4FIR

Crystal structure of pyridoxal biosynthesis lyase PdxS from Pyrococcus

Functional Information from GO Data

Chain	GOid	namespace	contents
A	0006520	biological_process	amino acid metabolic process
A	0008615	biological_process	pyridoxine biosynthetic process
A	0016843	molecular_function	amine-lyase activity
A	0036381	molecular_function	pyridoxal 5'-phosphate synthase (glutamine hydrolysing) activity
A	0042819	biological_process	vitamin B6 biosynthetic process
A	0042823	biological_process	pyridoxal 5'-phosphate biosynthetic process
B	0006520	biological_process	amino acid metabolic process
B	0008615	biological_process	pyridoxine biosynthetic process
B	0016843	molecular_function	amine-lyase activity
B	0036381	molecular_function	pyridoxal 5'-phosphate synthase (glutamine hydrolysing) activity
B	0042819	biological_process	vitamin B6 biosynthetic process
B	0042823	biological_process	pyridoxal 5'-phosphate biosynthetic process
C	0006520	biological_process	amino acid metabolic process
C	0008615	biological_process	pyridoxine biosynthetic process
C	0016843	molecular_function	amine-lyase activity
C	0036381	molecular_function	pyridoxal 5'-phosphate synthase (glutamine hydrolysing) activity
C	0042819	biological_process	vitamin B6 biosynthetic process
C	0042823	biological_process	pyridoxal 5'-phosphate biosynthetic process
D	0006520	biological_process	amino acid metabolic process
D	0008615	biological_process	pyridoxine biosynthetic process
D	0016843	molecular_function	amine-lyase activity
D	0036381	molecular_function	pyridoxal 5'-phosphate synthase (glutamine hydrolysing) activity
D	0042819	biological_process	vitamin B6 biosynthetic process
D	0042823	biological_process	pyridoxal 5'-phosphate biosynthetic process
E	0006520	biological_process	amino acid metabolic process
E	0008615	biological_process	pyridoxine biosynthetic process
E	0016843	molecular_function	amine-lyase activity
E	0036381	molecular_function	pyridoxal 5'-phosphate synthase (glutamine hydrolysing) activity
E	0042819	biological_process	vitamin B6 biosynthetic process
E	0042823	biological_process	pyridoxal 5'-phosphate biosynthetic process
F	0006520	biological_process	amino acid metabolic process
F	0008615	biological_process	pyridoxine biosynthetic process
F	0016843	molecular_function	amine-lyase activity
F	0036381	molecular_function	pyridoxal 5'-phosphate synthase (glutamine hydrolysing) activity
F	0042819	biological_process	vitamin B6 biosynthetic process
F	0042823	biological_process	pyridoxal 5'-phosphate biosynthetic process

Functional Information from PDB Data

site_id	AC1
Number of Residues	11
Details	BINDING SITE FOR RESIDUE R5P A 401

Chain	Residue
A	ASP30
A	GLY278
A	SER279
A	PRO55
A	LYS87
A	SER110
A	ARG153
A	ALA158
A	GLY159
A	GLY256
A	GLY257

---

site_id	AC2
Number of Residues	14
Details	BINDING SITE FOR RESIDUE R5P B 401

Chain	Residue
B	ASP30
B	PRO55
B	LYS87
B	ASP108
B	SER110
B	VAL112
B	ARG153
B	ALA158
B	GLY159
B	GLY256
B	GLY257
B	VAL277
B	GLY278
B	SER279

---

site_id	AC3
Number of Residues	10
Details	BINDING SITE FOR RESIDUE R5P C 401

Chain	Residue
C	ASP30
C	LYS87
C	ASP108
C	ARG153
C	ALA158
C	GLY159
C	GLY256
C	GLY257
C	GLY278
C	SER279

---

site_id	AC4
Number of Residues	13
Details	BINDING SITE FOR RESIDUE R5P D 401

Chain	Residue
D	ASP30
D	PRO55
D	LYS87
D	ASP108
D	SER110
D	VAL112
D	ALA158
D	GLY159
D	GLY256
D	GLY257
D	VAL277
D	GLY278
D	SER279

---

site_id	AC5
Number of Residues	13
Details	BINDING SITE FOR RESIDUE R5P E 401

Chain	Residue
E	ASP30
E	PRO55
E	LYS87
E	ASP108
E	VAL112
E	ARG153
E	ALA158
E	GLY159
E	GLY256
E	GLY257
E	VAL277
E	GLY278
E	SER279

---

site_id	AC6
Number of Residues	9
Details	BINDING SITE FOR RESIDUE R5P F 401

Chain	Residue
F	ASP30
F	LYS87
F	ARG153
F	ALA158
F	GLY159
F	GLY256
F	GLY257
F	GLY278
F	SER279

---

Functional Information from PROSITE/UniProt

site_id	PS01235
Number of Residues	19
Details	PDXS_SNZ_1 PdxS/SNZ family signature. LPVVNFAAGGVATPADAAL

Chain	Residue	Details
A	LEU248-LEU266

---

Functional Information from SwissProt/UniProt

site_id	SWS_FT_FI1
Number of Residues	6
Details	Active site: {"description":"Schiff-base intermediate with D-ribose 5-phosphate","evidences":[{"source":"HAMAP-Rule","id":"MF_01824","evidenceCode":"ECO:0000255"},{"source":"PubMed","id":"23104439","evidenceCode":"ECO:0000269"}]}

Chain

Residue

Details

---

site_id	SWS_FT_FI2
Number of Residues	24
Details	Binding site: {"evidences":[{"source":"HAMAP-Rule","id":"MF_01824","evidenceCode":"ECO:0000255"},{"source":"PubMed","id":"23104439","evidenceCode":"ECO:0000269"}]}

Chain

Residue

Details

---

site_id	SWS_FT_FI3
Number of Residues	6
Details	Binding site: {"evidences":[{"source":"HAMAP-Rule","id":"MF_01824","evidenceCode":"ECO:0000255"}]}

Chain

Residue

Details

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