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PDBsum entry 1cmq

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Oxidoreductase(h2o2(a)) PDB id
1cmq
Jmol
Contents
Protein chain
291 a.a. *
Ligands
HEM
Waters ×55
* Residue conservation analysis
PDB id:
1cmq
Name: Oxidoreductase(h2o2(a))
Title: Small molecule binding to an artificially created cavity at the active site of cytochromE C peroxidase
Structure: CytochromE C peroxidase. Chain: a. Engineered: yes
Source: Saccharomyces cerevisiae. Baker's yeast. Organism_taxid: 4932. Gene: potential
Resolution:
2.30Å     R-factor:   0.190    
Authors: M.M.Fitzgerald,D.E.Mcree,M.J.Churchill,D.B.Goodin
Key ref:
M.M.Fitzgerald et al. (1994). Small molecule binding to an artificially created cavity at the active site of cytochrome c peroxidase. Biochemistry, 33, 3807-3818. PubMed id: 8142383 DOI: 10.1021/bi00179a004
Date:
23-Nov-93     Release date:   31-Jan-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: 10.1021/bi00179a004 Biochemistry 33:3807-3818 (1994)
PubMed id: 8142383  
 
 
Small molecule binding to an artificially created cavity at the active site of cytochrome c peroxidase.
M.M.Fitzgerald, M.J.Churchill, D.E.McRee, D.B.Goodin.
 
  ABSTRACT  
 
In the oxidized "ES" state of cytochrome c peroxidase, Trp-191 is reversibly oxidized to a stable cation free radical by the hypervalent heme. To explore the potential for engineering a binding site for heterocyclic compounds at this site, the mutant W191G was constructed. Two independent crystal structures of W191G at 2.1- and 2.3-A resolution show that W191G contains a well-defined, approximately 180-A3 cavity at the Trp-191 site. The cavity is occupied by five ordered water molecules which participate in an extensive hydrogen-bonding network with each other, with polar main-chain atoms, and with the carboxylate of Asp-235. After a number of heterocyclic compounds were screened, evidence was obtained that substituted imidazoles bind to the cavity of W191G. Titration of W191G with imidazole resulted in a perturbation of the Soret absorption band that was not observed for W191H, W191F, or the native enzyme. The dissociation constants for binding of benzimidazole, imidazole, 2-ethylimidazole, 1-methylimidazole, 2-methylimidazole, and 1,2-dimethylimidazole to W191G were respectively 2.58, 0.70, 0.36, 0.057, 0.047, and 0.027 mM at pH 6.0. The highest binding affinity was exhibited by 1,2-dimethylimidazole, indicating that steric interactions and the efficiency of filling the cavity are important determinants for specificity. The Kd for imidazole binding increased from 0.7 mM at pH 6 to 3.0 mM at pH 8 and could be fit to a single proton ionization curve with a pKa of 7.4, demonstrating the preferential binding by the imidazolium ion (pKa = 7.3). The binding of a number of substituted imidazoles to the cavity of W191G was verified by X-ray crystallographic analysis. The most clearly defined density was observed for W191G crystals soaked in 1 mM 1,2-dimethylimidazole and was consistent with an oriented occupation in which the unsubstituted nitrogen forms a hydrogen bond or ion pair interaction with Asp-235. Thus, enhanced binding of positively charged molecules may be the result of interactions with this carboxylate. An analogous interaction may stabilize the developing positive charge on the Trp-191 radical of the wild-type enzyme. While the oxidation of imidazoles by the ferryl intermediate of W191G was neither expected nor observed, this study has defined the structural determinants for small molecule binding to an artificially created cavity near a heme center which is capable of generating oxidized species at a potential of over 1 V, and these results will guide future attempts for novel substrate oxidation by CCP.
 

