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PDBsum entry 1cce

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Oxidoreductase(h2o2(a)) PDB id
1cce
Jmol
Contents
Protein chain
291 a.a. *
Ligands
HEM
Waters ×86
* Residue conservation analysis
PDB id:
1cce
Name: Oxidoreductase(h2o2(a))
Title: Construction of a bis-aquo heme enzyme and replacement with exogenous ligand
Structure: CytochromE C peroxidase. Chain: a. Engineered: yes
Source: Saccharomyces cerevisiae. Baker's yeast. Organism_taxid: 4932
Resolution:
2.30Å     R-factor:   0.190    
Authors: D.E.Mcree,G.M.Jensen,M.M.Fitzgerald,H.A.Siegel,D.B.Goodin
Key ref: D.E.McRee et al. (1994). Construction of a bisaquo heme enzyme and binding by exogenous ligands. Proc Natl Acad Sci U S A, 91, 12847-12851. PubMed id: 7809133 DOI: 10.1073/pnas.91.26.12847
Date:
04-May-94     Release date:   31-Jul-94    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
P00431  (CCPR_YEAST) -  Cytochrome c peroxidase, mitochondrial
Seq:
Struc:
361 a.a.
291 a.a.*
Key:    PfamA domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 3 residue positions (black crosses)

 Enzyme reactions 
   Enzyme class: E.C.1.11.1.5  - Cytochrome-c peroxidase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: 2 ferrocytochrome c + H2O2 = 2 ferricytochrome c + 2 H2O
2 × ferrocytochrome c
+ H(2)O(2)
= 2 × ferricytochrome c
+ 2 × H(2)O
      Cofactor: Heme
Heme
Bound ligand (Het Group name = HEM) matches with 95.00% similarity
Molecule diagrams generated from .mol files obtained from the KEGG ftp site
 Gene Ontology (GO) functional annotation 
  GO annot!
  Biological process     oxidation-reduction process   2 terms 
  Biochemical function     peroxidase activity     2 terms  

 

 
    reference    
 
 
DOI no: 10.1073/pnas.91.26.12847 Proc Natl Acad Sci U S A 91:12847-12851 (1994)
PubMed id: 7809133  
 
 
Construction of a bisaquo heme enzyme and binding by exogenous ligands.
D.E.McRee, G.M.Jensen, M.M.Fitzgerald, H.A.Siegel, D.B.Goodin.
 
  ABSTRACT  
 
The crystal structure of the His-175-->Gly (H175G) mutant of cytochrome-c peroxidase (EC 1.11.1.5), missing its only heme ligand, reveals that the histidine is replaced by solvent to give a bisaquo heme protein. This protein retains some residual activity, which can be stimulated or inhibited by addition of exogenous ligands. Structural analysis confirms the binding of imidazole to the heme at the position of the wild-type histidine ligand. This imidazole complex reacts readily with hydrogen peroxide to produce a radical species with novel properties. However, reactivation in this complex is incomplete (approximately 5%), which, in view of the very similar structures of the wild-type and the H175G/imidazole forms, implies a critical role for tethering of the axial ligand in catalysis. This study demonstrates the feasibility of constructing heme enzymes with no covalent link to the protein and with unnatural ligand replacements. Such enzymes may prove useful in studies of electron transfer mechanisms and in the engineering of novel heme-based catalysts.
 

