skip to main content
OSTI.GOV title logo U.S. Department of Energy
Office of Scientific and Technical Information

Title: Crystal structure of the pristine peroxidase ferryl center and its relevance to proton-coupled electron transfer

Journal Article · · Proceedings of the National Academy of Sciences of the United States of America
 [1];  [2];  [2];  [2];  [2];  [2];  [1];  [2];  [3]
  1. Department of Molecular Biology and Biochemistry, University of California, Irvine, CA 92697-3900,
  2. Macromolecular Crystallographic Group, The Stanford Synchrotron Radiation Lightsource, National Accelerator Laboratory, Stanford University, Stanford, CA 94309,
  3. Department of Molecular Biology and Biochemistry, University of California, Irvine, CA 92697-3900,, Department of Pharmaceutical Sciences, University of California, Irvine, CA 92697-3900,, Department of Chemistry, University of California, Irvine, CA 92697-3900

Significance A major problem in determining the crystal structures of metalloenzymes is that the reducing power of X-rays often changes the oxidation state of the metal center, thereby complicating important mechanistic conclusions on enzyme function. This reduction is especially problematic in studying Fe(IV)=O intermediates, which are powerful oxidants used by many metalloenzymes. This problem can be circumvented using the Stanford Linear Coherent Light Source (LCLS), which generates intense X-ray pulses on the femtosecond time scale and enables structure determinations with no reduction of metal centers. Here, we report the crystal structure of the Fe(IV)=O peroxidase intermediate called compound I using data obtained from the LCLS. We also present kinetic and computational results that, together with crystal structures, provide important mechanistic insights.

Sponsoring Organization:
USDOE
Grant/Contract Number:
AC02-76SF00515
OSTI ID:
1236656
Journal Information:
Proceedings of the National Academy of Sciences of the United States of America, Journal Name: Proceedings of the National Academy of Sciences of the United States of America Vol. 113 Journal Issue: 5; ISSN 0027-8424
Publisher:
Proceedings of the National Academy of SciencesCopyright Statement
Country of Publication:
United States
Language:
English
Citation Metrics:
Cited by: 53 works
Citation information provided by
Web of Science

References (43)

Goniometer-based femtosecond crystallography with X-ray free electron lasers journal October 2014
Design of a Ruthenium−Cytochrome c Derivative To Measure Electron Transfer to the Radical Cation and Oxyferryl Heme in Cytochrome c Peroxidase journal January 1996
The crystal structure of cytochrome c peroxidase. journal January 1980
Free energy of charges in solvated proteins: microscopic calculations using a reversible charging process journal December 1986
Overview of the CCP 4 suite and current developments journal March 2011
Radiation damage in protein serial femtosecond crystallography using an x-ray free-electron laser journal December 2011
Crystal structure of the Leishmania major peroxidase-cytochrome c complex journal October 2012
Engineering Ascorbate Peroxidase Activity into Cytochrome c Peroxidase journal September 2008
Heme Enzyme Structure and Function journal January 2014
Crystal Structure of Leishmania major Peroxidase and Characterization of the Compound I Tryptophan Radical journal May 2011
Activation of a vinculin-binding site in the talin rod involves rearrangement of a five-helix bundle journal July 2004
Neutron cryo-crystallography captures the protonation state of ferryl heme in a peroxidase journal July 2014
Enzymatic Mechanism of Leishmania major Peroxidase and the Critical Role of Specific Ionic Interactions journal May 2015
Leishmania major Peroxidase Is a Cytochrome c Peroxidase journal March 2012
Processing of X-ray snapshots from crystals in random orientations journal July 2014
The stereochemistry of peroxidase catalysis. journal September 1980
Application of Badger's Rule to Heme and Non-Heme Iron−Oxygen Bonds:  An Examination of Ferryl Protonation States journal February 2006
REFMAC 5 for the refinement of macromolecular crystal structures journal March 2011
On the Role of Water in Peroxidase Catalysis: A Theoretical Investigation of HRP Compound I Formation journal April 2010
A hypothetical model of the cytochrome c peroxidase . cytochrome c electron transfer complex. journal November 1980
Femtosecond X-ray protein nanocrystallography journal February 2011
Crystal structure of a complex between electron transfer partners, cytochrome c peroxidase and cytochrome c journal December 1992
Taking snapshots of photosynthetic water oxidation using femtosecond X-ray diffraction and spectroscopy journal July 2014
Constant pH molecular dynamics in generalized Born implicit solvent journal December 2004
On the status of ferryl protonation journal April 2006
An automated system to mount cryo-cooled protein crystals on a synchrotron beamline, using compact sample cassettes and a small-scale robot journal November 2002
Resonance Raman spectroscopy of oxoiron(IV) porphyrin π-cation radical and oxoiron(IV) hemes in peroxidase intermediates journal April 2006
Proximal ligand effects on electronic structure and spectra of compound I of peroxidases journal March 2001
Leishmania major encodes an unusual peroxidase that is a close homologue of plant ascorbate peroxidase: a novel role of the transmembrane domain journal August 2005
Effects of Concerted Hydrogen Bonding of Distal Histidine on Active Site Structures of Horseradish Peroxidase. Resonance Raman Studies with Asn70 Mutants journal February 1997
A Complete Mechanism for Steady-State Oxidation of Yeast Cytochrome c by Yeast Cytochrome c Peroxidase journal January 1996
Resonance Raman evidence for oxygen exchange between the FeIV = O heme and bulk water during enzymic catalysis of horseradish peroxidase and its relation with the heme-linked ionization. journal April 1986
Crystallographic and Single-Crystal Spectral Analysis of the Peroxidase Ferryl Intermediate journal April 2010
MOLREP an Automated Program for Molecular Replacement journal December 1997
The catalytic pathway of horseradish peroxidase at high resolution journal May 2002
Potential for biomolecular imaging with femtosecond X-ray pulses journal August 2000
XDS journal January 2010
Electrostatic calculations of the pKa values of ionizable groups in bacteriorhodopsin journal March 1992
Proton Linkage in Formation of the Cytochrome c-Cytochrome c Peroxidase Complex: Electrostatic Properties of the High- and Low-Affinity Cytochrome Binding Sites on the Peroxidase journal October 1994
Exploiting structure similarity in refinement: automated NCS and target-structure restraints in BUSTER journal March 2012
Constant pH Replica Exchange Molecular Dynamics in Explicit Solvent Using Discrete Protonation States: Implementation, Testing, and Validation journal February 2014
Self-terminating diffraction gates femtosecond X-ray nanocrystallography measurements journal December 2011
High-Resolution Crystal Structures and Spectroscopy of Native and Compound I Cytochrome c Peroxidase journal May 2003