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
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)
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)
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)
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)
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)
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)
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)
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)
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)
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)
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)
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)
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)
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)
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)
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)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
P	SCOP2B Superfamily	Phosphoenolpyruvate/pyruvate domain	8082255	3000510	SCOP2B (2022-06-29)
O	SCOP2B Superfamily	Phosphoenolpyruvate/pyruvate domain	8082255	3000510	SCOP2B (2022-06-29)
N	SCOP2B Superfamily	Phosphoenolpyruvate/pyruvate domain	8082255	3000510	SCOP2B (2022-06-29)
M	SCOP2B Superfamily	Phosphoenolpyruvate/pyruvate domain	8082255	3000510	SCOP2B (2022-06-29)
L	SCOP2B Superfamily	Phosphoenolpyruvate/pyruvate domain	8082255	3000510	SCOP2B (2022-06-29)
K	SCOP2B Superfamily	Phosphoenolpyruvate/pyruvate domain	8082255	3000510	SCOP2B (2022-06-29)
J	SCOP2B Superfamily	Phosphoenolpyruvate/pyruvate domain	8082255	3000510	SCOP2B (2022-06-29)
I	SCOP2B Superfamily	Phosphoenolpyruvate/pyruvate domain	8082255	3000510	SCOP2B (2022-06-29)
H	SCOP2B Superfamily	Phosphoenolpyruvate/pyruvate domain	8082255	3000510	SCOP2B (2022-06-29)
G	SCOP2B Superfamily	Phosphoenolpyruvate/pyruvate domain	8082255	3000510	SCOP2B (2022-06-29)
F	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)
C	SCOP2B Superfamily	Phosphoenolpyruvate/pyruvate domain	8082255	3000510	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Phosphoenolpyruvate/pyruvate domain	8082255	3000510	SCOP2B (2022-06-29)
A	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)
P	PEP_mutase	e3fa3P1	A: a/b barrels	X: TIM beta/alpha-barrel	H: TIM barrels (From Topology)	T: TIM barrels	F: PEP_mutase	ECOD (1.6)
O	PEP_mutase	e3fa3O1	A: a/b barrels	X: TIM beta/alpha-barrel	H: TIM barrels (From Topology)	T: TIM barrels	F: PEP_mutase	ECOD (1.6)
N	PEP_mutase	e3fa3N1	A: a/b barrels	X: TIM beta/alpha-barrel	H: TIM barrels (From Topology)	T: TIM barrels	F: PEP_mutase	ECOD (1.6)
M	PEP_mutase	e3fa3M1	A: a/b barrels	X: TIM beta/alpha-barrel	H: TIM barrels (From Topology)	T: TIM barrels	F: PEP_mutase	ECOD (1.6)
L	PEP_mutase	e3fa3L1	A: a/b barrels	X: TIM beta/alpha-barrel	H: TIM barrels (From Topology)	T: TIM barrels	F: PEP_mutase	ECOD (1.6)
K	PEP_mutase	e3fa3K1	A: a/b barrels	X: TIM beta/alpha-barrel	H: TIM barrels (From Topology)	T: TIM barrels	F: PEP_mutase	ECOD (1.6)
J	PEP_mutase	e3fa3J1	A: a/b barrels	X: TIM beta/alpha-barrel	H: TIM barrels (From Topology)	T: TIM barrels	F: PEP_mutase	ECOD (1.6)
I	PEP_mutase	e3fa3I1	A: a/b barrels	X: TIM beta/alpha-barrel	H: TIM barrels (From Topology)	T: TIM barrels	F: PEP_mutase	ECOD (1.6)
H	PEP_mutase	e3fa3H1	A: a/b barrels	X: TIM beta/alpha-barrel	H: TIM barrels (From Topology)	T: TIM barrels	F: PEP_mutase	ECOD (1.6)
G	PEP_mutase	e3fa3G1	A: a/b barrels	X: TIM beta/alpha-barrel	H: TIM barrels (From Topology)	T: TIM barrels	F: PEP_mutase	ECOD (1.6)
F	PEP_mutase	e3fa3F1	A: a/b barrels	X: TIM beta/alpha-barrel	H: TIM barrels (From Topology)	T: TIM barrels	F: PEP_mutase	ECOD (1.6)
E	PEP_mutase	e3fa3E1	A: a/b barrels	X: TIM beta/alpha-barrel	H: TIM barrels (From Topology)	T: TIM barrels	F: PEP_mutase	ECOD (1.6)
D	PEP_mutase	e3fa3D1	A: a/b barrels	X: TIM beta/alpha-barrel	H: TIM barrels (From Topology)	T: TIM barrels	F: PEP_mutase	ECOD (1.6)
C	PEP_mutase	e3fa3C1	A: a/b barrels	X: TIM beta/alpha-barrel	H: TIM barrels (From Topology)	T: TIM barrels	F: PEP_mutase	ECOD (1.6)
B	PEP_mutase	e3fa3B1	A: a/b barrels	X: TIM beta/alpha-barrel	H: TIM barrels (From Topology)	T: TIM barrels	F: PEP_mutase	ECOD (1.6)
A	PEP_mutase	e3fa3A1	A: a/b barrels	X: TIM beta/alpha-barrel	H: TIM barrels (From Topology)	T: TIM barrels	F: PEP_mutase	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
P	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)
N	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)
L	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)
J	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)
H	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)
F	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)
C	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)
A	3.20.20.60	Alpha Beta	Alpha-Beta Barrel	TIM Barrel	Phosphoenolpyruvate-binding domains	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B, C, D, E A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P	PF13714	Phosphoenolpyruvate phosphomutase (PEP_mutase)	Phosphoenolpyruvate phosphomutase	This domain includes the enzyme Phosphoenolpyruvate phosphomutase (EC:5.4.2.9). This protein Swiss:O86937 has been characterised as catalysing the formation of a carbon-phosphorus bond by converting phosphoenolpyruvate (PEP) to phosphonopyruvate (P-P ...	This domain includes the enzyme Phosphoenolpyruvate phosphomutase (EC:5.4.2.9). This protein Swiss:O86937 has been characterised as catalysing the formation of a carbon-phosphorus bond by converting phosphoenolpyruvate (PEP) to phosphonopyruvate (P-Pyr) [1]. This enzyme has a TIM barrel fold.	Domain

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	hydrolase activity catalytic activity cation binding ion binding binding metal ion binding small molecule binding oxo-acid-lyase activity lyase activity carbon-carbon lyase activity	-	-

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.