6LD7 | pdb_00006ld7

Native Structure of cystathionine gamma synthase (XometB) from Xanthomonas oryzae pv. oryzae

External Resource: Annotation

Domain Annotation: SCOP/SCOPe Classification
Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
Protein Family Annotation
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)
A	d6ld7a_	Alpha and beta proteins (a/b)	PLP-dependent transferase-like	PLP-dependent transferases	automated matches	automated matches	(Xanthomonas oryzae pv. oryzae KACC 10331 ) [TaxId: 291331 ],	SCOPe (2.08)
D	d6ld7d_	Alpha and beta proteins (a/b)	PLP-dependent transferase-like	PLP-dependent transferases	automated matches	automated matches	(Xanthomonas oryzae pv. oryzae KACC 10331 ) [TaxId: 291331 ],	SCOPe (2.08)
C	d6ld7c_	Alpha and beta proteins (a/b)	PLP-dependent transferase-like	PLP-dependent transferases	automated matches	automated matches	(Xanthomonas oryzae pv. oryzae KACC 10331 ) [TaxId: 291331 ],	SCOPe (2.08)
B	d6ld7b_	Alpha and beta proteins (a/b)	PLP-dependent transferase-like	PLP-dependent transferases	automated matches	automated matches	(Xanthomonas oryzae pv. oryzae KACC 10331 ) [TaxId: 291331 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A	SCOP2B Superfamily	PLP-dependent transferases	8102180	3000954	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	PLP-dependent transferases	8102180	3000954	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	PLP-dependent transferases	8102180	3000954	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	PLP-dependent transferases	8102180	3000954	SCOP2B (2022-06-29)

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
A	e6ld7A1	A: Family A G protein-coupled receptor-like	X: Family A G protein-coupled receptor-like	H: Family A G protein-coupled receptor-like	T: Epimerase	F:	ECOD (20:10:01)
D	e6ld7D1	A: Family A G protein-coupled receptor-like	X: Family A G protein-coupled receptor-like	H: Family A G protein-coupled receptor-like	T: Epimerase	F:	ECOD (20:10:01)
C	e6ld7C1	A: Family A G protein-coupled receptor-like	X: Family A G protein-coupled receptor-like	H: Family A G protein-coupled receptor-like	T: Epimerase	F:	ECOD (20:10:01)
B	e6ld7B1	A: Family A G protein-coupled receptor-like	X: Family A G protein-coupled receptor-like	H: Family A G protein-coupled receptor-like	T: Epimerase	F:	ECOD (20:10:01)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B, C, D	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	Cystathionine gamma-synthase	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 L-cysteine 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 proteinogenic amino acid metabolic process non-proteinogenic amino acid metabolic process homocysteine metabolic process oxoacid metabolic process sulfur amino acid metabolic process L-cysteine 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 proteinogenic amino acid metabolic process non-proteinogenic amino acid metabolic process metabolic process cellular process small molecule metabolic process sulfur compound metabolic process L-cysteine biosynthetic process organic acid biosynthetic process carboxylic acid 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 L-cysteine biosynthetic process via L-cystathionine alpha-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	IPR015424	Pyridoxal phosphate-dependent transferase	Homologous Superfamily
A, B, C, D	IPR000277	Cys/Met metabolism, pyridoxal phosphate-dependent enzyme	Family
A, B, C, D	IPR015421	Pyridoxal phosphate-dependent transferase, major domain	Homologous Superfamily
A, B, C, D	IPR015422	Pyridoxal phosphate-dependent transferase, small domain	Homologous Superfamily
A, B, C, D	IPR011821	O-succinylhomoserine (thiol)-lyase	Family
A, B, C, D	IPR054542	Cys/Met metabolism enzyme, pyridoxal-phosphate attachment site	Conserved Site

Protein Modification Annotation

Modified Residue(s)
Chain	Residue(s)	Description
A, B, C, D	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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