4IYO

Crystal structure of cystathionine gamma lyase from Xanthomonas oryzae pv. oryzae (XometC) in complex with E-site serine, A-site serine, A-site external aldimine structure with aminoacrylate and A-site iminopropionate intermediates


Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

ChainsTypeFamily Name Domain Identifier Family IdentifierProvenance Source (Version)
ASCOP2B SuperfamilyPLP-dependent transferases 8059619 3000954 SCOP2B (2022-06-29)
BSCOP2B SuperfamilyPLP-dependent transferases 8059619 3000954 SCOP2B (2022-06-29)
CSCOP2B SuperfamilyPLP-dependent transferases 8059619 3000954 SCOP2B (2022-06-29)
DSCOP2B SuperfamilyPLP-dependent transferases 8059619 3000954 SCOP2B (2022-06-29)

Domain Annotation: ECOD Classification ECOD Database Homepage

ChainsFamily NameDomain Identifier ArchitecturePossible HomologyHomologyTopologyFamilyProvenance Source (Version)
ACys_Met_Meta_PP_Ce4iyoA2 A: a+b two layersX: 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 transferasesF: Cys_Met_Meta_PP_CECOD (1.6)
ACys_Met_Meta_PP_Ne4iyoA3 A: a/b three-layered sandwichesX: PLP-dependent transferases (From Topology)H: PLP-dependent transferases (From Topology)T: PLP-dependent transferasesF: Cys_Met_Meta_PP_NECOD (1.6)
BCys_Met_Meta_PP_Ce4iyoB2 A: a+b two layersX: 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 transferasesF: Cys_Met_Meta_PP_CECOD (1.6)
BCys_Met_Meta_PP_Ne4iyoB3 A: a/b three-layered sandwichesX: PLP-dependent transferases (From Topology)H: PLP-dependent transferases (From Topology)T: PLP-dependent transferasesF: Cys_Met_Meta_PP_NECOD (1.6)
CCys_Met_Meta_PP_Ce4iyoC2 A: a+b two layersX: 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 transferasesF: Cys_Met_Meta_PP_CECOD (1.6)
CCys_Met_Meta_PP_Ne4iyoC3 A: a/b three-layered sandwichesX: PLP-dependent transferases (From Topology)H: PLP-dependent transferases (From Topology)T: PLP-dependent transferasesF: Cys_Met_Meta_PP_NECOD (1.6)
DCys_Met_Meta_PP_Ce4iyoD3 A: a+b two layersX: 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 transferasesF: Cys_Met_Meta_PP_CECOD (1.6)
DCys_Met_Meta_PP_Ne4iyoD2 A: a/b three-layered sandwichesX: PLP-dependent transferases (From Topology)H: PLP-dependent transferases (From Topology)T: PLP-dependent transferasesF: Cys_Met_Meta_PP_NECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Protein Family Annotation Pfam Database Homepage

ChainsAccessionNameDescriptionCommentsSource
PF01053Cys/Met metabolism PLP-dependent enzyme (Cys_Met_Meta_PP)Cys/Met metabolism PLP-dependent enzymeThis 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
B, C, D
PF01053Cys/Met metabolism PLP-dependent enzyme (Cys_Met_Meta_PP)Cys/Met metabolism PLP-dependent enzymeThis 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

ChainsPolymerMolecular FunctionBiological ProcessCellular Component
Cystathionine gamma-lyase-like protein -
B, C, D
Cystathionine gamma-lyase-like protein, LYS201A modified -

Protein Modification Annotation

Modified Residue(s)
ChainResidue(s)Description
B, C, D
LLP Parent Component: LYS

RESIDAA0119

PSI-MOD :  N6-pyridoxal phosphate-L-lysine MOD:00128