3FA4 | pdb_00003fa4

Crystal structure of 2,3-dimethylmalate lyase, a PEP mutase/isocitrate lyase superfamily member, triclinic 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)
L	d3fa4l_	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	d3fa4k_	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	d3fa4j_	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	d3fa4i_	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	d3fa4h_	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	d3fa4g_	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	d3fa4f_	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	d3fa4e_	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	d3fa4d_	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	d3fa4c_	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	d3fa4b_	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	d3fa4a_	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)
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	SCOP2 Family	Phosphoenolpyruvate mutase/Isocitrate lyase-like	8082254	4003532	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	Phosphoenolpyruvate/pyruvate domain	8082255	3000510	SCOP2 (2022-06-29)

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
L	PEP_mutase	e3fa4L1	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	e3fa4K1	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	e3fa4J1	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	e3fa4I1	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	e3fa4H1	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	e3fa4G1	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	e3fa4F1	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	e3fa4E1	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	e3fa4D1	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	e3fa4C1	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	e3fa4B1	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	e3fa4A1	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)
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)

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	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	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	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	IPR039556	ICL/PEPM domain	Domain
A, B, C, D, E A, B, C, D, E, F, G, H, I, J, K, L	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.