3FA3 | pdb_00003fa3

Crystal structure of 2,3-dimethylmalate lyase, a PEP mutase/isocitrate lyase superfamily member, trigonal crystal form

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)
A	d3fa3a_	Alpha and beta proteins (a/b)	TIM beta/alpha-barrel	Phosphoenolpyruvate/pyruvate domain	automated matches	automated matches	(Aspergillus niger ) [TaxId: 5061 ],	SCOPe (2.08)
C	d3fa3c_	Alpha and beta proteins (a/b)	TIM beta/alpha-barrel	Phosphoenolpyruvate/pyruvate domain	automated matches	automated matches	(Aspergillus niger ) [TaxId: 5061 ],	SCOPe (2.08)
F	d3fa3f_	Alpha and beta proteins (a/b)	TIM beta/alpha-barrel	Phosphoenolpyruvate/pyruvate domain	automated matches	automated matches	(Aspergillus niger ) [TaxId: 5061 ],	SCOPe (2.08)
G	d3fa3g_	Alpha and beta proteins (a/b)	TIM beta/alpha-barrel	Phosphoenolpyruvate/pyruvate domain	automated matches	automated matches	(Aspergillus niger ) [TaxId: 5061 ],	SCOPe (2.08)
H	d3fa3h_	Alpha and beta proteins (a/b)	TIM beta/alpha-barrel	Phosphoenolpyruvate/pyruvate domain	automated matches	automated matches	(Aspergillus niger ) [TaxId: 5061 ],	SCOPe (2.08)
I	d3fa3i_	Alpha and beta proteins (a/b)	TIM beta/alpha-barrel	Phosphoenolpyruvate/pyruvate domain	automated matches	automated matches	(Aspergillus niger ) [TaxId: 5061 ],	SCOPe (2.08)
K	d3fa3k_	Alpha and beta proteins (a/b)	TIM beta/alpha-barrel	Phosphoenolpyruvate/pyruvate domain	automated matches	automated matches	(Aspergillus niger ) [TaxId: 5061 ],	SCOPe (2.08)
L	d3fa3l_	Alpha and beta proteins (a/b)	TIM beta/alpha-barrel	Phosphoenolpyruvate/pyruvate domain	automated matches	automated matches	(Aspergillus niger ) [TaxId: 5061 ],	SCOPe (2.08)
M	d3fa3m_	Alpha and beta proteins (a/b)	TIM beta/alpha-barrel	Phosphoenolpyruvate/pyruvate domain	automated matches	automated matches	(Aspergillus niger ) [TaxId: 5061 ],	SCOPe (2.08)
N	d3fa3n_	Alpha and beta proteins (a/b)	TIM beta/alpha-barrel	Phosphoenolpyruvate/pyruvate domain	automated matches	automated matches	(Aspergillus niger ) [TaxId: 5061 ],	SCOPe (2.08)
O	d3fa3o_	Alpha and beta proteins (a/b)	TIM beta/alpha-barrel	Phosphoenolpyruvate/pyruvate domain	automated matches	automated matches	(Aspergillus niger ) [TaxId: 5061 ],	SCOPe (2.08)
P	d3fa3p_	Alpha and beta proteins (a/b)	TIM beta/alpha-barrel	Phosphoenolpyruvate/pyruvate domain	automated matches	automated matches	(Aspergillus niger ) [TaxId: 5061 ],	SCOPe (2.08)
J	d3fa3j_	Alpha and beta proteins (a/b)	TIM beta/alpha-barrel	Phosphoenolpyruvate/pyruvate domain	automated matches	automated matches	(Aspergillus niger ) [TaxId: 5061 ],	SCOPe (2.08)
E	d3fa3e_	Alpha and beta proteins (a/b)	TIM beta/alpha-barrel	Phosphoenolpyruvate/pyruvate domain	automated matches	automated matches	(Aspergillus niger ) [TaxId: 5061 ],	SCOPe (2.08)
D	d3fa3d_	Alpha and beta proteins (a/b)	TIM beta/alpha-barrel	Phosphoenolpyruvate/pyruvate domain	automated matches	automated matches	(Aspergillus niger ) [TaxId: 5061 ],	SCOPe (2.08)