Literature references that cite this PDB file's key reference

  PubMed id Reference
21042820 S.El Ichi, A.Miodek, H.Sauriat-Dorizon, J.P.Mahy, C.Henry, M.N.Marzouki, and H.Korri-Youssoufi (2011).
Characterization of structure and activity of garlic peroxidase (POX(1B)).
  J Biol Inorg Chem, 16, 157-172.  
17534534 S.Schneider, J.Marles-Wright, K.H.Sharp, and M.Paoli (2007).
Diversity and conservation of interactions for binding heme in b-type heme proteins.
  Nat Prod Rep, 24, 621-630.  
16847742 K.Czarnecki, L.Chen, J.R.Diers, H.A.Frank, and D.F.Bocian (2006).
Low-frequency resonance Raman studies of the H(M202)G cavity mutant of bacterial photosynthetic reaction centers.
  Photosynth Res, 88, 31-41.  
12538891 A.M.Hays, H.B.Gray, and D.B.Goodin (2003).
Trapping of peptide-based surrogates in an artificially created channel of cytochrome c peroxidase.
  Protein Sci, 12, 278-287.  
12948779 P.D.Barker (2003).
Designing redox metalloproteins from bottom-up and top-down perspectives.
  Curr Opin Struct Biol, 13, 490-499.  
12012432 J.H.Dawson, A.E.Pond, and M.P.Roach (2002).
H93G myoglobin cavity mutant as versatile template for modeling heme proteins: magnetic circular dichroism studies of thiolate- and imidazole-ligated complexes.
  Biopolymers, 67, 200-206.  
11967381 R.J.Rosenfeld, A.M.Hays, R.A.Musah, and D.B.Goodin (2002).
Excision of a proposed electron transfer pathway in cytochrome c peroxidase and its replacement by a ligand-binding channel.
  Protein Sci, 11, 1251-1259.
PDB codes: 1kxm 1kxn
11170453 J.Hirst, S.K.Wilcox, J.Ai, P.Moënne-Loccoz, T.M.Loehr, and D.B.Goodin (2001).
Replacement of the axial histidine ligand with imidazole in cytochrome c peroxidase. 2. Effects on heme coordination and function.
  Biochemistry, 40, 1274-1283.  
11170452 J.Hirst, S.K.Wilcox, P.A.Williams, J.Blankenship, D.E.McRee, and D.B.Goodin (2001).
Replacement of the axial histidine ligand with imidazole in cytochrome c peroxidase. 1. Effects on structure.
  Biochemistry, 40, 1265-1273.
PDB codes: 1ds4 1dse 1dsg 1dso 1dsp
10852874 L.Meek, and D.J.Arp (2000).
The hydrogenase cytochrome b heme ligands of Azotobacter vinelandii are required for full H(2) oxidation capability.
  J Bacteriol, 182, 3429-3436.  
10684626 M.P.Roach, S.Ozaki, and Y.Watanabe (2000).
Investigations of the myoglobin cavity mutant H93G with unnatural imidazole proximal ligands as a modular peroxide O-O bond cleavage model system.
  Biochemistry, 39, 1446-1454.  
10360958 A.E.Pond, M.P.Roach, M.Sono, A.H.Rux, S.Franzen, R.Hu, M.R.Thomas, A.Wilks, Y.Dou, M.Ikeda-Saito, P.R.Ortiz de Montellano, W.H.Woodruff, S.G.Boxer, and J.H.Dawson (1999).
Assignment of the heme axial ligand(s) for the ferric myoglobin (H93G) and heme oxygenase (H25A) cavity mutants as oxygen donors using magnetic circular dichroism.
  Biochemistry, 38, 7601-7608.  
9698383 A.M.Hays, I.R.Vassiliev, J.H.Golbeck, and R.J.Debus (1998).
Role of D1-His190 in proton-coupled electron transfer reactions in photosystem II: a chemical complementation study.
  Biochemistry, 37, 11352-11365.  
9521770 Y.Zhao, J.P.Schelvis, G.T.Babcock, and M.A.Marletta (1998).
Identification of histidine 105 in the beta1 subunit of soluble guanylate cyclase as the heme proximal ligand.
  Biochemistry, 37, 4502-4509.  
9235990 A.K.Abelskov, A.T.Smith, C.B.Rasmussen, H.B.Dunford, and K.G.Welinder (1997).
