spacer
spacer

PDBsum entry 1ccp

Go to PDB code: 
protein ligands links
Oxidoreductase PDB id
1ccp
Jmol
Contents
Protein chain
293 a.a. *
Ligands
HEM
Waters ×233
* Residue conservation analysis
PDB id:
1ccp
Name: Oxidoreductase
Title: X-ray structures of recombinant yeast cytochromE C peroxidas three heme-cleft mutants prepared by site-directed mutagene
Structure: Yeast cytochromE C peroxidase. Chain: a. Engineered: yes
Source: Saccharomyces cerevisiae. Baker's yeast. Organism_taxid: 4932
Resolution:
2.20Å     R-factor:   0.155    
Authors: J.Wang,J.M.Mauro,S.L.Edwards,S.J.Oatley,L.A.Fishel,V.A.Ashfo H.Xuong,J.Kraut
Key ref:
J.M.Wang et al. (1990). X-ray structures of recombinant yeast cytochrome c peroxidase and three heme-cleft mutants prepared by site-directed mutagenesis. Biochemistry, 29, 7160-7173. PubMed id: 2169873 DOI: 10.1021/bi00483a003
Date:
28-Feb-90     Release date:   15-Jul-91    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
P00431  (CCPR_YEAST) -  Cytochrome c peroxidase, mitochondrial
Seq:
Struc:
361 a.a.
293 a.a.*
Key:    PfamA domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 2 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 95.45% 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: 10.1021/bi00483a003 Biochemistry 29:7160-7173 (1990)
PubMed id: 2169873  
 
 
X-ray structures of recombinant yeast cytochrome c peroxidase and three heme-cleft mutants prepared by site-directed mutagenesis.
J.M.Wang, M.Mauro, S.L.Edwards, S.J.Oatley, L.A.Fishel, V.A.Ashford, N.H.Xuong, J.Kraut.
 
  ABSTRACT  
 
The 2.2-A X-ray structure for CCP(MI), a plasmid-encoded form of Saccharomyces cerevisiae cytochrome c peroxidase (CCP) expressed in Escherichia coli [Fishel, L.A., Villafranca, J. E., Mauro, J. M., & Kraut, J. (1987) Biochemistry 26, 351-360], has been solved, together with the structures of three specifically designed single-site heme-cleft mutants. The structure of CCP(MI) was solved by using molecular replacement methods, since its crystals grow differently from the crystals of CCP isolated from bakers' yeast used previously for structural solution. Small distal-side differences between CCP(MI) and bakers' yeast CCP are observed, presumably due to a strain-specific Thr-53----Ile substitution in CCP(MI). A Trp-51----Phe mutant remains pentacoordinated and exhibits only minor distal structural adjustments. The observation of a vacant sixth coordination site in this structure differs from the results of solution resonance Raman studies, which predict hexacoordinated high-spin iron [Smulevich, G., Mauro, J.M., Fishel, L. A., English, A. M., Kraut, J., & Spiro, T. G. (1988) Biochemistry 27, 5477-5485]. The coordination behavior of this W51F mutant is apparently altered in the presence of a precipitating agent, 30% 2-methyl-2,4-pentanediol. A proximal Trp-191----Phe mutant that has substantially diminished enzyme activity and altered magnetic properties [Mauro, J. M., Fishel, L. F., Hazzard, J. T., Meyer, T. E., Tollin, G., Cusanovich, M. A., & Kraut, J. (1988) Biochemistry 27, 6243-6256] accommodates the substitution by allowing the side chain of Phe-191, together with the segment of backbone to which it is attached, to move toward the heme. This relatively large (ca. 1 A) local perturbation is accompanied by numerous small adjustments resulting in a slight overall compression of the enzyme's proximal domain; however, the iron coordination sphere is essentially unchanged. This structure rules out a major alteration in protein conformation as a reason for the dramatically decreased activity of the W191F mutant. Changing proximal Asp-235 to Asn results in two significant localized structural changes. First, the heme iron moves toward the porphyrin plane, and distal water 595 now clearly resides in the iron coordination sphere at a distance of 2.0 A. The observation of hexacoordinated iron for the D235N mutant is in accord with previous resonance Raman results. Second, the indole side chain of Trp-191 has flipped over as a result of the mutation; the tryptophan N epsilon takes part in a new hydrogen bond with the backbone carbonyl oxygen of Leu-177.(ABSTRACT TRUNCATED AT 400 WORDS)
 

