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Abeyawardhane DL, Fernández RD, Heitger DR, Crozier MK, Wolver JC, Lucas HR. Copper Induced Radical Dimerization of α-Synuclein Requires Histidine. J Am Chem Soc 2018; 140:17086-17094. [DOI: 10.1021/jacs.8b08947] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Affiliation(s)
| | - Ricardo D. Fernández
- Department of Chemistry, Virginia Commonwealth University, Richmond, Virginia 23284, United States
| | - Denver R. Heitger
- Department of Chemistry, Virginia Commonwealth University, Richmond, Virginia 23284, United States
| | - Madeleine K. Crozier
- Department of Chemistry, Virginia Commonwealth University, Richmond, Virginia 23284, United States
| | - Julia C. Wolver
- Department of Chemistry, Virginia Commonwealth University, Richmond, Virginia 23284, United States
| | - Heather R. Lucas
- Department of Chemistry, Virginia Commonwealth University, Richmond, Virginia 23284, United States
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2
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Rudolph J, Erbse AH, Behlen LS, Copley SD. A radical intermediate in the conversion of pentachlorophenol to tetrachlorohydroquinone by Sphingobium chlorophenolicum. Biochemistry 2014; 53:6539-49. [PMID: 25238136 PMCID: PMC4204890 DOI: 10.1021/bi5010427] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
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Pentachlorophenol
(PCP) hydroxylase, the first enzyme in the pathway
for degradation of PCP in Sphingobium chlorophenolicum, is an unusually slow flavin-dependent monooxygenase (kcat = 0.02 s–1) that converts PCP to
a highly reactive product, tetrachlorobenzoquinone (TCBQ). Using stopped-flow
spectroscopy, we have shown that the steps up to and including formation
of TCBQ are rapid (5–30 s–1). Before products
can be released from the active site, the strongly oxidizing TCBQ
abstracts an electron from a donor at the active site, possibly a
cysteine residue, resulting in an off-pathway diradical state that
only slowly reverts to an intermediate capable of completing the catalytic
cycle. TCBQ reductase, the second enzyme in the PCP degradation pathway,
rescues this nonproductive complex via two fast sequential one-electron
transfers. These studies demonstrate how adoption of an ancestral
catalytic strategy for conversion of a substrate with different steric
and electronic properties can lead to subtle yet (literally) radical
changes in enzymatic reaction mechanisms.
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Affiliation(s)
- Johannes Rudolph
- Department of Molecular, Cellular and Developmental Biology and the Cooperative Institute for Research in Environmental Sciences, and ‡Department of Chemistry and Biochemistry, University of Colorado Boulder , Boulder, Colorado 80309, United States
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De Luna P, Bushnell EAC, Gauld JW. A Molecular Dynamics Examination on Mutation-Induced Catalase Activity in Coral Allene Oxide Synthase. J Phys Chem B 2013; 117:14635-41. [DOI: 10.1021/jp408486n] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Phil De Luna
- Department
of Chemistry and
Biochemistry, University of Windsor, Windsor, Ontario N9B 3P4, Canada
| | - Eric A. C. Bushnell
- Department
of Chemistry and
Biochemistry, University of Windsor, Windsor, Ontario N9B 3P4, Canada
| | - James W. Gauld
- Department
of Chemistry and
Biochemistry, University of Windsor, Windsor, Ontario N9B 3P4, Canada
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Promponas VJ, Ouzounis CA, Iliopoulos I. Experimental evidence validating the computational inference of functional associations from gene fusion events: a critical survey. Brief Bioinform 2012; 15:443-54. [PMID: 23220349 PMCID: PMC4017328 DOI: 10.1093/bib/bbs072] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
More than a decade ago, a number of methods were proposed for the inference of protein interactions, using whole-genome information from gene clusters, gene fusions and phylogenetic profiles. This structural and evolutionary view of entire genomes has provided a valuable approach for the functional characterization of proteins, especially those without sequence similarity to proteins of known function. Furthermore, this view has raised the real possibility to detect functional associations of genes and their corresponding proteins for any entire genome sequence. Yet, despite these exciting developments, there have been relatively few cases of real use of these methods outside the computational biology field, as reflected from citation analysis. These methods have the potential to be used in high-throughput experimental settings in functional genomics and proteomics to validate results with very high accuracy and good coverage. In this critical survey, we provide a comprehensive overview of 30 most prominent examples of single pairwise protein interaction cases in small-scale studies, where protein interactions have either been detected by gene fusion or yielded additional, corroborating evidence from biochemical observations. Our conclusion is that with the derivation of a validated gold-standard corpus and better data integration with big experiments, gene fusion detection can truly become a valuable tool for large-scale experimental biology.
