4U2H | pdb_00004u2h

The crystal structure of apo CalE6, a methionine gamma lyase from Micromonospora echinospora

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)
H	d4u2hh_	Alpha and beta proteins (a/b)	PLP-dependent transferase-like	PLP-dependent transferases	automated matches	automated matches	(Micromonospora echinospora ) [TaxId: 1877 ],	SCOPe (2.08)
G	d4u2hg_	Alpha and beta proteins (a/b)	PLP-dependent transferase-like	PLP-dependent transferases	automated matches	automated matches	(Micromonospora echinospora ) [TaxId: 1877 ],	SCOPe (2.08)
F	d4u2hf_	Alpha and beta proteins (a/b)	PLP-dependent transferase-like	PLP-dependent transferases	automated matches	automated matches	(Micromonospora echinospora ) [TaxId: 1877 ],	SCOPe (2.08)
E	d4u2he_	Alpha and beta proteins (a/b)	PLP-dependent transferase-like	PLP-dependent transferases	automated matches	automated matches	(Micromonospora echinospora ) [TaxId: 1877 ],	SCOPe (2.08)
D	d4u2hd_	Alpha and beta proteins (a/b)	PLP-dependent transferase-like	PLP-dependent transferases	automated matches	automated matches	(Micromonospora echinospora ) [TaxId: 1877 ],	SCOPe (2.08)
C	d4u2hc_	Alpha and beta proteins (a/b)	PLP-dependent transferase-like	PLP-dependent transferases	automated matches	automated matches	(Micromonospora echinospora ) [TaxId: 1877 ],	SCOPe (2.08)
B	d4u2hb_	Alpha and beta proteins (a/b)	PLP-dependent transferase-like	PLP-dependent transferases	automated matches	automated matches	(Micromonospora echinospora ) [TaxId: 1877 ],	SCOPe (2.08)
A	d4u2ha_	Alpha and beta proteins (a/b)	PLP-dependent transferase-like	PLP-dependent transferases	automated matches	automated matches	(Micromonospora echinospora ) [TaxId: 1877 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
H	SCOP2B Superfamily	PLP-dependent transferases	8059637	3000954	SCOP2B (2022-06-29)
G	SCOP2B Superfamily	PLP-dependent transferases	8059637	3000954	SCOP2B (2022-06-29)
F	SCOP2B Superfamily	PLP-dependent transferases	8059637	3000954	SCOP2B (2022-06-29)
E	SCOP2B Superfamily	PLP-dependent transferases	8059637	3000954	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	PLP-dependent transferases	8059637	3000954	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	PLP-dependent transferases	8059637	3000954	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	PLP-dependent transferases	8059637	3000954	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	PLP-dependent transferases	8059637	3000954	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)
H	U-box	e4u2hH1	A: a/b three-layered sandwiches	X: Rubredoxin-like	H: Rubredoxin-related	T: Rubredoxin-related	F: U-box	ECOD (v294.1)
G	U-box	e4u2hG1	A: a/b three-layered sandwiches	X: Rubredoxin-like	H: Rubredoxin-related	T: Rubredoxin-related	F: U-box	ECOD (v294.1)
F	U-box	e4u2hF1	A: a/b three-layered sandwiches	X: Rubredoxin-like	H: Rubredoxin-related	T: Rubredoxin-related	F: U-box	ECOD (v294.1)
E	U-box	e4u2hE1	A: a/b three-layered sandwiches	X: Rubredoxin-like	H: Rubredoxin-related	T: Rubredoxin-related	F: U-box	ECOD (v294.1)
D	U-box	e4u2hD1	A: a/b three-layered sandwiches	X: Rubredoxin-like	H: Rubredoxin-related	T: Rubredoxin-related	F: U-box	ECOD (v294.1)
C	U-box	e4u2hC1	A: a/b three-layered sandwiches	X: Rubredoxin-like	H: Rubredoxin-related	T: Rubredoxin-related	F: U-box	ECOD (v294.1)
C		e4u2hC2	A: a/b three-layered sandwiches	X: Rubredoxin-like	H: Ferritin/Heme oxygenase	T: Heme oxygenase/Ribonucleotide reductase	F:	ECOD (v294.1)
B	U-box	e4u2hB1	A: a/b three-layered sandwiches	X: Rubredoxin-like	H: Rubredoxin-related	T: Rubredoxin-related	F: U-box	ECOD (v294.1)
A	U-box	e4u2hA1	A: a/b three-layered sandwiches	X: Rubredoxin-like	H: Rubredoxin-related	T: Rubredoxin-related	F: U-box	ECOD (v294.1)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