Literature references that cite this PDB file's key reference

  PubMed id Reference
21334283 C.M.DiCarlo, L.B.Vitello, and J.E.Erman (2011).
Reduction potential of yeast cytochrome c peroxidase and three distal histidine mutants: dependence on pH.
  J Inorg Biochem, 105, 532-537.  
17881827 V.de Serrano, Z.Chen, M.F.Davis, and S.Franzen (2007).
X-ray crystal structural analysis of the binding site in the ferric and oxyferrous forms of the recombinant heme dehaloperoxidase cloned from Amphitrite ornata.
  Acta Crystallogr D Biol Crystallogr, 63, 1094-1101.
PDB codes: 2qfk 2qfn
15231844 R.Pierattelli, L.Banci, N.A.Eady, J.Bodiguel, J.N.Jones, P.C.Moody, E.L.Raven, B.Jamart-Grégoire, and K.A.Brown (2004).
Enzyme-catalyzed mechanism of isoniazid activation in class I and class III peroxidases.
  J Biol Chem, 279, 39000-39009.  
14645223 S.Hirotsu, G.C.Chu, M.Unno, D.S.Lee, T.Yoshida, S.Y.Park, Y.Shiro, and M.Ikeda-Saito (2004).
The crystal structures of the ferric and ferrous forms of the heme complex of HmuO, a heme oxygenase of Corynebacterium diphtheriae.
  J Biol Chem, 279, 11937-11947.
PDB codes: 1iw0 1iw1
15231843 T.Bertrand, N.A.Eady, J.N.Jones, Jesmin, J.M.Nagy, B.Jamart-Grégoire, E.L.Raven, and K.A.Brown (2004).
Crystal structure of Mycobacterium tuberculosis catalase-peroxidase.
  J Biol Chem, 279, 38991-38999.
PDB code: 1sj2
12543676 C.J.Wei, B.Lei, J.M.Musser, and S.C.Tu (2003).
Isoniazid activation defects in recombinant Mycobacterium tuberculosis catalase-peroxidase (KatG) mutants evident in InhA inhibitor production.
  Antimicrob Agents Chemother, 47, 670-675.  
12119039 H.A.Heering, C.Indiani, G.Regelsberger, C.Jakopitsch, C.Obinger, and G.Smulevich (2002).
New insights into the heme cavity structure of catalase-peroxidase: a spectroscopic approach to the recombinant synechocystis enzyme and selected distal cavity mutants.
  Biochemistry, 41, 9237-9247.  
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
11141052 R.A.Edwards, M.M.Whittaker, J.W.Whittaker, E.N.Baker, and G.B.Jameson (2001).
Outer sphere mutations perturb metal reactivity in manganese superoxide dismutase.
  Biochemistry, 40, 15-27.
PDB codes: 1en4 1en5 1en6
11425320 S.D.Zarić, D.M.Popović, and E.W.Knapp (2001).
Factors determining the orientation of axially coordinated imidazoles in heme proteins.
  Biochemistry, 40, 7914-7928.  
11567104 X.J.Morelli, P.N.Palma, F.Guerlesquin, and A.C.Rigby (2001).
A novel approach for assessing macromolecular complexes combining soft-docking calculations with NMR data.
  Protein Sci, 10, 2131-2137.  
10828979 S.A.Seibold, J.F.Cerda, A.M.Mulichak, I.Song, R.M.Garavito, T.Arakawa, W.L.Smith, and G.T.Babcock (2000).
Peroxidase activity in prostaglandin endoperoxide H synthase-1 occurs with a neutral histidine proximal heme ligand.
  Biochemistry, 39, 6616-6624.  
10388773 B.D.Howes, C.B.Schiodt, K.G.Welinder, M.P.Marzocchi, J.G.Ma, J.Zhang, J.A.Shelnutt, and G.Smulevich (1999).
The quantum mixed-spin heme state of barley peroxidase: A paradigm for class III peroxidases.
  Biophys J, 77, 478-492.  
10387022 F.Neri, C.Indiani, B.Baldi, J.Vind, K.G.Welinder, and G.Smulevich (1999).
Role of the distal phenylalanine 54 on the structure, stability, and ligand binding of Coprinus cinereus peroxidase.
  Biochemistry, 38, 7819-7827.  
10606521 X.Wang, and G.J.Pielak (1999).
Equilibrium thermodynamics of a physiologically-relevant heme-protein complex.
  Biochemistry, 38, 16876-16881.  
9694833 D.P.Molloy, A.E.Milner, I.K.Yakub, G.Chinnadurai, P.H.Gallimore, and R.J.Grand (1998).
Structural determinants present in the C-terminal binding protein binding site of adenovirus early region 1A proteins.
  J Biol Chem, 273, 20867-20876.  
9788999 L.Wan, M.B.Twitchett, L.D.Eltis, A.G.Mauk, and M.Smith (1998).
In vitro evolution of horse heart myoglobin to increase peroxidase activity.
  Proc Natl Acad Sci U S A, 95, 12825-12831.  
9694851 M.Ekberg, S.Pötsch, E.Sandin, M.Thunnissen, P.Nordlund, M.Sahlin, and B.M.Sjöberg (1998).
