5X30 | pdb_00005x30

Crystal structure of Pseudomonas putida methionine gamma-lyase C116H mutant with L-homocysteine intermediates.

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
Protein Modification Annotation

Domain Annotation: SCOP/SCOPe Classification SCOP-e Database Homepage

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
D	d5x30d_	Alpha and beta proteins (a/b)	PLP-dependent transferase-like	PLP-dependent transferases	Cystathionine synthase-like	Methionine gamma-lyase, MGL	(Pseudomonas putida ) [TaxId: 303 ],	SCOPe (2.08)
B	d5x30b_	Alpha and beta proteins (a/b)	PLP-dependent transferase-like	PLP-dependent transferases	Cystathionine synthase-like	Methionine gamma-lyase, MGL	(Pseudomonas putida ) [TaxId: 303 ],	SCOPe (2.08)
C	d5x30c_	Alpha and beta proteins (a/b)	PLP-dependent transferase-like	PLP-dependent transferases	Cystathionine synthase-like	Methionine gamma-lyase, MGL	(Pseudomonas putida ) [TaxId: 303 ],	SCOPe (2.08)
A	d5x30a_	Alpha and beta proteins (a/b)	PLP-dependent transferase-like	PLP-dependent transferases	Cystathionine synthase-like	Methionine gamma-lyase, MGL	(Pseudomonas putida ) [TaxId: 303 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
D	SCOP2B Superfamily	PLP-dependent transferases	8035032	3000954	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	PLP-dependent transferases	8035032	3000954	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	PLP-dependent transferases	8035032	3000954	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	PLP-dependent transferases	8035032	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)
D	Cys_Met_Meta_PP_C	e5x30D1	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	e5x30D2	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	e5x30B1	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	e5x30B2	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	e5x30C2	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	e5x30C1	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	e5x30A1	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	e5x30A2	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)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
D	3.40.640.10	Alpha Beta	3-Layer(aba) Sandwich	Aspartate Aminotransferase	domain 2	CATH (utative)
D	3.90.1150.10	Alpha Beta	Alpha-Beta Complex	Aspartate Aminotransferase, domain 1	Aspartate Aminotransferase, domain 1	CATH (utative)
B	3.40.640.10	Alpha Beta	3-Layer(aba) Sandwich	Aspartate Aminotransferase	domain 2	CATH (utative)
B	3.90.1150.10	Alpha Beta	Alpha-Beta Complex	Aspartate Aminotransferase, domain 1	Aspartate Aminotransferase, domain 1	CATH (utative)
C	3.40.640.10	Alpha Beta	3-Layer(aba) Sandwich	Aspartate Aminotransferase	domain 2	CATH (utative)
C	3.90.1150.10	Alpha Beta	Alpha-Beta Complex	Aspartate Aminotransferase, domain 1	Aspartate Aminotransferase, domain 1	CATH (utative)
A	3.40.640.10	Alpha Beta	3-Layer(aba) Sandwich	Aspartate Aminotransferase	domain 2	CATH (utative)
A	3.90.1150.10	Alpha Beta	Alpha-Beta Complex	Aspartate Aminotransferase, domain 1	Aspartate Aminotransferase, domain 1	CATH (utative)

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
B, D	L-methionine gamma-lyase	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 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	cellular anatomical structure intracellular anatomical structure cytoplasm
A, C	L-methionine gamma-lyase	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 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	cellular anatomical structure intracellular anatomical structure cytoplasm

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
B, D	IPR015424	Pyridoxal phosphate-dependent transferase	Homologous Superfamily
B, D	IPR000277	Cys/Met metabolism, pyridoxal phosphate-dependent enzyme	Family
B, D	IPR015421	Pyridoxal phosphate-dependent transferase, major domain	Homologous Superfamily
B, D	IPR015422	Pyridoxal phosphate-dependent transferase, small domain	Homologous Superfamily
B, D	IPR006237	L-methionine gamma-lyase	Family
B, D	IPR054542	Cys/Met metabolism enzyme, pyridoxal-phosphate attachment site	Conserved Site
A, C	IPR015424	Pyridoxal phosphate-dependent transferase	Homologous Superfamily
A, C	IPR000277	Cys/Met metabolism, pyridoxal phosphate-dependent enzyme	Family
A, C	IPR015421	Pyridoxal phosphate-dependent transferase, major domain	Homologous Superfamily
A, C	IPR015422	Pyridoxal phosphate-dependent transferase, small domain	Homologous Superfamily
A, C	IPR006237	L-methionine gamma-lyase	Family
A, C	IPR054542	Cys/Met metabolism enzyme, pyridoxal-phosphate attachment site	Conserved Site

Protein Modification Annotation

Modified Residue(s)
Chain	Residue(s)	Description
A, C	LLP	Parent Component: LYS RESID: AA0119 PSI-MOD : N6-pyridoxal phosphate-L-lysine MOD:00128

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.

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