Literature references that cite this PDB file's key reference

  PubMed id Reference
18831031 D.J.Huggins, M.D.Altman, and B.Tidor (2009).
Evaluation of an inverse molecular design algorithm in a model binding site.
  Proteins, 75, 168-186.  
18280498 A.P.Graves, D.M.Shivakumar, S.E.Boyce, M.P.Jacobson, D.A.Case, and B.K.Shoichet (2008).
Rescoring docking hit lists for model cavity sites: predictions and experimental testing.
  J Mol Biol, 377, 914-934.
PDB codes: 2ray 2raz 2rb0 2rb1 2rb2 2rbn 2rbo 2rbp 2rbq 2rbr 2rbs 2rbt 2rbu 2rbv 2rbw 2rbx 2rby 2rbz 2rc0 2rc1 2rc2
18196463 R.E.Amaro, R.Baron, and J.A.McCammon (2008).
An improved relaxed complex scheme for receptor flexibility in computer-aided drug design.
  J Comput Aided Mol Des, 22, 693-705.  
18821750 W.Deng, and C.L.Verlinde (2008).
Evaluation of different virtual screening programs for docking in a charged binding pocket.
  J Chem Inf Model, 48, 2010-2020.  
17334823 K.H.Kim (2007).
Outliers in SAR and QSAR: is unusual binding mode a possible source of outliers?
  J Comput Aided Mol Des, 21, 63-86.  
16490206 R.Brenk, S.W.Vetter, S.E.Boyce, D.B.Goodin, and B.K.Shoichet (2006).
Probing molecular docking in a charged model binding site.
  J Mol Biol, 357, 1449-1470.
PDB codes: 2anz 2aqd 2as1 2as2 2as3 2as4 2as6 2eun 2euo 2eup 2euq 2eur 2eus 2eut 2euu
15738411 B.M.Hoffman, L.M.Celis, D.A.Cull, A.D.Patel, J.L.Seifert, K.E.Wheeler, J.Wang, J.Yao, I.V.Kurnikov, and J.M.Nocek (2005).
Differential influence of dynamic processes on forward and reverse electron transfer across a protein-protein interface.
  Proc Natl Acad Sci U S A, 102, 3564-3569.  
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.  
11900539 H.Mei, L.Geren, M.A.Miller, B.Durham, and F.Millett (2002).
Role of the low-affinity binding site in electron transfer from cytochrome C to cytochrome C peroxidase.
  Biochemistry, 41, 3968-3976.  
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
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
10813812 D.Barrick (2000).
Trans-substitution of the proximal hydrogen bond in myoglobin: II. Energetics, functional consequences, and implications for hemoglobin allostery.
  Proteins, 39, 291-308.  
10722697 J.Hirst, and D.B.Goodin (2000).
Unusual oxidative chemistry of N(omega)-hydroxyarginine and N-hydroxyguanidine catalyzed at an engineered cavity in a heme peroxidase.
  J Biol Chem, 275, 8582-8591.
PDB codes: 1dj1 1dj5
10608846 C.A.Bonagura, B.Bhaskar, M.Sundaramoorthy, and T.L.Poulos (1999).
Conversion of an engineered potassium-binding site into a calcium-selective site in cytochrome c peroxidase.
  J Biol Chem, 274, 37827-37833.
PDB code: 1krj
10220341 C.A.Bonagura, M.Sundaramoorthy, B.Bhaskar, and T.L.Poulos (1999).
The effects of an engineered cation site on the structure, activity, and EPR properties of cytochrome c peroxidase.
  Biochemistry, 38, 5538-5545.
PDB code: 1jdr
10346906 H.Mei, K.Wang, N.Peffer, G.Weatherly, D.S.Cohen, M.Miller, G.Pielak, B.Durham, and F.Millett (1999).
Role of configurational gating in intracomplex electron transfer from cytochrome c to the radical cation in cytochrome c peroxidase.
  Biochemistry, 38, 6846-6854.  
9915834 Y.Bourne, P.Taylor, P.E.Bougis, and P.Marchot (1999).
Crystal structure of mouse acetylcholinesterase. A peripheral site-occluding loop in a tetrameric assembly.
