Literature DB >> 8528082

The role of aspartate-235 in the binding of cations to an artificial cavity at the radical site of cytochrome c peroxidase.

M M Fitzgerald1, M L Trester, G M Jensen, D E McRee, D B Goodin.   

Abstract

The activated state of cytochrome c peroxidase, compound ES, contains a cation radical on the Trp-191 side chain. We recently reported that replacing this tryptophan with glycine creates a buried cavity at the active site that contains ordered solvent and that will specifically bind substituted imidazoles in their protonated cationic forms (Fitzgerald MM, Churchill MJ, McRee DE, Goodin DB, 1994, Biochemistry 33:3807-3818). Proposals that a nearby carboxylate, Asp-235, and competing monovalent cations should modulate the affinity of the W191G cavity for ligand binding are addressed in this study. Competitive binding titrations of the imidazolium ion to W191G as a function of [K+] show that potassium competes weakly with the binding of imidazoles. The dissociation constant observed for potassium binding (18 mM) is more than 3,000-fold higher than that for 1,2-dimethylimidazole (5.5 microM) in the absence of competing cations. Significantly, the W191G-D235N double mutant shows no evidence for binding imidazoles in their cationic or neutral forms, even though the structure of the cavity remains largely unperturbed by replacement of the carboxylate. Refined crystallographic B-values of solvent positions indicate that the weakly bound potassium in W191G is significantly depopulated in the double mutant. These results demonstrate that the buried negative charge of Asp-235 is an essential feature of the cation binding determinant and indicate that this carboxylate plays a critical role in stabilizing the formation of the Trp-191 radical cation.

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Year:  1995        PMID: 8528082      PMCID: PMC2143207          DOI: 10.1002/pro.5560040919

Source DB:  PubMed          Journal:  Protein Sci        ISSN: 0961-8368            Impact factor:   6.725


  13 in total

Review 1.  Probing protein structure and dynamics with resonance Raman spectroscopy: cytochrome c peroxidase and hemoglobin.

Authors:  T G Spiro; G Smulevich; C Su
Journal:  Biochemistry       Date:  1990-05-15       Impact factor: 3.162

2.  Identification by ENDOR of Trp191 as the free-radical site in cytochrome c peroxidase compound ES.

Authors:  M Sivaraja; D B Goodin; M Smith; B M Hoffman
Journal:  Science       Date:  1989-08-18       Impact factor: 47.728

3.  Comprehensive explanation of the anomalous EPR spectra of wild-type and mutant cytochrome c peroxidase compound ES.

Authors:  A L Houseman; P E Doan; D B Goodin; B M Hoffman
Journal:  Biochemistry       Date:  1993-04-27       Impact factor: 3.162

4.  Comparative proton NMR analysis of wild-type cytochrome c peroxidase from yeast, the recombinant enzyme from Escherichia coli, and an Asp-235----Asn-235 mutant.

Authors:  J D Satterlee; J E Erman; J M Mauro; J Kraut
Journal:  Biochemistry       Date:  1990-09-18       Impact factor: 3.162

5.  X-ray structures of recombinant yeast cytochrome c peroxidase and three heme-cleft mutants prepared by site-directed mutagenesis.

Authors:  J M Wang; M Mauro; S L Edwards; S J Oatley; L A Fishel; V A Ashford; N H Xuong; J Kraut
Journal:  Biochemistry       Date:  1990-08-07       Impact factor: 3.162

6.  Identification of a porphyrin pi cation radical in ascorbate peroxidase compound I.

Authors:  W R Patterson; T L Poulos; D B Goodin
Journal:  Biochemistry       Date:  1995-04-04       Impact factor: 3.162

7.  Compound I radical in site-directed mutants of cytochrome c peroxidase as probed by electron paramagnetic resonance and electron-nuclear double resonance.

Authors:  L A Fishel; M F Farnum; J M Mauro; M A Miller; J Kraut; Y J Liu; X L Tan; C P Scholes
Journal:  Biochemistry       Date:  1991-02-19       Impact factor: 3.162

8.  A cation binding motif stabilizes the compound I radical of cytochrome c peroxidase.

Authors:  M A Miller; G W Han; J Kraut
Journal:  Proc Natl Acad Sci U S A       Date:  1994-11-08       Impact factor: 11.205

9.  Crystal structure of yeast cytochrome c peroxidase refined at 1.7-A resolution.

Authors:  B C Finzel; T L Poulos; J Kraut
Journal:  J Biol Chem       Date:  1984-11-10       Impact factor: 5.157

10.  The Asp-His-Fe triad of cytochrome c peroxidase controls the reduction potential, electronic structure, and coupling of the tryptophan free radical to the heme.

Authors:  D B Goodin; D E McRee
Journal:  Biochemistry       Date:  1993-04-06       Impact factor: 3.162

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  10 in total

1.  Excision of a proposed electron transfer pathway in cytochrome c peroxidase and its replacement by a ligand-binding channel.

Authors:  Robin J Rosenfeld; Anna-Maria A Hays; Rabi A Musah; David B Goodin
Journal:  Protein Sci       Date:  2002-05       Impact factor: 6.725

2.  Trapping of peptide-based surrogates in an artificially created channel of cytochrome c peroxidase.

Authors:  Anna-Maria A Hays; Harry B Gray; David B Goodin
Journal:  Protein Sci       Date:  2003-02       Impact factor: 6.725

Review 3.  Thirty years of heme peroxidase structural biology.

Authors:  Thomas L Poulos
Journal:  Arch Biochem Biophys       Date:  2010-03-03       Impact factor: 4.013

4.  Replacement of an electron transfer pathway in cytochrome c peroxidase with a surrogate peptide.

Authors:  Anna-Maria A Hays Putnam; Young-Tae Lee; David B Goodin
Journal:  Biochemistry       Date:  2009-01-13       Impact factor: 3.162

5.  Impact of Proximal and Distal Pocket Site-Directed Mutations on the Ferric/Ferrous Heme Redox Potential of Yeast Cytochrome-c-Peroxidase.

Authors:  G M Jensen; D B Goodin
Journal:  Theor Chem Acc       Date:  2011-12       Impact factor: 1.702

6.  Automated docking of ligands to an artificial active site: augmenting crystallographic analysis with computer modeling.

Authors:  Robin J Rosenfeld; David S Goodsell; Rabi A Musah; Garrett M Morris; David B Goodin; Arthur J Olson
Journal:  J Comput Aided Mol Des       Date:  2003-08       Impact factor: 3.686

7.  Predictive power of molecular dynamics receptor structures in virtual screening.

Authors:  Sara E Nichols; Riccardo Baron; Anthony Ivetac; J Andrew McCammon
Journal:  J Chem Inf Model       Date:  2011-05-12       Impact factor: 4.956

8.  Roles for ordered and bulk solvent in ligand recognition and docking in two related cavities.

Authors:  Sarah Barelier; Sarah E Boyce; Inbar Fish; Marcus Fischer; David B Goodin; Brian K Shoichet
Journal:  PLoS One       Date:  2013-07-18       Impact factor: 3.240

9.  An improved relaxed complex scheme for receptor flexibility in computer-aided drug design.

Authors:  Rommie E Amaro; Riccardo Baron; J Andrew McCammon
Journal:  J Comput Aided Mol Des       Date:  2008-01-15       Impact factor: 3.686

10.  Computational analysis of the tryptophan cation radical energetics in peroxidase Compound I.

Authors:  Thomas L Poulos; Jenny S Kim; Vidhi C Murarka
Journal:  J Biol Inorg Chem       Date:  2022-01-21       Impact factor: 3.358

  10 in total

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