B	d3fa3b_	Alpha and beta proteins (a/b)	TIM beta/alpha-barrel	Phosphoenolpyruvate/pyruvate domain	automated matches	automated matches	(Aspergillus niger ) [TaxId: 5061 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A	SCOP2B Superfamily	Phosphoenolpyruvate/pyruvate domain	8082255	3000510	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	Phosphoenolpyruvate/pyruvate domain	8082255	3000510	SCOP2B (2022-06-29)
F	SCOP2B Superfamily	Phosphoenolpyruvate/pyruvate domain	8082255	3000510	SCOP2B (2022-06-29)
G	SCOP2B Superfamily	Phosphoenolpyruvate/pyruvate domain	8082255	3000510	SCOP2B (2022-06-29)
H	SCOP2B Superfamily	Phosphoenolpyruvate/pyruvate domain	8082255	3000510	SCOP2B (2022-06-29)
I	SCOP2B Superfamily	Phosphoenolpyruvate/pyruvate domain	8082255	3000510	SCOP2B (2022-06-29)
K	SCOP2B Superfamily	Phosphoenolpyruvate/pyruvate domain	8082255	3000510	SCOP2B (2022-06-29)
L	SCOP2B Superfamily	Phosphoenolpyruvate/pyruvate domain	8082255	3000510	SCOP2B (2022-06-29)
M	SCOP2B Superfamily	Phosphoenolpyruvate/pyruvate domain	8082255	3000510	SCOP2B (2022-06-29)
N	SCOP2B Superfamily	Phosphoenolpyruvate/pyruvate domain	8082255	3000510	SCOP2B (2022-06-29)
O	SCOP2B Superfamily	Phosphoenolpyruvate/pyruvate domain	8082255	3000510	SCOP2B (2022-06-29)
P	SCOP2B Superfamily	Phosphoenolpyruvate/pyruvate domain	8082255	3000510	SCOP2B (2022-06-29)
J	SCOP2B Superfamily	Phosphoenolpyruvate/pyruvate domain	8082255	3000510	SCOP2B (2022-06-29)
E	SCOP2B Superfamily	Phosphoenolpyruvate/pyruvate domain	8082255	3000510	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	Phosphoenolpyruvate/pyruvate domain	8082255	3000510	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Phosphoenolpyruvate/pyruvate domain	8082255	3000510	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	PEP_mutase	e3fa3A1	A: a/b three-layered sandwiches	X: Ribonuclease H-like	H: TIM barrels	T: TIM barrels	F: PEP_mutase	ECOD (v294.1)
C	NusG	e3fa3C1	A: a/b three-layered sandwiches	X: HTH	H: Nudix	T: Nudix	F: NusG	ECOD (v294.1)
F	NusG	e3fa3F1	A: a/b three-layered sandwiches	X: HTH	H: Nudix	T: Nudix	F: NusG	ECOD (v294.1)
G	NusG	e3fa3G1	A: a/b three-layered sandwiches	X: HTH	H: Nudix	T: Nudix	F: NusG	ECOD (v294.1)
H	NusG	e3fa3H1	A: a/b three-layered sandwiches	X: HTH	H: Nudix	T: Nudix	F: NusG	ECOD (v294.1)
I	NusG	e3fa3I1	A: a/b three-layered sandwiches	X: HTH	H: Nudix	T: Nudix	F: NusG	ECOD (v294.1)
K	NusG	e3fa3K1	A: a/b three-layered sandwiches	X: HTH	H: Nudix	T: Nudix	F: NusG	ECOD (v294.1)
L	NusG	e3fa3L1	A: a/b three-layered sandwiches	X: HTH	H: Nudix	T: Nudix	F: NusG	ECOD (v294.1)
M	NusG	e3fa3M1	A: a/b three-layered sandwiches	X: HTH	H: Nudix	T: Nudix	F: NusG	ECOD (v294.1)
N	NusG	e3fa3N1	A: a/b three-layered sandwiches	X: HTH	H: Nudix	T: Nudix	F: NusG	ECOD (v294.1)
O	NusG	e3fa3O1	A: a/b three-layered sandwiches	X: HTH	H: Nudix	T: Nudix	F: NusG	ECOD (v294.1)
P	NusG	e3fa3P1	A: a/b three-layered sandwiches	X: HTH	H: Nudix	T: Nudix	F: NusG	ECOD (v294.1)
J	NusG	e3fa3J1	A: a/b three-layered sandwiches	X: HTH	H: Nudix	T: Nudix	F: NusG	ECOD (v294.1)