pH dependence and structural interpretation of the reactions of Coprinus cinereus peroxidase with hydrogen peroxide, ferulic acid, and 2,2'-azinobis.
  Biochemistry, 36, 9453-9463.  
8989328 D.Barrick, N.T.Ho, V.Simplaceanu, F.W.Dahlquist, and C.Ho (1997).
A test of the role of the proximal histidines in the Perutz model for cooperativity in haemoglobin.
  Nat Struct Biol, 4, 78-83.  
9030724 J.Bujons, A.Dikiy, J.C.Ferrer, L.Banci, and A.G.Mauk (1997).
Charge reversal of a critical active-site residue of cytochrome-c peroxidase: characterization of the Arg48-->Glu variant.
  Eur J Biochem, 243, 72-84.  
9305956 R.A.Musah, and D.B.Goodin (1997).
Introduction of novel substrate oxidation into cytochrome c peroxidase by cavity complementation: oxidation of 2-aminothiazole and covalent modification of the enzyme.
  Biochemistry, 36, 11665-11674.
PDB code: 1aev
8634269 G.van Pouderoyen, C.R.Andrew, T.M.Loehr, J.Sanders-Loehr, S.Mazumdar, H.A.Hill, and G.W.Canters (1996).
Spectroscopic and mechanistic studies of type-1 and type-2 copper sites in Pseudomonas aeruginosa azurin as obtained by addition of external ligands to mutant His46Gly.
  Biochemistry, 35, 1397-1407.  
8855959 G.van Pouderoyen, T.den Blaauwen, J.Reedijk, and G.W.Canters (1996).
Dimerization of a His117Gly azurin mutant by external addition of 1,omega-di(imidazol-1-yl)alkanes.
  Biochemistry, 35, 13205-13211.  
8841402 J.Foerster, C.Harteneck, J.Malkewitz, G.Schultz, and D.Koesling (1996).
A functional heme-binding site of soluble guanylyl cyclase requires intact N-termini of alpha 1 and beta 1 subunits.
  Eur J Biochem, 240, 380-386.  
8652585 J.O.Goldsmith, B.King, and S.G.Boxer (1996).
Mg coordination by amino acid side chains is not required for assembly and function of the special pair in bacterial photosynthetic reaction centers.
  Biochemistry, 35, 2421-2428.  
8664277 S.K.Wilcox, G.M.Jensen, M.M.Fitzgerald, D.E.McRee, and D.B.Goodin (1996).
Altering substrate specificity at the heme edge of cytochrome c peroxidase.
  Biochemistry, 35, 4858-4866.
PDB codes: 3ccx 4ccx
8841121 S.L.Newmyer, J.Sun, T.M.Loehr, and P.R.Ortiz de Montellano (1996).
Rescue of the horseradish peroxidase His-170-->Ala mutant activity by imidazole: importance of proximal ligand tethering.
  Biochemistry, 35, 12788-12795.  
8855949 T.Matsui, S.Nagano, K.Ishimori, Y.Watanabe, and I.Morishima (1996).
Preparation and reactions of myoglobin mutants bearing both proximal cysteine ligand and hydrophobic distal cavity: protein models for the active site of P-450.
  Biochemistry, 35, 13118-13124.  
7579651 D.Barrick (1995).
Depletion and replacement of protein metal ligands.
  Curr Opin Biotechnol, 6, 411-418.  
  8528082 M.M.Fitzgerald, M.L.Trester, G.M.Jensen, D.E.McRee, and D.B.Goodin (1995).
The role of aspartate-235 in the binding of cations to an artificial cavity at the radical site of cytochrome c peroxidase.
  Protein Sci, 4, 1844-1850.
PDB codes: 1cmt 1cmu
The most recent references are shown first. Citation data come partly from CiteXplore and partly from an automated harvesting procedure. Note that this is likely to be only a partial list as not all journals are covered by either method. However, we are continually building up the citation data so more and more references will be included with time. Where a reference describes a PDB structure, the PDB codes are shown on the right.