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Affiliation(s)
- Vasilis J Promponas
- Institute of Agrobiotechnology, Centre for Research & Technology Hellas (CERTH), 57001 Thessaloniki, Greece.
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Coordination modes of tyrosinate-ligated catalase-type heme enzymes: magnetic circular dichroism studies of Plexaura homomalla allene oxide synthase, Mycobacterium avium ssp. paratuberculosis protein-2744c, and bovine liver catalase in their ferric and ferrous states. J Inorg Biochem 2011; 105:1786-94. [PMID: 22104301 DOI: 10.1016/j.jinorgbio.2011.09.026] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2011] [Revised: 09/15/2011] [Accepted: 09/15/2011] [Indexed: 11/20/2022]
Abstract
Bovine liver catalase (BLC), catalase-related allene oxide synthase (cAOS) from Plexaura homomalla, and a recently isolated protein from the cattle pathogen Mycobacterium avium ssp. paratuberculosis (MAP-2744c (MAP)) are all tyrosinate-ligated heme enzymes whose crystal structures have been reported. cAOS and MAP have low (<20%) sequence similarity to, and significantly different catalytic functions from, BLC. cAOS transforms 8R-hydroperoxy-eicosatetraenoic acid to an allene epoxide, whereas the MAP protein is a putative organic peroxide-dependent peroxidase. To elucidate factors influencing the functions of these and related heme proteins, we have investigated the heme iron coordination properties of these tyrosinate-ligated heme enzymes in their ferric and ferrous states using magnetic circular dichroism and UV-visible absorption spectroscopy. The MAP protein shows remarkable spectral similarities to cAOS and BLC in its native Fe(III) state, but clear differences from ferric proximal heme ligand His93Tyr Mb (myoglobin) mutant, which may be attributed to the presence of an Arg(+)-N(ω)-H···¯O-Tyr (proximal heme axial ligand) hydrogen bond in the first three heme proteins. Furthermore, the spectra of Fe(III)-CN¯, Fe(III)-NO, Fe(II)-NO (except for five-coordinate MAP), Fe(II)-CO, and Fe(II)-O(2) states of cAOS and MAP, but not H93Y Mb, are also similar to the corresponding six-coordinate complexes of BLC, suggesting that a tyrosinate (Tyr-O¯) is the heme axial ligand trans to the bound ligands in these complexes. The Arg(+)-N(ω)-H to ¯O-Tyr hydrogen bond would be expected to modulate the donor properties of the proximal tyrosinate oxyanion and, combined with the subtle differences in the catalytic site structures, affect the activities of cAOS, MAP and BLC.
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Dey M, Li X, Kunz RC, Ragsdale SW. Detection of Organometallic and Radical Intermediates in the Catalytic Mechanism of Methyl-Coenzyme M Reductase Using the Natural Substrate Methyl-Coenzyme M and a Coenzyme B Substrate Analogue. Biochemistry 2010; 49:10902-11. [DOI: 10.1021/bi101562m] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Mishtu Dey
- Department of Biological Chemistry, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Xianghui Li
- Department of Biological Chemistry, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Ryan C. Kunz
- Department of Biological Chemistry, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Stephen W. Ragsdale
- Department of Biological Chemistry, University of Michigan, Ann Arbor, Michigan 48109, United States
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Wu F, Gaffney BJ. Dynamic behavior of fatty acid spin labels within a binding site of soybean lipoxygenase-1. Biochemistry 2006; 45:12510-8. [PMID: 17029406 PMCID: PMC2515559 DOI: 10.1021/bi061415l] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
The putative substrate-binding site in lipoxygenases is long and internal. There is little direct evidence about how the unsaturated fatty acid substrates enter and move within the cavity to position themselves correctly for electron transfer reactions with the catalytic non-heme iron. An EPR spectroscopy approach, with spin-labeled fatty acids, is taken here to investigate dynamic behavior of fatty acids bound to soybean lipoxygenase-1. The probes are labeled on C5, C8, C10, C12, and C16 of stearic acid. The EPR-determined affinity for the enzyme increases as the length of the alkyl end of the probe increases, with a DeltaDeltaG of -190 cal/methylene. The probes in the series exhibit similar enhanced paramagnetic relaxation by the iron center. These results indicate that the members of the series have a common binding site. All of the bound probes undergo considerable local mobility. The stearate spin-labeled at C5 has the highest affinity for the lipoxygenase, and it is a competitive inhibitor, with a K(i) of 9 muM. Surprisingly, this stearate labeled near the carboxyl end undergoes more local motion than those labeled in the middle of the chain, when it is bound. This shows that the carboxyl end of the fatty-acid spin label is not rigidly docked on the protein. During catalysis, repositioning of the substrate carboxyl on the protein surface may be coupled to motion of portions of the chain undergoing reaction.
