Summary Structural details Experimental details Functional details Sequence Neighbor History Downloads

5JYX

Crystal structure of the covalent thioimide intermediate of the archaeosine synthase QueF-Like

Functional Information from GO Data

Chain	GOid	namespace	contents
A	0008033	biological_process	tRNA processing
A	0008616	biological_process	tRNA queuosine(34) biosynthetic process
A	0016740	molecular_function	transferase activity
A	0033739	molecular_function	preQ1 synthase activity
B	0008033	biological_process	tRNA processing
B	0008616	biological_process	tRNA queuosine(34) biosynthetic process
B	0016740	molecular_function	transferase activity
B	0033739	molecular_function	preQ1 synthase activity
C	0008033	biological_process	tRNA processing
C	0008616	biological_process	tRNA queuosine(34) biosynthetic process
C	0016740	molecular_function	transferase activity
C	0033739	molecular_function	preQ1 synthase activity
D	0008033	biological_process	tRNA processing
D	0008616	biological_process	tRNA queuosine(34) biosynthetic process
D	0016740	molecular_function	transferase activity
D	0033739	molecular_function	preQ1 synthase activity
E	0008033	biological_process	tRNA processing
E	0008616	biological_process	tRNA queuosine(34) biosynthetic process
E	0016740	molecular_function	transferase activity
E	0033739	molecular_function	preQ1 synthase activity
F	0008033	biological_process	tRNA processing
F	0008616	biological_process	tRNA queuosine(34) biosynthetic process
F	0016740	molecular_function	transferase activity
F	0033739	molecular_function	preQ1 synthase activity
G	0008033	biological_process	tRNA processing
G	0008616	biological_process	tRNA queuosine(34) biosynthetic process
G	0016740	molecular_function	transferase activity
G	0033739	molecular_function	preQ1 synthase activity
H	0008033	biological_process	tRNA processing
H	0008616	biological_process	tRNA queuosine(34) biosynthetic process
H	0016740	molecular_function	transferase activity
H	0033739	molecular_function	preQ1 synthase activity
I	0008033	biological_process	tRNA processing
I	0008616	biological_process	tRNA queuosine(34) biosynthetic process
I	0016740	molecular_function	transferase activity
I	0033739	molecular_function	preQ1 synthase activity
J	0008033	biological_process	tRNA processing
J	0008616	biological_process	tRNA queuosine(34) biosynthetic process
J	0016740	molecular_function	transferase activity
J	0033739	molecular_function	preQ1 synthase activity
K	0008033	biological_process	tRNA processing
K	0008616	biological_process	tRNA queuosine(34) biosynthetic process
K	0016740	molecular_function	transferase activity
K	0033739	molecular_function	preQ1 synthase activity
L	0008033	biological_process	tRNA processing
L	0008616	biological_process	tRNA queuosine(34) biosynthetic process
L	0016740	molecular_function	transferase activity
L	0033739	molecular_function	preQ1 synthase activity
M	0008033	biological_process	tRNA processing
M	0008616	biological_process	tRNA queuosine(34) biosynthetic process
M	0016740	molecular_function	transferase activity
M	0033739	molecular_function	preQ1 synthase activity
N	0008033	biological_process	tRNA processing
N	0008616	biological_process	tRNA queuosine(34) biosynthetic process
N	0016740	molecular_function	transferase activity
N	0033739	molecular_function	preQ1 synthase activity
O	0008033	biological_process	tRNA processing
O	0008616	biological_process	tRNA queuosine(34) biosynthetic process
O	0016740	molecular_function	transferase activity
O	0033739	molecular_function	preQ1 synthase activity

Functional Information from PDB Data

site_id	AC1
Number of Residues	10
Details	binding site for residue GD1 A 201

Chain	Residue
A	CYS21
C	GLU46
A	ASP28
A	LEU61
A	HIS62
A	GLU63
A	TYR90
C	VAL42
C	LEU43
C	ILE45

site_id	AC2
Number of Residues	4
Details	binding site for residue NA C 202

Chain	Residue
C	GLU31
C	SER33
C	THR85
C	HOH308

site_id	AC3
Number of Residues	4
Details	binding site for residue NA E 202

Chain	Residue
E	GLU31
E	SER33
E	THR85
E	HOH305

site_id	AC4
Number of Residues	1
Details	binding site for residue NA L 202

Chain	Residue
L	SER33

site_id	AC5
Number of Residues	14
Details	binding site for Di-peptide GD1 B 201 and CYS B 21

Chain	Residue
B	VAL20
B	PRO22
B	ILE23
B	SER24
B	LYS25
B	THR26
B	ASP28
B	LEU61
B	HIS62
B	GLU63
B	TYR90
E	LEU43
E	ILE45
E	GLU46

site_id	AC6
Number of Residues	14
Details	binding site for Di-peptide GD1 C 201 and CYS C 21

Chain	Residue
C	VAL20
C	PRO22
C	ILE23
C	SER24
C	LYS25
C	THR26
C	ASP28
C	LEU61
C	HIS62
C	GLU63
C	TYR90
J	LEU43
J	ILE45
J	GLU46

site_id	AC7
Number of Residues	15
Details	binding site for Di-peptide GD1 D 201 and CYS D 21

Chain	Residue
D	VAL20
D	PRO22
D	ILE23
D	SER24
D	LYS25
D	THR26
D	ASP28
D	LEU61
D	HIS62
D	GLU63
D	TYR90
H	VAL42
H	LEU43
H	ILE45
H	GLU46

site_id	AC8
Number of Residues	14
Details	binding site for Di-peptide GD1 E 201 and CYS E 21

