4L9Y | pdb_00004l9y

Crystal Structure of Rhodobacter sphaeroides malyl-CoA lyase in complex with magnesium, glyoxylate, and propionyl-CoA

External Resource: Annotation

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: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
D	SCOP2B Superfamily	Phosphoenolpyruvate/pyruvate domain	8083972	3000510	SCOP2B (2022-06-29)
F	SCOP2B Superfamily	Phosphoenolpyruvate/pyruvate domain	8083972	3000510	SCOP2B (2022-06-29)
E	SCOP2B Superfamily	Phosphoenolpyruvate/pyruvate domain	8083972	3000510	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	Phosphoenolpyruvate/pyruvate domain	8083972	3000510	SCOP2B (2022-06-29)
B	SCOP2 Family	HpcH/HpaI aldolase	8083971	4003274	SCOP2 (2022-06-29)
B	SCOP2 Superfamily	Phosphoenolpyruvate/pyruvate domain	8083972	3000510	SCOP2 (2022-06-29)
A	SCOP2B Superfamily	Phosphoenolpyruvate/pyruvate domain	8083972	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)
D	FKBP_C	e4l9yD1	A: alpha bundles	X: CCHHC domain	H: CCHHC domain	T: CCHHC domain	F: FKBP_C	ECOD (develop294)
F	ERG4_ERG24	e4l9yF2	A: alpha bundles	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: N-terminal domain of Delta(14)-sterol reductase, MaSR1	F: ERG4_ERG24	ECOD (develop294)
E	FKBP_C	e4l9yE1	A: alpha bundles	X: CCHHC domain	H: CCHHC domain	T: CCHHC domain	F: FKBP_C	ECOD (develop294)
C	XdhC_CoxI	e4l9yC1	A: alpha bundles	X: Single-stranded left-handed beta-helix	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: XdhC_CoxI	ECOD (develop294)
B	FKBP_C	e4l9yB1	A: alpha bundles	X: CCHHC domain	H: CCHHC domain	T: CCHHC domain	F: FKBP_C	ECOD (develop294)
A	ERG4_ERG24	e4l9yA2	A: alpha bundles	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: N-terminal domain of Delta(14)-sterol reductase, MaSR1	F: ERG4_ERG24	ECOD (develop294)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
D	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)
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	PF03328	HpcH/HpaI aldolase/citrate lyase (HpcH_HpaI)	HpcH/HpaI aldolase/citrate lyase	This family includes 2,4-dihydroxyhept-2-ene-1,7-dioic acid aldolase and 4-hydroxy-2-oxovalerate aldolase.	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	Malyl-CoA lyase	cation binding magnesium ion binding ion binding binding metal ion binding small molecule binding (S)-citramalyl-CoA lyase activity oxo-acid-lyase activity lyase activity catalytic activity carbon-carbon lyase activity L-erythro-3-methylmalyl-CoA lyase activity malyl-CoA lyase activity	oxoacid metabolic process dicarboxylic acid metabolic process carboxylic acid metabolic process small molecule metabolic process metabolic process cellular process organic acid metabolic process oxaloacetate metabolic process	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B, C, D, E A, B, C, D, E, F	IPR015813	Pyruvate/Phosphoenolpyruvate kinase-like domain superfamily	Homologous Superfamily
A, B, C, D, E A, B, C, D, E, F	IPR040442	Pyruvate kinase-like domain superfamily	Homologous Superfamily
A, B, C, D, E A, B, C, D, E, F	IPR005000	HpcH/HpaI aldolase/citrate lyase domain	Domain
A, B, C, D, E A, B, C, D, E, F	IPR011206	Citrate lyase beta subunit-like	Family

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.