H	3.40.640.10	Alpha Beta	3-Layer(aba) Sandwich	Aspartate Aminotransferase	domain 2	CATH (4.3.0)
H	3.90.1150.10	Alpha Beta	Alpha-Beta Complex	Aspartate Aminotransferase, domain 1	Aspartate Aminotransferase, domain 1	CATH (4.3.0)
G	3.40.640.10	Alpha Beta	3-Layer(aba) Sandwich	Aspartate Aminotransferase	domain 2	CATH (4.3.0)
G	3.90.1150.10	Alpha Beta	Alpha-Beta Complex	Aspartate Aminotransferase, domain 1	Aspartate Aminotransferase, domain 1	CATH (4.3.0)
F	3.40.640.10	Alpha Beta	3-Layer(aba) Sandwich	Aspartate Aminotransferase	domain 2	CATH (4.3.0)
F	3.90.1150.10	Alpha Beta	Alpha-Beta Complex	Aspartate Aminotransferase, domain 1	Aspartate Aminotransferase, domain 1	CATH (4.3.0)
E	3.40.640.10	Alpha Beta	3-Layer(aba) Sandwich	Aspartate Aminotransferase	domain 2	CATH (4.3.0)
E	3.90.1150.10	Alpha Beta	Alpha-Beta Complex	Aspartate Aminotransferase, domain 1	Aspartate Aminotransferase, domain 1	CATH (4.3.0)
D	3.40.640.10	Alpha Beta	3-Layer(aba) Sandwich	Aspartate Aminotransferase	domain 2	CATH (4.3.0)
D	3.90.1150.10	Alpha Beta	Alpha-Beta Complex	Aspartate Aminotransferase, domain 1	Aspartate Aminotransferase, domain 1	CATH (4.3.0)
C	3.40.640.10	Alpha Beta	3-Layer(aba) Sandwich	Aspartate Aminotransferase	domain 2	CATH (4.3.0)
C	3.90.1150.10	Alpha Beta	Alpha-Beta Complex	Aspartate Aminotransferase, domain 1	Aspartate Aminotransferase, domain 1	CATH (4.3.0)
B	3.40.640.10	Alpha Beta	3-Layer(aba) Sandwich	Aspartate Aminotransferase	domain 2	CATH (4.3.0)
B	3.90.1150.10	Alpha Beta	Alpha-Beta Complex	Aspartate Aminotransferase, domain 1	Aspartate Aminotransferase, domain 1	CATH (4.3.0)
A	3.40.640.10	Alpha Beta	3-Layer(aba) Sandwich	Aspartate Aminotransferase	domain 2	CATH (4.3.0)
A	3.90.1150.10	Alpha Beta	Alpha-Beta Complex	Aspartate Aminotransferase, domain 1	Aspartate Aminotransferase, domain 1	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	CalE6	carbon-sulfur lyase activity methionine gamma-lyase activity lyase activity catalytic activity homocysteine desulfhydrase activity vitamin binding vitamin B6 binding pyridoxal phosphate binding ion binding binding anion binding heterocyclic compound binding small molecule binding	homocysteine metabolic process oxoacid metabolic process sulfur amino acid metabolic process carboxylic acid metabolic process amino acid metabolic process primary metabolic process organic acid metabolic process transsulfuration alpha-amino acid metabolic process L-amino acid metabolic process non-proteinogenic amino acid metabolic process proteinogenic amino acid metabolic process metabolic process cellular process homocysteine metabolic process oxoacid metabolic process sulfur amino acid metabolic process carboxylic acid metabolic process amino acid metabolic process primary metabolic process organic acid metabolic process transsulfuration alpha-amino acid metabolic process L-amino acid metabolic process non-proteinogenic amino acid metabolic process proteinogenic amino acid metabolic process metabolic process cellular process small molecule metabolic process sulfur compound metabolic process	cellular anatomical structure intracellular anatomical structure cytoplasm

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B, C, D, E A, B, C, D, E, F, G, H	IPR015424	Pyridoxal phosphate-dependent transferase	Homologous Superfamily
A, B, C, D, E A, B, C, D, E, F, G, H	IPR000277	Cys/Met metabolism, pyridoxal phosphate-dependent enzyme	Family
A, B, C, D, E A, B, C, D, E, F, G, H	IPR015421	Pyridoxal phosphate-dependent transferase, major domain	Homologous Superfamily
A, B, C, D, E A, B, C, D, E, F, G, H	IPR015422	Pyridoxal phosphate-dependent transferase, small domain	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.