  J Biol Chem, 274, 2963-2970.
PDB code: 1maa
9814755 A.Peracchi, J.Matulic-Adamic, S.Wang, L.Beigelman, and D.Herschlag (1998).
Structure-function relationships in the hammerhead ribozyme probed by base rescue.
  RNA, 4, 1332-1346.  
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
  9514261 Y.Cao, R.A.Musah, S.K.Wilcox, D.B.Goodin, and D.E.McRee (1998).
Protein conformer selection by ligand binding observed with crystallography.
  Protein Sci, 7, 72-78.
PDB code: 1ccj
9100022 K.Kishi, D.P.Hildebrand, M.Kusters-van Someren, J.Gettemy, A.G.Mauk, and M.H.Gold (1997).
Site-directed mutations at phenylalanine-190 of manganese peroxidase: effects on stability, function, and coordination.
  Biochemistry, 36, 4268-4277.  
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
9405625 S.Kim, J.Liang, and B.A.Barry (1997).
Chemical complementation identifies a proton acceptor for redox-active tyrosine D in photosystem II.
  Proc Natl Acad Sci U S A, 94, 14406-14411.  
8634253 C.A.Bonagura, M.Sundaramoorthy, H.S.Pappa, W.R.Patterson, and T.L.Poulos (1996).
An engineered cation site in cytochrome c peroxidase alters the reactivity of the redox active tryptophan.
  Biochemistry, 35, 6107-6115.  
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.  
8961943 H.Mei, K.Wang, S.McKee, X.Wang, J.L.Waldner, G.J.Pielak, B.Durham, and F.Millett (1996).
Control of formation and dissociation of the high-affinity complex between cytochrome c and cytochrome c peroxidase by ionic strength and the low-affinity binding site.
  Biochemistry, 35, 15800-15806.  
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.  
8673607 M.M.Fitzgerald, R.A.Musah, D.E.McRee, and D.B.Goodin (1996).
A ligand-gated, hinged loop rearrangement opens a channel to a buried artificial protein cavity.
  Nat Struct Biol, 3, 626-631.
PDB codes: 1aa4 1ac4 1ac8 1aes 1aet 1aeu 1cci 1ryc
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
8634279 V.Helms, E.Deprez, E.Gill, C.Barret, G.Hui Bon Hoa, and R.C.Wade (1996).
Improved binding of cytochrome P450cam substrate analogues designed to fill extra space in the substrate binding pocket.
  Biochemistry, 35, 1485-1499.  
7579651 D.Barrick (1995).
Depletion and replacement of protein metal ligands.
  Curr Opin Biotechnol, 6, 411-418.  
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
7765803 P.Holliger, and H.R.Hoogenboom (1995).
Artificial antibodies and enzymes: mimicking nature and beyond.
  Trends Biotechnol, 13, 7-9.  
7579646 S.J.Hubbard, and P.Argos (1995).
Evidence on close packing and cavities in proteins.
  Curr Opin Biotechnol, 6, 375-381.  
8519982 V.Helms, and R.C.Wade (1995).
Thermodynamics of water mediating protein-ligand interactions in cytochrome P450cam: a molecular dynamics study.
  Biophys J, 69, 810-824.  
7629167 V.P.Miller, D.B.Goodin, A.E.Friedman, C.Hartmann, and P.R.Ortiz de Montellano (1995).
Horseradish peroxidase Phe172-->Tyr mutant. Sequential formation of compound I with a porphyrin radical cation and a protein radical.
  J Biol Chem, 270, 18413-18419.  
7809133 D.E.McRee, G.M.Jensen, M.M.Fitzgerald, H.A.Siegel, and D.B.Goodin (1994).
Construction of a bisaquo heme enzyme and binding by exogenous ligands.
  Proc Natl Acad Sci U S A, 91, 12847-12851.
PDB codes: 1cce 1ccg
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
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.