Preserved catalytic activity in an engineered ribonucleotide reductase R2 protein with a nonphysiological radical transfer pathway. The importance of hydrogen bond connections between the participating residues.
  J Biol Chem, 273, 21003-21008.  
9609702 M.Nissum, F.Neri, D.Mandelman, T.L.Poulos, and G.Smulevich (1998).
Spectroscopic characterization of recombinant pea cytosolic ascorbate peroxidase: similarities and differences with cytochrome c peroxidase.
  Biochemistry, 37, 8080-8087.  
9836578 S.K.Wilcox, C.D.Putnam, M.Sastry, J.Blankenship, W.J.Chazin, D.E.McRee, and D.B.Goodin (1998).
Rational design of a functional metalloenzyme: introduction of a site for manganese binding and oxidation into a heme peroxidase.
  Biochemistry, 37, 16853-16862.
PDB code: 1bva
8756714 G.Smulevich, F.Neri, M.P.Marzocchi, and K.G.Welinder (1996).
Versatility of heme coordination demonstrated in a fungal peroxidase. Absorption and resonance Raman studies of Coprinus cinereus peroxidase and the Asp245-->Asn mutant at various pH values.
  Biochemistry, 35, 10576-10585.  
8611540 I.E.Holzbaur, A.M.English, and A.A.Ismail (1996).
FTIR study of the thermal denaturation of horseradish and cytochrome c peroxidases in D2O.
  Biochemistry, 35, 5488-5494.  
8555215 J.Wang, R.W.Larsen, S.J.Moench, J.D.Satterlee, D.L.Rousseau, and M.R.Ondrias (1996).
Cytochrome c peroxidase complexed with cytochrome c has an unperturbed heme moiety.
  Biochemistry, 35, 453-463.  
8942678 K.Wang, H.Mei, L.Geren, M.A.Miller, A.Saunders, X.Wang, J.L.Waldner, G.J.Pielak, B.Durham, and F.Millett (1996).
Design of a ruthenium-cytochrome c derivative to measure electron transfer to the radical cation and oxyferryl heme in cytochrome c peroxidase.
  Biochemistry, 35, 15107-15119.  
8916924 N.C.Veitch, Y.Gao, and K.G.Welinder (1996).
The Asp245-->Asn mutant of Coprinus cinereus peroxidase. Characterization by 1H-NMR spectroscopy and comparison with the wild-type enzyme.
  Biochemistry, 35, 14370-14380.  
8942679 R.Sinclair, S.Hallam, M.Chen, B.Chance, and L.Powers (1996).
Active site structure in cytochrome c peroxidase and myoglobin mutants: effects of altered hydrogen bonding to the proximal histidine.
  Biochemistry, 35, 15120-15128.  
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
8847347 F.Millett, M.A.Miller, L.Geren, and B.Durham (1995).
Electron transfer between cytochrome c and cytochrome c peroxidase.
  J Bioenerg Biomembr, 27, 341-351.  
  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
7759477 M.Sahlin, G.Lassmann, S.Pötsch, B.M.Sjöberg, and A.Gräslund (1995).
Transient free radicals in iron/oxygen reconstitution of mutant protein R2 Y122F. Possible participants in electron transfer chains in ribonucleotide reductase.
  J Biol Chem, 270, 12361-12372.  
8076654 J.D.Satterlee, S.L.Alam, J.M.Mauro, J.E.Erman, and T.L.Poulos (1994).
The effect of the Asn82-->Asp mutation in yeast cytochrome c peroxidase studied by proton NMR spectroscopy.
  Eur J Biochem, 224, 81-87.  
7664080 M.A.Miller, A.Shaw, and J.Kraut (1994).
2.2 A structure of oxy-peroxidase as a model for the transient enzyme: peroxide complex.
  Nat Struct Biol, 1, 524-531.
PDB code: 1dcc
7972020 M.A.Miller, G.W.Han, and J.Kraut (1994).
A cation binding motif stabilizes the compound I radical of cytochrome c peroxidase.
  Proc Natl Acad Sci U S A, 91, 11118-11122.
PDB codes: 1cpd 1cpe 1cpf 1cpg
8502724 B.A.Barry (1993).
The role of redox-active amino acids in the photosynthetic water-oxidizing complex.
  Photochem Photobiol, 57, 179-188.  
1518925 D.Shortle (1992).
Mutational studies of protein structures and their stabilities.
  Q Rev Biophys, 25, 205-250.  
1633807 N.C.Veitch, R.J.Williams, R.C.Bray, J.F.Burke, S.A.Sanders, R.N.Thorneley, and A.T.Smith (1992).
Structural studies by proton-NMR spectroscopy of plant horseradish peroxidase C, the wild-type recombinant protein from Escherichia coli and two protein variants, Phe41----Val and Arg38----Lys.
  Eur J Biochem, 207, 521-531.  
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.