Summary Structural details Experimental details Functional details Sequence Neighbor History Downloads

1PG8

Crystal Structure of L-methionine alpha-, gamma-lyase

Functional Information from GO Data

Chain	GOid	namespace	contents
A	0003824	molecular_function	catalytic activity
A	0005737	cellular_component	cytoplasm
A	0009086	biological_process	methionine biosynthetic process
A	0016829	molecular_function	lyase activity
A	0016846	molecular_function	carbon-sulfur lyase activity
A	0018826	molecular_function	methionine gamma-lyase activity
A	0019346	biological_process	transsulfuration
A	0030170	molecular_function	pyridoxal phosphate binding
A	0047982	molecular_function	homocysteine desulfhydrase activity
B	0003824	molecular_function	catalytic activity
B	0005737	cellular_component	cytoplasm
B	0009086	biological_process	methionine biosynthetic process
B	0016829	molecular_function	lyase activity
B	0016846	molecular_function	carbon-sulfur lyase activity
B	0018826	molecular_function	methionine gamma-lyase activity
B	0019346	biological_process	transsulfuration
B	0030170	molecular_function	pyridoxal phosphate binding
B	0047982	molecular_function	homocysteine desulfhydrase activity
C	0003824	molecular_function	catalytic activity
C	0005737	cellular_component	cytoplasm
C	0009086	biological_process	methionine biosynthetic process
C	0016829	molecular_function	lyase activity
C	0016846	molecular_function	carbon-sulfur lyase activity
C	0018826	molecular_function	methionine gamma-lyase activity
C	0019346	biological_process	transsulfuration
C	0030170	molecular_function	pyridoxal phosphate binding
C	0047982	molecular_function	homocysteine desulfhydrase activity
D	0003824	molecular_function	catalytic activity
D	0005737	cellular_component	cytoplasm
D	0009086	biological_process	methionine biosynthetic process
D	0016829	molecular_function	lyase activity
D	0016846	molecular_function	carbon-sulfur lyase activity
D	0018826	molecular_function	methionine gamma-lyase activity
D	0019346	biological_process	transsulfuration
D	0030170	molecular_function	pyridoxal phosphate binding
D	0047982	molecular_function	homocysteine desulfhydrase activity

Functional Information from PDB Data

site_id	AC1
Number of Residues	8
Details	BINDING SITE FOR RESIDUE SO4 C 1146

Chain	Residue
C	TYR114
C	LYS211
C	VAL339
C	SER340
C	GLN349
C	ARG375
C	HOH1284
C	HOH1285

site_id	AC2
Number of Residues	8
Details	BINDING SITE FOR RESIDUE SO4 A 1124

Chain	Residue
A	ASN161
A	LYS211
A	VAL339
A	SER340
A	ARG375
A	HOH1495
A	HOH1496
A	TYR114

site_id	AC3
Number of Residues	8
Details	BINDING SITE FOR RESIDUE SO4 B 1138

Chain	Residue
B	TYR114
B	LYS211
B	VAL339
B	SER340
B	LEU341
B	GLN349
B	ARG375
B	PLP1799

site_id	AC4
Number of Residues	6
Details	BINDING SITE FOR RESIDUE SO4 D 1147

Chain	Residue
D	TYR114
D	LYS211
D	VAL339
D	SER340
D	GLN349
D	ARG375

site_id	AC5
Number of Residues	12
Details	BINDING SITE FOR RESIDUE PLP A 1399

Chain	Residue
A	SER88
A	GLY89
A	MET90
A	ILE93
A	TYR114
A	ASP186
A	SER208
A	THR210
A	LYS211
A	HOH1495
C	TYR59
C	ARG61

site_id	AC6
Number of Residues	13
Details	BINDING SITE FOR RESIDUE PLP B 1799

Chain	Residue
B	SER88
B	GLY89
B	MET90
B	TYR114
B	ASP186
B	TYR189
B	SER208
B	THR210
B	LYS211
B	LEU341
B	SO41138
D	TYR59
D	ARG61

