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Catalytic Site Atlas

CSA LITERATURE entry for 1nml

E.C. namecytochrome-c peroxidase
SpeciesMarinobacter hydrocarbonoclasticus ()
E.C. Number (IntEnz) 1.11.1.5
CSA Homologues of 1nml
CSA Entries With UniProtID
CSA Entries With EC Number 1.11.1.5
PDBe Entry 1nml
PDBSum Entry 1nml
MACiE Entry 1nml

Literature Report

IntroductionCytochrome c peroxidase (CCP) catalyses the reduction of hydrogen peroxide to water, an important step in the cellular detoxification process. Two cytochrome c molecules serve as the electron donors. Di-heme CCPs are found in bacteria including Pseudomonas aeruginosa, Paracoccus denitrificans and Pseudomonas nautica.
The overall reaction is:
2 cyt c (Fe2+) + H2O2 -> 2 cyt c (Fe3+) + 2 H2O
The enzyme has two heme cofactors, referred to as high and low potential hemes (HP heme and LP heme), located in the C and N terminal domains respectively.
The enzyme requires Ca2+ for activation; calcium causes structural changes and removal of a heme ligand, allowing peroxide approach.
MechansimThe mechanism is not yet clearly understood, but a mechanism using a oxo-ferryl intermediate is consistent with spectroscopic, mutagenic and structural evidence. LP heme is the peroxidatic heme, and HP heme is the route of electron transfer from the cytochromes to the LP heme. Trp 94 is likely to function as an electron transfer residue, connecting the propionate groups of the two heme cofactors.
The most supported model for the redox mechanism is:
1) The inactive form of the enzyme has no calcium, HP heme with Fe(III) in high / low spin equilibrium, and LP heme with low spin Fe(III).
2) Calcium binds; cytochrome c delivers an electron to HP heme which becomes low spin with Fe(II). The enzyme is now activated.
3) Hydrogen peroxide binds to LP heme. Glu 114 acts as an acid/base catalyst to transfer one of the protons of H2O2 to the other oxygen atom, thus encouraging O-O bond cleavage and loss of water. An LP heme Fe(IV)=O oxo-ferryl species is formed. HP heme is oxidised to Fe(III).
4) A second cytochrome c delivers an electron to LP heme (via HP heme and Trp 94); along with two protons (method of proton delivery not known), this reduces the Fe(IV)=O into Fe(III) and water.
5) A third cytochrome c delivers an electron to HP heme, reducing its Fe(III) into Fe(II). The enzyme is now back in the active mixed valence form.
Reaction

Catalytic Sites for 1nml

Annotated By Reference To The Literature - Site 1 (Perform Site Search)
ResidueChainNumberUniProtKB NumberFunctional PartFunctionTargetDescription
GluA114114macie:sideChainGlu 114 may act to promote cleavage of the peroxide O-O bond, by facilitating proton transfer from one oxygen of the substrate to the other.

Literature References

Notes:
Dias JM
Structural basis for the mechanism of Ca(2+) activation of the di-heme cytochrome c peroxidase from Pseudomonas nautica 617.
Structure 2004 12 961-973
PubMed: 15274917
De Smet L
Structural and mutagenesis studies on the cytochrome c peroxidase from Rhodobacter capsulatus provide new insights into structure-function relationships of bacterial di-heme peroxidases.
J Biol Chem 2006 281 4371-4379
PubMed: 16314410
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