E	NusG	e3fa3E1	A: a/b three-layered sandwiches	X: HTH	H: Nudix	T: Nudix	F: NusG	ECOD (v294.1)
D	NusG	e3fa3D1	A: a/b three-layered sandwiches	X: HTH	H: Nudix	T: Nudix	F: NusG	ECOD (v294.1)
B	NusG	e3fa3B1	A: a/b three-layered sandwiches	X: HTH	H: Nudix	T: Nudix	F: NusG	ECOD (v294.1)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	3.20.20.60	Alpha Beta	Alpha-Beta Barrel	TIM Barrel	Phosphoenolpyruvate-binding domains	CATH (4.3.0)
C	3.20.20.60	Alpha Beta	Alpha-Beta Barrel	TIM Barrel	Phosphoenolpyruvate-binding domains	CATH (4.3.0)
F	3.20.20.60	Alpha Beta	Alpha-Beta Barrel	TIM Barrel	Phosphoenolpyruvate-binding domains	CATH (4.3.0)
G	3.20.20.60	Alpha Beta	Alpha-Beta Barrel	TIM Barrel	Phosphoenolpyruvate-binding domains	CATH (4.3.0)
H	3.20.20.60	Alpha Beta	Alpha-Beta Barrel	TIM Barrel	Phosphoenolpyruvate-binding domains	CATH (4.3.0)
I	3.20.20.60	Alpha Beta	Alpha-Beta Barrel	TIM Barrel	Phosphoenolpyruvate-binding domains	CATH (4.3.0)
K	3.20.20.60	Alpha Beta	Alpha-Beta Barrel	TIM Barrel	Phosphoenolpyruvate-binding domains	CATH (4.3.0)
L	3.20.20.60	Alpha Beta	Alpha-Beta Barrel	TIM Barrel	Phosphoenolpyruvate-binding domains	CATH (4.3.0)
M	3.20.20.60	Alpha Beta	Alpha-Beta Barrel	TIM Barrel	Phosphoenolpyruvate-binding domains	CATH (4.3.0)
N	3.20.20.60	Alpha Beta	Alpha-Beta Barrel	TIM Barrel	Phosphoenolpyruvate-binding domains	CATH (4.3.0)
O	3.20.20.60	Alpha Beta	Alpha-Beta Barrel	TIM Barrel	Phosphoenolpyruvate-binding domains	CATH (4.3.0)
P	3.20.20.60	Alpha Beta	Alpha-Beta Barrel	TIM Barrel	Phosphoenolpyruvate-binding domains	CATH (4.3.0)
J	3.20.20.60	Alpha Beta	Alpha-Beta Barrel	TIM Barrel	Phosphoenolpyruvate-binding domains	CATH (4.3.0)
E	3.20.20.60	Alpha Beta	Alpha-Beta Barrel	TIM Barrel	Phosphoenolpyruvate-binding domains	CATH (4.3.0)
D	3.20.20.60	Alpha Beta	Alpha-Beta Barrel	TIM Barrel	Phosphoenolpyruvate-binding domains	CATH (4.3.0)
B	3.20.20.60	Alpha Beta	Alpha-Beta Barrel	TIM Barrel	Phosphoenolpyruvate-binding domains	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, I, J, K, L, M, N, O, P	2,3-dimethylmalate lyase	oxo-acid-lyase activity methylisocitrate lyase activity lyase activity catalytic activity carbon-carbon lyase activity hydrolase activity cation binding ion binding binding metal ion binding small molecule binding	-	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B, C, D, E A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P	IPR015813	Pyruvate/Phosphoenolpyruvate kinase-like domain superfamily	Homologous Superfamily
A, B, C, D, E A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P	IPR018523	Isocitrate lyase/phosphorylmutase, conserved site	Conserved Site
A, B, C, D, E A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P	IPR039556	ICL/PEPM domain	Domain
A, B, C, D, E A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P	IPR040442	Pyruvate kinase-like domain superfamily	Homologous Superfamily

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.