4L0O

Structure determination of cystathionine gamma-synthase from Helicobacter pylori

External Resource: Annotation

Domain Annotation: SCOP/SCOPe Classification
Domain Annotation: ECOD Classification
Domain Annotation: CATH
Protein Family Annotation
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)
B [auth A]	d4l0oa_	Alpha and beta proteins (a/b)	PLP-dependent transferase-like	PLP-dependent transferases	automated matches	automated matches	(Helicobacter pylori 26695 ) [TaxId: 85962 ],	SCOPe (2.08)
C	d4l0oc_	Alpha and beta proteins (a/b)	PLP-dependent transferase-like	PLP-dependent transferases	automated matches	automated matches	(Helicobacter pylori 26695 ) [TaxId: 85962 ],	SCOPe (2.08)
D [auth E]	d4l0oe_	Alpha and beta proteins (a/b)	PLP-dependent transferase-like	PLP-dependent transferases	automated matches	automated matches	(Helicobacter pylori 26695 ) [TaxId: 85962 ],	SCOPe (2.08)
F [auth K]	d4l0ok_	Alpha and beta proteins (a/b)	PLP-dependent transferase-like	PLP-dependent transferases	automated matches	automated matches	(Helicobacter pylori 26695 ) [TaxId: 85962 ],	SCOPe (2.08)
H [auth O]	d4l0oo_	Alpha and beta proteins (a/b)	PLP-dependent transferase-like	PLP-dependent transferases	automated matches	automated matches	(Helicobacter pylori 26695 ) [TaxId: 85962 ],	SCOPe (2.08)
A [auth H]	d4l0oh_	Alpha and beta proteins (a/b)	PLP-dependent transferase-like	PLP-dependent transferases	automated matches	automated matches	(Helicobacter pylori 26695 ) [TaxId: 85962 ],	SCOPe (2.08)
E [auth G]	d4l0og_	Alpha and beta proteins (a/b)	PLP-dependent transferase-like	PLP-dependent transferases	automated matches	automated matches	(Helicobacter pylori 26695 ) [TaxId: 85962 ],	SCOPe (2.08)
G [auth M]	d4l0om_	Alpha and beta proteins (a/b)	PLP-dependent transferase-like	PLP-dependent transferases	automated matches	automated matches	(Helicobacter pylori 26695 ) [TaxId: 85962 ],	SCOPe (2.08)