site_id	AC7
Number of Residues	12
Details	BINDING SITE FOR RESIDUE PLP C 1199

Chain	Residue
A	TYR59
A	ARG61
C	SER88
C	GLY89
C	MET90
C	TYR114
C	ASP186
C	TYR189
C	SER208
C	THR210
C	LYS211
C	HOH1284

site_id	AC8
Number of Residues	13
Details	BINDING SITE FOR RESIDUE PLP D 1599

Chain	Residue
B	TYR59
B	ARG61
D	SER88
D	GLY89
D	MET90
D	TYR114
D	ASP186
D	THR188
D	TYR189
D	SER208
D	THR210
D	LYS211
D	LEU341

site_id	AC9
Number of Residues	5
Details	BINDING SITE FOR RESIDUE PEG A 1001

Chain	Residue
A	SER4
A	LYS6
A	PEG1002
A	HOH1404
D	ASP385

site_id	BC1
Number of Residues	8
Details	BINDING SITE FOR RESIDUE PEG A 1002

Chain	Residue
A	PRO8
A	THR12
A	ARG13
A	HIS17
A	PEG1001
A	PEG1003
A	HOH1404
A	HOH1499

site_id	BC2
Number of Residues	3
Details	BINDING SITE FOR RESIDUE PEG A 1003

Chain	Residue
A	HIS16
A	TYR19
A	PEG1002

site_id	BC3
Number of Residues	4
Details	BINDING SITE FOR RESIDUE PEG A 1004

Chain	Residue
B	GLY25
A	HIS24
A	TYR33
A	HIS57

site_id	BC4
Number of Residues	2
Details	BINDING SITE FOR RESIDUE PEG A 1005

Chain	Residue
A	GLY25
B	HIS24

site_id	BC5
Number of Residues	8
Details	BINDING SITE FOR RESIDUE PEG B 1006

Chain	Residue
B	GLY18
B	TYR19
B	HIS24
B	PRO30
B	PRO31
B	VAL32
B	PRO65
B	THR66

site_id	BC6
Number of Residues	11
Details	BINDING SITE FOR RESIDUE PEG A 1007

Chain	Residue
A	ALA295
A	SER296
A	PHE297
A	PRO298
A	TYR300
A	THR301
C	ALA271
C	GLN274
C	VAL275
C	GLU278
C	HOH1281

site_id	BC7
Number of Residues	12
Details	BINDING SITE FOR RESIDUE PEG A 1008

Chain	Residue
A	GLY110
A	ASN111
A	THR112
A	LEU113
A	VAL135
A	ASP136
A	MET137
A	PHE156
A	GLU157
A	ALA160
A	HIS165
A	HOH1431

site_id	BC8
Number of Residues	9
Details	BINDING SITE FOR RESIDUE PEG C 1009

Chain	Residue
B	ALA11
B	ASN263
C	ARG268
C	ASN272
C	LEU380
C	GLU381
C	ASP382
C	ILE383
C	HOH1265

site_id	BC9
Number of Residues	2
Details	BINDING SITE FOR RESIDUE PEG B 1010

Chain	Residue
B	PRO8
B	HIS17

site_id	CC1
Number of Residues	6
Details	BINDING SITE FOR RESIDUE PEG C 1012

Chain	Residue
B	HIS16
B	ASP20
C	GLN333
C	LEU334
C	SER336
C	HOH1216

Functional Information from PROSITE/UniProt

site_id	PS00868
Number of Residues	15
Details	CYS_MET_METAB_PP Cys/Met metabolism enzymes pyridoxal-phosphate attachment site. DLvvhSATKYLsGHG

Chain	Residue	Details
A	ASP203-GLY217

Functional Information from SwissProt/UniProt

site_id	SWS_FT_FI1
Number of Residues	8
Details	Binding site: {"evidences":[{"source":"Reference","evidenceCode":"ECO:0000269","citation":{"citationType":"submission","publicationDate":"MAY-2003","submissionDatabase":"PDB data bank","title":"Crystal structure of L-methionine alpha-, gamma-lyase.","authors":["Allen T.W.","Sridhar V.","Prasad G.S.","Han Q.","Xu M.","Tan Y.","Hoffman R.M.","Ramaswamy S."]}}]}

