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PDBsum entry 7xbn
Go to PDB code:
Oxidoreductase
PDB id
7xbn
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Contents
Protein chains
393 a.a.
Ligands
HEM
×2
PXI
×2
GOL
×4
PEG
×3
Waters
×877
PDB id:
7xbn
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Name:
Oxidoreductase
Title:
Crystal structure of yc-17-bound cytochrome p450 pikc with the unnatural amino acid p-acetyl-l-phenylalanine incorporated at position 238
Structure:
Cytochrome p450 monooxygenase pikc. Chain: a, b. Synonym: cytochrome p450 monooxygenase pick,narbomycin c-12 hydroxylase,pikromycin synthase cyp107l1. Engineered: yes
Source:
Streptomyces venezuelae. Organism_taxid: 54571. Gene: pikc, pick. Expressed in: escherichia coli. Expression_system_taxid: 562
Resolution:
2.00Å
R-factor:
0.176
R-free:
0.210
Authors:
G.B.Li,Y.J.Pan,S.Y.Li,X.Gao
Key ref:
Y.J.Pan et al. New mechanistic insight of cytochrome p450 pikc gaine site-Specific mutagenesis by non-Coding amino acids.
Nat commun
, .
Date:
21-Mar-22
Release date:
15-Feb-23
PROCHECK
Headers
References
Protein chains
?
O87605
(PIKC_STRVZ) - Cytochrome P450 monooxygenase PikC from Streptomyces venezuelae
Seq:
Struc:
416 a.a.
393 a.a.
*
Key:
PfamA domain
Secondary structure
*
PDB and UniProt seqs differ at 1 residue position (black cross)
Enzyme reactions
Enzyme class:
E.C.1.14.15.33
- pikromycin synthase.
[IntEnz]
[ExPASy]
[KEGG]
[BRENDA]
Reaction:
1.
narbomycin + 2 reduced [2Fe-2S]-[ferredoxin] + O2 + 2 H
+
= pikromycin + 2 oxidized [2Fe-2S]-[ferredoxin] + H2O
2.
narbomycin + 2 reduced [2Fe-2S]-[ferredoxin] + O2 + 2 H
+
= neopikromycin + 2 oxidized [2Fe-2S]-[ferredoxin] + H2O
3.
narbomycin + 4 reduced [2Fe-2S]-[ferredoxin] + 2 O2 + 4 H
+
= novapikromycin + 4 oxidized [2Fe-2S]-[ferredoxin] + 2 H2O
4.
10-deoxymethymycin + 2 reduced [2Fe-2S]-[ferredoxin] + O2 + 2 H
+
= methymycin + 2 oxidized [2Fe-2S]-[ferredoxin] + H2O
5.
10-deoxymethymycin + 2 reduced [2Fe-2S]-[ferredoxin] + O2 + 2 H
+
= neomethymycin + 2 oxidized [2Fe-2S]-[ferredoxin] + H2O
6.
10-deoxymethymycin +
narbomycin
+
2 × reduced [2Fe-2S]-[ferredoxin]
Bound ligand (Het Group name =
PXI
)
matches with 88.89% similarity
+
O2
+
2 × H(+)
=
pikromycin
+
2 × oxidized [2Fe-2S]-[ferredoxin]
+
H2O
narbomycin
+
2 × reduced [2Fe-2S]-[ferredoxin]
Bound ligand (Het Group name =
PXI
)
matches with 88.89% similarity
+
O2
+
2 × H(+)
=
neopikromycin
+
2 × oxidized [2Fe-2S]-[ferredoxin]
+
H2O
narbomycin
+
4 × reduced [2Fe-2S]-[ferredoxin]
Bound ligand (Het Group name =
PXI
)
matches with 88.89% similarity
+
2 × O2
+
4 × H(+)
=
novapikromycin
+
4 × oxidized [2Fe-2S]-[ferredoxin]
+
2 × H2O
10-deoxymethymycin
Bound ligand (Het Group name =
PXI
)
corresponds exactly
+
2 × reduced [2Fe-2S]-[ferredoxin]
+
O2
+
2 × H(+)
=
methymycin
+
2 × oxidized [2Fe-2S]-[ferredoxin]
+
H2O
10-deoxymethymycin
Bound ligand (Het Group name =
PXI
)
corresponds exactly
+
2 × reduced [2Fe-2S]-[ferredoxin]
+
O2
+
2 × H(+)
=
neomethymycin
+
2 × oxidized [2Fe-2S]-[ferredoxin]
+
H2O
10-deoxymethymycin
Bound ligand (Het Group name =
PXI
)
corresponds exactly
+
Cofactor:
Heme-thiolate
Molecule diagrams generated from .mol files obtained from the
KEGG ftp site
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