5X2Z

Crystal structure of Pseudomonas putida methionine gamma-lyase C116H mutant with L-methionine intermediates

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	15
Details	binding site for residue 3LM A 401

Chain	Residue
A	SER88
A	SER340
A	LEU341
A	THR355
A	ARG375
A	HOH510
A	HOH552
A	GLY89
A	MET90
A	TYR114
A	ASP186
A	SER208
A	THR210
A	LYS211
A	VAL339

---

site_id	AC2
Number of Residues	16
Details	binding site for residue 3LM B 401

Chain	Residue
B	SER88
B	GLY89
B	MET90
B	TYR114
B	ASN161
B	ASP186
B	SER208
B	THR210
B	LYS211
B	VAL339
B	SER340
B	LEU341
B	THR355
B	ARG375
B	HOH518
B	HOH552

---

site_id	AC3
Number of Residues	15
Details	binding site for residue 3LM C 401

Chain	Residue
C	SER88
C	GLY89
C	MET90
C	TYR114
C	ASP186
C	SER208
C	THR210
C	LYS211
C	VAL339
C	SER340
C	LEU341
C	ARG375
C	HOH505
C	HOH549
C	HOH563

---

site_id	AC4
Number of Residues	16
Details	binding site for residue 3LM D 401

Chain	Residue
D	SER88
D	GLY89
D	MET90
D	TYR114
D	ASN161
D	ASP186
D	SER208
D	THR210
D	LYS211
D	VAL339
D	SER340
D	LEU341
D	THR355
D	ARG375
D	HOH515
D	HOH522

---

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

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