6LDO | pdb_00006ldo

Crystal structure of cystathionine gamma-lyase from Lactobacillus plantarum complexed with L-serine

External Resource: Annotation

Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
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)
F	SCOP2B Superfamily	PLP-dependent transferases	8096390	3000954	SCOP2B (2022-06-29)
E	SCOP2B Superfamily	PLP-dependent transferases	8096390	3000954	SCOP2B (2022-06-29)
D	SCOP2 Family	Cystathionine synthase-like	8096389	4000672	SCOP2 (2022-06-29)
D	SCOP2 Superfamily	PLP-dependent transferases	8096390	3000954	SCOP2 (2022-06-29)
C	SCOP2B Superfamily	PLP-dependent transferases	8096390	3000954	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	PLP-dependent transferases	8096390	3000954	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	PLP-dependent transferases	8096390	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)
F	Cys_Met_Meta_PP_C	e6ldoF1	A: a+b two layers	X: C-terminal domain in some PLP-dependent transferases (From Topology)	H: C-terminal domain in some PLP-dependent transferases (From Topology)	T: C-terminal domain in some PLP-dependent transferases	F: Cys_Met_Meta_PP_C	ECOD (1.6)
F	Cys_Met_Meta_PP_N	e6ldoF2	A: a/b three-layered sandwiches	X: PLP-dependent transferases (From Topology)	H: PLP-dependent transferases (From Topology)	T: PLP-dependent transferases	F: Cys_Met_Meta_PP_N	ECOD (1.6)
E	Cys_Met_Meta_PP_C	e6ldoE2	A: a+b two layers	X: C-terminal domain in some PLP-dependent transferases (From Topology)	H: C-terminal domain in some PLP-dependent transferases (From Topology)	T: C-terminal domain in some PLP-dependent transferases	F: Cys_Met_Meta_PP_C	ECOD (1.6)
E	Cys_Met_Meta_PP_N	e6ldoE1	A: a/b three-layered sandwiches	X: PLP-dependent transferases (From Topology)	H: PLP-dependent transferases (From Topology)	T: PLP-dependent transferases	F: Cys_Met_Meta_PP_N	ECOD (1.6)
D	Cys_Met_Meta_PP_C	e6ldoD2	A: a+b two layers	X: C-terminal domain in some PLP-dependent transferases (From Topology)	H: C-terminal domain in some PLP-dependent transferases (From Topology)	T: C-terminal domain in some PLP-dependent transferases	F: Cys_Met_Meta_PP_C	ECOD (1.6)
D	Cys_Met_Meta_PP_N	e6ldoD1	A: a/b three-layered sandwiches	X: PLP-dependent transferases (From Topology)	H: PLP-dependent transferases (From Topology)	T: PLP-dependent transferases	F: Cys_Met_Meta_PP_N	ECOD (1.6)
C	Cys_Met_Meta_PP_C	e6ldoC2	A: a+b two layers	X: C-terminal domain in some PLP-dependent transferases (From Topology)	H: C-terminal domain in some PLP-dependent transferases (From Topology)	T: C-terminal domain in some PLP-dependent transferases	F: Cys_Met_Meta_PP_C	ECOD (1.6)
C	Cys_Met_Meta_PP_N	e6ldoC1	A: a/b three-layered sandwiches	X: PLP-dependent transferases (From Topology)	H: PLP-dependent transferases (From Topology)	T: PLP-dependent transferases	F: Cys_Met_Meta_PP_N	ECOD (1.6)
B	Cys_Met_Meta_PP_C	e6ldoB1	A: a+b two layers	X: C-terminal domain in some PLP-dependent transferases (From Topology)	H: C-terminal domain in some PLP-dependent transferases (From Topology)	T: C-terminal domain in some PLP-dependent transferases	F: Cys_Met_Meta_PP_C	ECOD (1.6)
B	Cys_Met_Meta_PP_N	e6ldoB2	A: a/b three-layered sandwiches	X: PLP-dependent transferases (From Topology)	H: PLP-dependent transferases (From Topology)	T: PLP-dependent transferases	F: Cys_Met_Meta_PP_N	ECOD (1.6)
A	Cys_Met_Meta_PP_C	e6ldoA1	A: a+b two layers	X: C-terminal domain in some PLP-dependent transferases (From Topology)	H: C-terminal domain in some PLP-dependent transferases (From Topology)	T: C-terminal domain in some PLP-dependent transferases	F: Cys_Met_Meta_PP_C	ECOD (1.6)
A	Cys_Met_Meta_PP_N	e6ldoA2	A: a/b three-layered sandwiches	X: PLP-dependent transferases (From Topology)	H: PLP-dependent transferases (From Topology)	T: PLP-dependent transferases	F: Cys_Met_Meta_PP_N	ECOD (1.6)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B, C, D, E A, B, C, D, E, F	PF01053	Cys/Met metabolism PLP-dependent enzyme (Cys_Met_Meta_PP)	Cys/Met metabolism PLP-dependent enzyme	This family includes enzymes involved in cysteine and methionine metabolism. The following are members: Cystathionine gamma-lyase, Cystathionine gamma-synthase, Cystathionine beta-lyase, Methionine gamma-lyase, OAH/OAS sulfhydrylase, O-succinylhomose ...	This family includes enzymes involved in cysteine and methionine metabolism. The following are members: Cystathionine gamma-lyase, Cystathionine gamma-synthase, Cystathionine beta-lyase, Methionine gamma-lyase, OAH/OAS sulfhydrylase, O-succinylhomoserine sulfhydrylase All of these members participate is slightly different reactions. All these enzymes use PLP (pyridoxal-5'-phosphate) as a cofactor.	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	Cystathionine gamma-lyase	carbon-sulfur lyase activity lyase activity catalytic activity cystathionine gamma-lyase activity vitamin binding vitamin B6 binding pyridoxal phosphate binding ion binding binding anion binding heterocyclic compound binding small molecule binding cystathionine gamma-synthase activity transferase activity carbon-sulfur lyase activity lyase activity catalytic activity cystathionine gamma-lyase activity vitamin binding vitamin B6 binding pyridoxal phosphate binding ion binding binding anion binding heterocyclic compound binding small molecule binding cystathionine gamma-synthase activity transferase activity transferase activity, transferring alkyl or aryl (other than methyl) groups	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 cysteine metabolic process non-proteinogenic amino acid metabolic process metabolic process cellular process small molecule metabolic 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 cysteine metabolic process non-proteinogenic amino acid metabolic process metabolic process cellular process small molecule metabolic process sulfur compound metabolic process homoserine metabolic process cysteine biosynthetic process via cystathionine organic acid biosynthetic process carboxylic acid biosynthetic process cysteine biosynthetic process small molecule biosynthetic process amino acid biosynthetic process sulfur compound biosynthetic process biosynthetic process serine family amino acid biosynthetic process sulfur amino acid biosynthetic process alpha-amino acid biosynthetic process aspartate family amino acid biosynthetic process methionine biosynthetic process L-amino acid biosynthetic process methionine metabolic process L-amino acid metabolic process proteinogenic amino acid metabolic process proteinogenic amino acid biosynthetic 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	IPR015424	Pyridoxal phosphate-dependent transferase	Homologous Superfamily
A, B, C, D, E A, B, C, D, E, F	IPR000277	Cys/Met metabolism, pyridoxal phosphate-dependent enzyme	Family
A, B, C, D, E A, B, C, D, E, F	IPR015421	Pyridoxal phosphate-dependent transferase, major domain	Homologous Superfamily
A, B, C, D, E A, B, C, D, E, F	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.