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
B [auth A]	PF01053	e4l0oA2	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: PF01053	ECOD (1.6)
B [auth A]	PF01053	e4l0oA3	A: a/b three-layered sandwiches	X: PLP-dependent transferases (From Topology)	H: PLP-dependent transferases (From Topology)	T: PLP-dependent transferases	F: PF01053	ECOD (1.6)
C	PF01053	e4l0oC2	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: PF01053	ECOD (1.6)
C	PF01053	e4l0oC3	A: a/b three-layered sandwiches	X: PLP-dependent transferases (From Topology)	H: PLP-dependent transferases (From Topology)	T: PLP-dependent transferases	F: PF01053	ECOD (1.6)
D [auth E]	PF01053	e4l0oE2	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: PF01053	ECOD (1.6)
D [auth E]	PF01053	e4l0oE3	A: a/b three-layered sandwiches	X: PLP-dependent transferases (From Topology)	H: PLP-dependent transferases (From Topology)	T: PLP-dependent transferases	F: PF01053	ECOD (1.6)
F [auth K]	PF01053	e4l0oK2	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: PF01053	ECOD (1.6)
F [auth K]	PF01053	e4l0oK3	A: a/b three-layered sandwiches	X: PLP-dependent transferases (From Topology)	H: PLP-dependent transferases (From Topology)	T: PLP-dependent transferases	F: PF01053	ECOD (1.6)
H [auth O]	PF01053	e4l0oO2	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: PF01053	ECOD (1.6)
H [auth O]	PF01053	e4l0oO3	A: a/b three-layered sandwiches	X: PLP-dependent transferases (From Topology)	H: PLP-dependent transferases (From Topology)	T: PLP-dependent transferases	F: PF01053	ECOD (1.6)
A [auth H]	PF01053	e4l0oH2	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: PF01053	ECOD (1.6)
A [auth H]	PF01053	e4l0oH3	A: a/b three-layered sandwiches	X: PLP-dependent transferases (From Topology)	H: PLP-dependent transferases (From Topology)	T: PLP-dependent transferases	F: PF01053	ECOD (1.6)
E [auth G]	PF01053	e4l0oG2	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: PF01053	ECOD (1.6)
E [auth G]	PF01053	e4l0oG3	A: a/b three-layered sandwiches	X: PLP-dependent transferases (From Topology)	H: PLP-dependent transferases (From Topology)	T: PLP-dependent transferases	F: PF01053	ECOD (1.6)
G [auth M]	PF01053	e4l0oM2	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: PF01053	ECOD (1.6)
G [auth M]	PF01053	e4l0oM3	A: a/b three-layered sandwiches	X: PLP-dependent transferases (From Topology)	H: PLP-dependent transferases (From Topology)	T: PLP-dependent transferases	F: PF01053	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
B [auth A]	3.40.640.10	Alpha Beta	3-Layer(aba) Sandwich	Aspartate Aminotransferase	domain 2	CATH (4.3.0)
B [auth A]	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)
D [auth E]	3.40.640.10	Alpha Beta	3-Layer(aba) Sandwich	Aspartate Aminotransferase	domain 2	CATH (4.3.0)
D [auth E]	3.90.1150.10	Alpha Beta	Alpha-Beta Complex	Aspartate Aminotransferase, domain 1	Aspartate Aminotransferase, domain 1	CATH (4.3.0)
F [auth K]	3.40.640.10	Alpha Beta	3-Layer(aba) Sandwich	Aspartate Aminotransferase	domain 2	CATH (4.3.0)
F [auth K]	3.90.1150.10	Alpha Beta	Alpha-Beta Complex	Aspartate Aminotransferase, domain 1	Aspartate Aminotransferase, domain 1	CATH (4.3.0)
H [auth O]	3.40.640.10	Alpha Beta	3-Layer(aba) Sandwich	Aspartate Aminotransferase	domain 2	CATH (4.3.0)
H [auth O]	3.90.1150.10	Alpha Beta	Alpha-Beta Complex	Aspartate Aminotransferase, domain 1	Aspartate Aminotransferase, domain 1	CATH (4.3.0)
A [auth H]	3.40.640.10	Alpha Beta	3-Layer(aba) Sandwich	Aspartate Aminotransferase	domain 2	CATH (4.3.0)
A [auth H]	3.90.1150.10	Alpha Beta	Alpha-Beta Complex	Aspartate Aminotransferase, domain 1	Aspartate Aminotransferase, domain 1	CATH (4.3.0)
E [auth G]	3.40.640.10	Alpha Beta	3-Layer(aba) Sandwich	Aspartate Aminotransferase	domain 2	CATH (4.3.0)
E [auth G]	3.90.1150.10	Alpha Beta	Alpha-Beta Complex	Aspartate Aminotransferase, domain 1	Aspartate Aminotransferase, domain 1	CATH (4.3.0)
G [auth M]	3.40.640.10	Alpha Beta	3-Layer(aba) Sandwich	Aspartate Aminotransferase	domain 2	CATH (4.3.0)
G [auth M]	3.90.1150.10	Alpha Beta	Alpha-Beta Complex	Aspartate Aminotransferase, domain 1	Aspartate Aminotransferase, domain 1	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A [auth H], B [auth A], C, D [auth E], E [auth G], A [auth H], B [auth A], C, D [auth E], E [auth G], F [auth K], G [auth M], H [auth O]	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-succinylhomos ...	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 [auth H], B [auth A], C, D [auth E], E [auth G], A [auth H], B [auth A], C, D [auth E], E [auth G], F [auth K], G [auth M], H [auth O]	Cystathionine gamma-synthase	carbon-sulfur lyase activity lyase activity catalytic activity cystathionine gamma-lyase activity cystathionine gamma-synthase activity (acts on O-phosphohomoserine) transferase activity transferase activity, transferring alkyl or aryl (other than methyl) groups vitamin binding vitamin B6 binding pyridoxal phosphate binding ion binding binding organic cyclic compound binding anion binding carbon-sulfur lyase activity lyase activity catalytic activity cystathionine gamma-lyase activity cystathionine gamma-synthase activity (acts on O-phosphohomoserine) transferase activity transferase activity, transferring alkyl or aryl (other than methyl) groups vitamin binding vitamin B6 binding pyridoxal phosphate binding ion binding binding organic cyclic compound binding anion binding heterocyclic compound binding small molecule binding cystathionine gamma-synthase activity	homocysteine metabolic process organonitrogen compound metabolic process serine family amino acid metabolic process oxoacid metabolic process sulfur amino acid metabolic process cellular 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 cysteine metabolic process non-proteinogenic amino acid metabolic process homocysteine metabolic process organonitrogen compound metabolic process serine family amino acid metabolic process oxoacid metabolic process sulfur amino acid metabolic process cellular 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 cysteine metabolic process non-proteinogenic amino acid metabolic process proteinogenic amino acid metabolic process organic substance metabolic process metabolic process small molecule metabolic process cellular process sulfur compound metabolic process homoserine metabolic process cellular biosynthetic process cysteine biosynthetic process via cystathionine organonitrogen compound biosynthetic process organic acid biosynthetic process carboxylic acid biosynthetic process cysteine biosynthetic process organic substance biosynthetic process small molecule biosynthetic process L-amino acid biosynthetic process amino acid biosynthetic process sulfur compound biosynthetic process biosynthetic process proteinogenic amino acid biosynthetic process serine family amino acid biosynthetic process sulfur amino acid biosynthetic process alpha-amino acid biosynthetic process aspartate family amino acid biosynthetic process aspartate family amino acid metabolic process methionine biosynthetic process methionine metabolic process	intracellular anatomical structure cytoplasm cellular anatomical entity

InterPro: Protein Family Classification InterPro Database Homepage

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

RCSB PDB Core Operations are funded by the National Science Foundation (DBI-1832184), 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 R01GM133198.