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Affiliation(s)
- Fayi Wu
- Department of Biological Sciences, BIO Unit I, Florida State University, Tallahassee, FL 32306-4370.
| | - Betty J. Gaffney
- Department of Biological Sciences, BIO Unit I, Florida State University, Tallahassee, FL 32306-4370.
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Tosha T, Uchida T, Brash AR, Kitagawa T. On the Relationship of Coral Allene Oxide Synthase to Catalase. J Biol Chem 2006; 281:12610-7. [PMID: 16513636 DOI: 10.1074/jbc.m600061200] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
A heme domain of coral allene oxide synthase (cAOS) catalyzes the formation of allene oxide from fatty acid hydroperoxide. Although cAOS has a similar heme active site to that of catalase, cAOS is completely lacking in catalase activity. A close look at the hydrogen-bonding possibilities around the distal His in cAOS suggested that the imidazole ring is rotated by 180 degrees relative to that of catalase because of the hydrogen bond between Thr-66 and the distal His-67. This could contribute to the functional differences between cAOS and catalase, and to examine this possibility, we mutated Thr-66 in cAOS to Val, the corresponding residue in catalase. In contrast to the complete absence of catalase activity in wild type (WT) cAOS, T66V had a modest catalase activity. On the other hand, the mutation suppressed the native enzymatic activity of the formation of allene oxide to 14% of that of WT cAOS. In the resonance Raman spectrum, whereas WT cAOS has only a 6-coordinate/high spin heme, T66V has a 5-coordinate/high spin heme as a minor species. Because catalase adopts a 5-coordinate/high spin structure, probably the 5-coordinate/high spin portion of T66V showed the catalase activity. Furthermore, in accord with the fact that the CN affinity of catalase is higher than that of WT cAOS, the CN affinity of T66V was 8-fold higher than that of WT cAOS, indicating that the mutation could mimic the heme active site in catalase. We, therefore, propose that the hydrogen bond between Thr-66 and distal His-67 could modulate the orientation of distal His, thereby regulating the enzymatic activity in cAOS.
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Affiliation(s)
- Takehiko Tosha
- Okazaki Institute for Integrative Bioscience, National Institutes of Natural Sciences, Okazaki 444-8787, Japan
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Oldham ML, Brash AR, Newcomer ME. The structure of coral allene oxide synthase reveals a catalase adapted for metabolism of a fatty acid hydroperoxide. Proc Natl Acad Sci U S A 2004; 102:297-302. [PMID: 15625113 PMCID: PMC544295 DOI: 10.1073/pnas.0406352102] [Citation(s) in RCA: 65] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
8R-Lipoxygenase and allene oxide synthase (AOS) are parts of a naturally occurring fusion protein from the coral Plexaura homomalla. AOS catalyses the production of an unstable epoxide (an allene oxide) from the fatty acid hydroperoxide generated by the lipoxygenase activity. Here, we report the structure of the AOS domain and its striking structural homology to catalase. Whereas nominal sequence identity between the enzymes had been previously described, the extent of structural homology observed was not anticipated, given that this enzyme activity had been exclusively associated with the P450 superfamily, and conservation of a catalase fold without catalase activity is unprecedented. Whereas the heme environment is largely conserved, the AOS heme is planar and the distal histidine is flanked by two hydrogen-bonding residues. These critical differences likely facilitate the switch from a catalatic activity to that of a fatty acid hydroperoxidase.
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Affiliation(s)
- Michael L Oldham
- Department of Biological Sciences, Louisiana State University, Baton Rouge, LA 70803, USA
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