Chain

Residue

Details

site_id	SWS_FT_FI2
Number of Residues	12
Details	Binding site: {"description":"in other chain","evidences":[{"source":"Reference","evidenceCode":"ECO:0000269","citation":{"citationType":"submission","publicationDate":"MAY-2003","submissionDatabase":"PDB data bank","title":"Crystal structure of L-methionine alpha-, gamma-lyase.","authors":["Allen T.W.","Sridhar V.","Prasad G.S.","Han Q.","Xu M.","Tan Y.","Hoffman R.M.","Ramaswamy S."]}}]}

Chain

Residue

Details

site_id	SWS_FT_FI3
Number of Residues	8
Details	Binding site: {"evidences":[{"source":"PubMed","id":"22785484","evidenceCode":"ECO:0000269"},{"source":"PDB","id":"3VK3","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"3VK4","evidenceCode":"ECO:0007744"}]}

Chain

Residue

Details

site_id	SWS_FT_FI4
Number of Residues	4
Details	Modified residue: {"description":"N6-(pyridoxal phosphate)lysine","evidences":[{"source":"PubMed","id":"17289792","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"22785484","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"3365412","evidenceCode":"ECO:0000269"},{"source":"Reference","evidenceCode":"ECO:0000269","citation":{"citationType":"submission","publicationDate":"MAY-2003","submissionDatabase":"PDB data bank","title":"Crystal structure of L-methionine alpha-, gamma-lyase.","authors":["Allen T.W.","Sridhar V.","Prasad G.S.","Han Q.","Xu M.","Tan Y.","Hoffman R.M.","Ramaswamy S."]}},{"source":"Reference","evidenceCode":"ECO:0000269","citation":{"citationType":"submission","publicationDate":"AUG-2003","submissionDatabase":"PDB data bank","title":"Detailed structure of L-methionine-lyase from Pseudomonas putida.","authors":["Misaki S.","Takimoto A.","Takakura T.","Yoshioka T.","Yamashita M.","Tamura T.","Tanaka H.","Inagaki K."]}},{"source":"PDB","id":"1UKJ","evidenceCode":"ECO:0007744"}]}

Chain

Residue

Details

Catalytic Information from CSA

site_id	CSA1
Number of Residues	3
Details	Annotated By Reference To The Literature 1b8g

Chain	Residue	Details
A	LYS211
A	ASP186
A	TYR114

site_id	CSA2
Number of Residues	3
Details	Annotated By Reference To The Literature 1b8g

Chain	Residue	Details
B	LYS211
B	ASP186
B	TYR114

site_id	CSA3
Number of Residues	3
Details	Annotated By Reference To The Literature 1b8g

Chain	Residue	Details
C	LYS211
C	ASP186
C	TYR114

site_id	CSA4
Number of Residues	3
Details	Annotated By Reference To The Literature 1b8g

Chain	Residue	Details
D	LYS211
D	ASP186
D	TYR114

site_id	CSA5
Number of Residues	3
Details	Annotated By Reference To The Literature 1b8g

Chain	Residue	Details
A	ARG61
C	ASP186
C	TYR114

site_id	CSA6
Number of Residues	3
Details	Annotated By Reference To The Literature 1b8g

Chain	Residue	Details
D	ASP186
D	TYR114
B	ARG61

site_id	CSA7
Number of Residues	3
Details	Annotated By Reference To The Literature 1b8g

Chain	Residue	Details
A	ASP186
A	TYR114
C	ARG61

site_id	CSA8
Number of Residues	3
Details	Annotated By Reference To The Literature 1b8g

Chain	Residue	Details
D	ARG61
B	ASP186
B	TYR114

		Sequence (fasta)
		PDBx/mmCIF
		PDBML format (no-atom)
		PDB format (full)
		Validation report (PDF)
		EDMap 2fo-fc (MTZ)