P-loop domains-like	H: ARM repeat	T: ARM repeat	F: EPSP_synthase	ECOD (v294.1)
G	tRNA-synt_1b	e1smkG2	A: a/b three-layered sandwiches	X: HTH	H: Nudix	T: winged helix domain	F: tRNA-synt_1b	ECOD (v294.1)
G	EPSP_synthase	e1smkG3	A: a/b three-layered sandwiches	X: P-loop domains-like	H: ARM repeat	T: ARM repeat	F: EPSP_synthase	ECOD (v294.1)
E	tRNA-synt_1b	e1smkE2	A: a/b three-layered sandwiches	X: HTH	H: Nudix	T: winged helix domain	F: tRNA-synt_1b	ECOD (v294.1)
E	EPSP_synthase	e1smkE1	A: a/b three-layered sandwiches	X: P-loop domains-like	H: ARM repeat	T: ARM repeat	F: EPSP_synthase	ECOD (v294.1)
D	tRNA-synt_1b	e1smkD2	A: a/b three-layered sandwiches	X: HTH	H: Nudix	T: winged helix domain	F: tRNA-synt_1b	ECOD (v294.1)
D	EPSP_synthase	e1smkD1	A: a/b three-layered sandwiches	X: P-loop domains-like	H: ARM repeat	T: ARM repeat	F: EPSP_synthase	ECOD (v294.1)
B	tRNA-synt_1b	e1smkB2	A: a/b three-layered sandwiches	X: HTH	H: Nudix	T: winged helix domain	F: tRNA-synt_1b	ECOD (v294.1)
B	EPSP_synthase	e1smkB1	A: a/b three-layered sandwiches	X: P-loop domains-like	H: ARM repeat	T: ARM repeat	F: EPSP_synthase	ECOD (v294.1)
A	tRNA-synt_1b	e1smkA2	A: a/b three-layered sandwiches	X: HTH	H: Nudix	T: winged helix domain	F: tRNA-synt_1b	ECOD (v294.1)
A	EPSP_synthase	e1smkA3	A: a/b three-layered sandwiches	X: P-loop domains-like	H: ARM repeat	T: ARM repeat	F: EPSP_synthase	ECOD (v294.1)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
C	3.40.50.720	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	NAD(P)-binding Rossmann-like Domain	CATH (4.3.0)
C	3.90.110.10	Alpha Beta	Alpha-Beta Complex	L-2-Hydroxyisocaproate Dehydrogenase	Chain A, 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	3.90.110.10	Alpha Beta	Alpha-Beta Complex	L-2-Hydroxyisocaproate Dehydrogenase	Chain A, 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	3.90.110.10	Alpha Beta	Alpha-Beta Complex	L-2-Hydroxyisocaproate Dehydrogenase	Chain A, domain 2	CATH (4.3.0)
G	3.40.50.720	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	NAD(P)-binding Rossmann-like Domain	CATH (4.3.0)
G	3.90.110.10	Alpha Beta	Alpha-Beta Complex	L-2-Hydroxyisocaproate Dehydrogenase	Chain A, domain 2	CATH (4.3.0)
E	3.40.50.720	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	NAD(P)-binding Rossmann-like Domain	CATH (4.3.0)
E	3.90.110.10	Alpha Beta	Alpha-Beta Complex	L-2-Hydroxyisocaproate Dehydrogenase	Chain A, 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	3.90.110.10	Alpha Beta	Alpha-Beta Complex	L-2-Hydroxyisocaproate Dehydrogenase	Chain A, domain 2	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	3.90.110.10	Alpha Beta	Alpha-Beta Complex	L-2-Hydroxyisocaproate Dehydrogenase	Chain A, domain 2	CATH (4.3.0)
A	3.40.50.720	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	NAD(P)-binding Rossmann-like Domain	CATH (4.3.0)
A	3.90.110.10	Alpha Beta	Alpha-Beta Complex	L-2-Hydroxyisocaproate Dehydrogenase	Chain A, domain 2	CATH (4.3.0)

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B, C, D, E A, B, C, D, E, F, G, H	Malate dehydrogenase, glyoxysomal	L-malate dehydrogenase (NAD+) activity oxidoreductase activity oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor oxidoreductase activity, acting on CH-OH group of donors malate dehydrogenase activity catalytic activity	aerobic respiration cellular respiration tricarboxylic acid cycle energy derivation by oxidation of organic compounds primary metabolic process metabolic process cellular process generation of precursor metabolites and energy carbohydrate metabolic process glyoxylate metabolic process glyoxylate cycle oxoacid metabolic process carboxylic acid metabolic process organic acid metabolic process aerobic respiration cellular respiration tricarboxylic acid cycle energy derivation by oxidation of organic compounds primary metabolic process metabolic process cellular process generation of precursor metabolites and energy carbohydrate metabolic process glyoxylate metabolic process glyoxylate cycle oxoacid metabolic process carboxylic acid metabolic process organic acid metabolic process aldehyde metabolic process small molecule metabolic process monocarboxylic acid metabolic process malate metabolic process dicarboxylic acid metabolic process	membrane-bounded organelle intracellular organelle cellular anatomical structure intracellular anatomical structure organelle glyoxysome peroxisome microbody cytoplasm intracellular membrane-bounded organelle plastid chloroplast

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B, C, D, E A, B, C, D, E, F, G, H	IPR015955	Lactate dehydrogenase/glycoside hydrolase, family 4, C-terminal	Homologous Superfamily
A, B, C, D, E A, B, C, D, E, F, G, H	IPR001252	Malate dehydrogenase, active site	Active Site
A, B, C, D, E A, B, C, D, E, F, G, H	IPR001557	L-lactate/malate dehydrogenase	Family
A, B, C, D, E A, B, C, D, E, F, G, H	IPR010097	Malate dehydrogenase, type 1	Family
A, B, C, D, E A, B, C, D, E, F, G, H	IPR001236	Lactate/malate dehydrogenase, N-terminal	Domain
A, B, C, D, E A, B, C, D, E, F, G, H	IPR036291	NAD(P)-binding domain superfamily	Homologous Superfamily
A, B, C, D, E A, B, C, D, E, F, G, H	IPR022383	Lactate/malate dehydrogenase, C-terminal	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. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.