PDBsum entry 4b7d

Oxidoreductase

PDB id: 4b7d

Contents

Protein chains

393 a.a.

Ligands

GOL ×3

HEM ×2

QLE ×2

Waters ×446

PDB id:

4b7d

Name:

Oxidoreductase

Title:

Pikc bound to the 10-dml analog with the 3-(n,n-dimethylamino) propanoate anchoring group

Structure:

Cytochrome p450 hydroxylase pikc. Chain: a, b. Synonym: cytochrome p450 monooxygenase. Engineered: yes. Other_details: thiolate link between c 354 and hem 1407

Source:

Streptomyces venezuelae. Organism_taxid: 54571. Expressed in: escherichia coli. Expression_system_taxid: 562.

Resolution:

1.89Å R-factor: 0.203 R-free: 0.257

Authors:

L.M.Podust

Key ref:

L.M.Podust Recognition of synthetic substrates by p450 pikc. To be published, .

Date:

17-Aug-12 Release date: 28-Aug-13

Protein chains

O87605  (PIKC_STRVZ) -  Cytochrome P450 monooxygenase PikC from Streptomyces venezuelae

Seq: 416 a.a.

Struc: 393 a.a.

Enzyme reactions

• Enzyme class: E.C.1.14.15.33 - pikromycin synthase.
• 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 = QLE) matches with 68.42% similarity) + O2 + 2 × H(+) = pikromycin + 2 × oxidized [2Fe-2S]-[ferredoxin] + H2O

narbomycin + 2 × reduced [2Fe-2S]-[ferredoxin] (Bound ligand (Het Group name = QLE) matches with 68.42% similarity) + O2 + 2 × H(+) = neopikromycin + 2 × oxidized [2Fe-2S]-[ferredoxin] + H2O

narbomycin + 4 × reduced [2Fe-2S]-[ferredoxin] (Bound ligand (Het Group name = QLE) matches with 68.42% similarity) + 2 × O2 + 4 × H(+) = novapikromycin + 4 × oxidized [2Fe-2S]-[ferredoxin] + 2 × H2O

10-deoxymethymycin (Bound ligand (Het Group name = QLE) matches with 87.50% similarity) + 2 × reduced [2Fe-2S]-[ferredoxin] + O2 + 2 × H(+) = methymycin + 2 × oxidized [2Fe-2S]-[ferredoxin] + H2O

10-deoxymethymycin (Bound ligand (Het Group name = QLE) matches with 87.50% similarity) + 2 × reduced [2Fe-2S]-[ferredoxin] + O2 + 2 × H(+) = neomethymycin + 2 × oxidized [2Fe-2S]-[ferredoxin] + H2O

10-deoxymethymycin (Bound ligand (Het Group name = QLE) matches with 87.50% similarity) +

• Cofactor: Heme-thiolate

Molecule diagrams generated from .mol files obtained from the KEGG ftp site