Annotations: 4IXZ

Native structure of cystathionine gamma lyase (XometC) from xanthomonas oryzae pv. oryzae at pH 9.0

External Resource: Annotation

Domain Annotation: SCOP/SCOPe Classification
Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
Domain Annotation: CATH
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)
D	d4ixzd_	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	d4ixzc_	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	d4ixzb_	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)
A	d4ixza_	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)
D	SCOP2 Family	Cystathionine synthase-like	8059618	4000672	SCOP2 (2022-06-29)
D	SCOP2 Superfamily	PLP-dependent transferases	8059619	3000954	SCOP2 (2022-06-29)
C	SCOP2B Superfamily	PLP-dependent transferases	8059619	3000954	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	PLP-dependent transferases	8059619	3000954	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	PLP-dependent transferases	8059619	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	EF-hand_1, EF-hand_5, EF-hand_7	e4ixzD2	A: beta barrels	X: Subtilisin-like	H: Subtilisin-like	T: Subtilisin-like	F: EF-hand_1, EF-hand_5, EF-hand_7	ECOD (v294.2)
C	EF-hand_1, EF-hand_5, EF-hand_7	e4ixzC2	A: beta barrels	X: Subtilisin-like	H: Subtilisin-like	T: Subtilisin-like	F: EF-hand_1, EF-hand_5, EF-hand_7	ECOD (v294.2)
B	EF-hand_1, EF-hand_5, EF-hand_7	e4ixzB2	A: beta barrels	X: Subtilisin-like	H: Subtilisin-like	T: Subtilisin-like	F: EF-hand_1, EF-hand_5, EF-hand_7	ECOD (v294.2)
A	EF-hand_1, EF-hand_5, EF-hand_7	e4ixzA2	A: beta barrels	X: Subtilisin-like	H: Subtilisin-like	T: Subtilisin-like	F: EF-hand_1, EF-hand_5, EF-hand_7	ECOD (v294.2)

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 (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)

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-lyase-like protein	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 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	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	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 : AA0119 : N6-pyridoxal phosphate-L-lysine MOD:00128

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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.