Chain	Residue
E	VAL20
E	PRO22
E	ILE23
E	SER24
E	LYS25
E	THR26
E	ASP28
E	LEU61
E	HIS62
E	GLU63
E	TYR90
F	LEU43
F	ILE45
F	GLU46

site_id	AC9
Number of Residues	15
Details	binding site for Di-peptide GD1 F 201 and CYS F 21

Chain	Residue
F	VAL20
F	PRO22
F	ILE23
F	SER24
F	LYS25
F	THR26
F	ASP28
F	LEU61
F	HIS62
F	GLU63
F	TYR90
O	LEU43
O	ALA44
O	ILE45
O	GLU46

site_id	AD1
Number of Residues	14
Details	binding site for Di-peptide GD1 G 201 and CYS G 21

Chain	Residue
G	LYS25
G	THR26
G	ASP28
G	HIS62
G	GLU63
G	TYR90
D	VAL42
D	LEU43
D	ILE45
D	GLU46
G	VAL20
G	PRO22
G	ILE23
G	SER24

site_id	AD2
Number of Residues	16
Details	binding site for Di-peptide GD1 H 201 and CYS H 21

Chain	Residue
H	VAL20
H	PRO22
H	ILE23
H	SER24
H	LYS25
H	THR26
H	ASP28
H	LEU61
H	HIS62
H	GLU63
H	TYR90
L	VAL42
L	LEU43
L	ALA44
L	ILE45
L	GLU46

site_id	AD3
Number of Residues	15
Details	binding site for Di-peptide GD1 I 201 and CYS I 21

Chain	Residue
B	VAL42
B	LEU43
B	ILE45
B	GLU46
I	VAL20
I	PRO22
I	ILE23
I	SER24
I	LYS25
I	THR26
I	ASP28
I	LEU61
I	HIS62
I	GLU63
I	TYR90

site_id	AD4
Number of Residues	14
Details	binding site for Di-peptide GD1 J 201 and CYS J 21

Chain	Residue
J	VAL20
J	PRO22
J	ILE23
J	SER24
J	LYS25
J	THR26
J	ASP28
J	LEU61
J	HIS62
J	GLU63
J	TYR90
N	LEU43
N	ILE45
N	GLU46

site_id	AD5
Number of Residues	14
Details	binding site for Di-peptide GD1 K 201 and CYS K 21

Chain	Residue
G	LEU43
G	ILE45
G	GLU46
K	VAL20
K	PRO22
K	ILE23
K	SER24
K	LYS25
K	THR26
K	ASP28
K	LEU61
K	HIS62
K	GLU63
K	TYR90

site_id	AD6
Number of Residues	16
Details	binding site for Di-peptide GD1 L 201 and CYS L 21

Chain	Residue
K	LEU2
K	LEU43
K	ALA44
K	ILE45
K	GLU46
L	VAL20
L	PRO22
L	ILE23
L	SER24
L	LYS25
L	THR26
L	ASP28
L	LEU61
L	HIS62
L	GLU63
L	TYR90

site_id	AD7
Number of Residues	16
Details	binding site for Di-peptide GD1 M 201 and CYS M 21

Chain	Residue
A	VAL42
A	LEU43
A	ALA44
A	ILE45
A	GLU46
M	VAL20
M	PRO22
M	ILE23
M	SER24
M	LYS25
M	THR26
M	ASP28
M	LEU61
M	HIS62
M	GLU63
M	TYR90

site_id	AD8
Number of Residues	16
Details	binding site for Di-peptide GD1 N 201 and CYS N 21

Chain	Residue
M	LEU2
M	VAL42
M	LEU43
M	ILE45
M	GLU46
N	VAL20
N	PRO22
N	ILE23
N	SER24
N	LYS25
N	THR26
N	ASP28
N	LEU61
N	HIS62
N	GLU63
N	TYR90

site_id	AD9
Number of Residues	14
Details	binding site for Di-peptide GD1 O 201 and CYS O 21

Chain	Residue
I	LEU43
I	ILE45
I	GLU46
O	VAL20
O	PRO22
O	ILE23
O	SER24
O	LYS25
O	THR26
O	ASP28
O	LEU61
O	HIS62
O	GLU63
O	TYR90

Functional Information from PROSITE/UniProt

site_id	PS00092
Number of Residues	7
Details	N6_MTASE N-6 Adenine-specific DNA methylases signature. AAVNPPY

Chain	Residue	Details
A	ALA75-TYR81

Functional Information from SwissProt/UniProt

site_id	SWS_FT_FI1
Number of Residues	15
Details	Active site: {"description":"Thioimide intermediate","evidences":[{"source":"PubMed","id":"27802572","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"28383498","evidenceCode":"ECO:0000269"}]}

Chain

Residue

Details

site_id	SWS_FT_FI2
Number of Residues	15
Details	Active site: {"description":"Proton donor/acceptor","evidences":[{"source":"PubMed","id":"27802572","evidenceCode":"ECO:0000305"}]}

Chain

Residue

Details

site_id	SWS_FT_FI3
Number of Residues	30
Details	Binding site: {"description":"in other chain","evidences":[{"source":"PubMed","id":"27802572","evidenceCode":"ECO:0000269"}]}

Chain

Residue

Details

site_id	SWS_FT_FI4
Number of Residues	45
Details	Binding site: {"evidences":[{"source":"PubMed","id":"27802572","evidenceCode":"ECO:0000269"}]}

Chain

Residue

Details

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