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Catalytic Site Atlas

CSA LITERATURE entry for 1apx

E.C. nameL-ascorbate peroxidase
SpeciesPisum sativum (Garden pea)
E.C. Number (IntEnz) 1.11.1.11
CSA Homologues of 1apxThere are 191 Homologs
CSA Entries With UniProtID P48534
CSA Entries With EC Number 1.11.1.11
PDBe Entry 1apx
PDBSum Entry 1apx
MACiE Entry 1apx

Literature Report

IntroductionThis entry covers the haem peroxidases (EC 1.11.1.5, 1.11.1.7, 1.11.1.11, 1.11.1.13, 1.11.1.14). This group of enzyme catalyse the reduction of hydrogen peroxide (H2O2) to water and the concurrent oxidisation of a range of substrates depending on the specific EC number. EC 1.11.1.5 (cytochrome C peroxidase) catalyses the oxidation of ferrocytochrome C to ferricytochrome C, EC 1.11.1.7 (myeloperoxidase) catalyses the oxidation of a wide range of organic and inorganic substrates, EC 1.11.1.11 (L-ascorbate peroxidases) oxidises L-ascorbate, EC 1.11.1.13 (Manganese peroxide) oxidises Mn2+ to Mn3+, EC 1.11.1.14 (lignin peroxide) breaks down lignin by oxidising veratryl alcohol. Note that the mammalian myeloperoxidases (EC 1.11.1.7) have a different orientation of the active site residues.
Mechansim[REF: 8] (1apx numbering) Despite the wide range of substrates of the heme peroxidases the mechanism can be broken down into 3 steps which are repeated in all of them: 1. Peroxidase (FE3+) + H2O2 = Compound I (FE4+') + H20 2. Compound I (FE4+') + AH2 = Compound II (FE4+) + AH' 3. Compound II (FE4+) + AH2 = Peroxidase (FE3+) + AH' 4. 2AH' = A2H2 or A + AH2 The first step is carried out by a common mechanism through all the heme peroxidases whilst 2-4 vary depending on substrate. The first step is catalysed by residues on the distal side of the heme group. H2O2 enters the active site and binds to the heme Fe, histidine 42, and arginine 38. The oxygen of H2O2 that is bound to the Fe donates a proton to the NE of the histidine. The histidine then in turn donates the proton to the other H2O2 oxygen bound to the arginine. This leaves water bound to arginine and the oxidised Compound I. The mechanism of oxidisation of the substrate varies in steps 2-4.
Reaction

Catalytic Sites for 1apx

Annotated By Reference To The Literature - Site 1 (Perform Site Search)
ResidueChainNumberUniProtKB NumberFunctional PartFunctionTargetDescription
ArgA3838macie:sideChain
HisA4242macie:sideChain
AsnA7171macie:sideChain

Annotated By Reference To The Literature - Site 2 (Perform Site Search)
ResidueChainNumberUniProtKB NumberFunctional PartFunctionTargetDescription
ArgB3838macie:sideChain
HisB4242macie:sideChain
AsnB7171macie:sideChain

Annotated By Reference To The Literature - Site 3 (Perform Site Search)
ResidueChainNumberUniProtKB NumberFunctional PartFunctionTargetDescription
ArgC3838macie:sideChain
HisC4242macie:sideChain
AsnC7171macie:sideChain

Annotated By Reference To The Literature - Site 4 (Perform Site Search)
ResidueChainNumberUniProtKB NumberFunctional PartFunctionTargetDescription
ArgD3838macie:sideChain
HisD4242macie:sideChain
AsnD7171macie:sideChain

Literature References

Notes:Catalase (EC 1.11.1.6) is also a heme peroxidase and uses a similar mechanism, including a catalytic histidine, however the orientation of the histidine and the other catalytic residues is markedly different. Some chloroperoxidases (EC 1.11.1.10) also use a heme group, however in these the catalytic residue is a glutamate. In lactate dehydrogenase and malate dehydrogenase (EC 1.1.1.27, 1.1.1.37 respectively), a similar set of catalytic residues is used though without the heme group. The role of the residues: histidine as acid/base, arginine binding substrate, asparagine controlling orientation of histidine, is conserved though LDH and MDH use aspartate instead of asparagine.
Edwards SL
Crystal structure of cytochrome c peroxidase compound I.
Biochemistry 1987 26 1503-1511
PubMed: 3036202
Peretz M
Amino acid sequence of alcohol dehydrogenase from the thermophilic bacterium Thermoanaerobium brockii.
Biochemistry 1989 28 6549-6555
PubMed: 2790012
Wang JM
X-ray structures of recombinant yeast cytochrome c peroxidase and three heme-cleft mutants prepared by site-directed mutagenesis.
Biochemistry 1990 29 7160-7173
PubMed: 2169873
Patterson WR
Crystal structure of recombinant pea cytosolic ascorbate peroxidase.
Biochemistry 1995 34 4331-4341
PubMed: 7703247
Fukuyama K
Crystal structures of cyanide- and triiodide-bound forms of Arthromyces ramosus peroxidase at different pH values. Perturbations of active site residues and their implication in enzyme catalysis.
J Biol Chem 1995 270 21884-21892
PubMed: 7665612
Gajhede M
Crystal structure of horseradish peroxidase C at 2.15 A resolution.
Nat Struct Biol 1997 4 1032-1038
PubMed: 9406554
Choinowski T
The crystal structure of lignin peroxidase at 1.70 A resolution reveals a hydroxy group on the cbeta of tryptophan 171: a novel radical site formed during the redox cycle.
J Mol Biol 1999 286 809-827
PubMed: 10024453
Camarero S
Description of a versatile peroxidase involved in the natural degradation of lignin that has both manganese peroxidase and lignin peroxidase substrate interaction sites.
J Biol Chem 1999 274 10324-10330
PubMed: 10187820
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