1
|
Mechanism for the synthesis of medium-chain 1-alkenes from fatty acids catalyzed by binuclear iron UndA decarboxylase. J Catal 2023. [DOI: 10.1016/j.jcat.2023.02.021] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/05/2023]
|
2
|
Du WGH, Götz AW, Noodleman L. Mössbauer Property Calculations on Fea33+∙∙∙H2O∙∙∙CuB2+ Dinuclear Center Models of the Resting Oxidized as-Isolated Cytochrome c Oxidase. Chemphyschem 2022; 23:e202100831. [PMID: 35142420 PMCID: PMC9054037 DOI: 10.1002/cphc.202100831] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2021] [Revised: 02/03/2022] [Indexed: 11/24/2022]
Abstract
Mössbauer isomer shift and quadrupole splitting properties have been calculated using the OLYP‐D3(BJ) density functional method on previously obtained (W.‐G. Han Du, et al., Inorg Chem. 2020, 59, 8906–8915) geometry optimized Fea33+−H2O−CuB2+ dinuclear center (DNC) clusters of the resting oxidized (O state) “as‐isolated” cytochrome c oxidase (CcO). The calculated results are highly consistent with the available experimental observations. The calculations have also shown that the structural heterogeneities of the O state DNCs implicated by the Mössbauer experiments are likely consequences of various factors, particularly the variable positions of the central H2O molecule between the Fea33+ and CuB2+ sites in different DNCs, whether or not this central H2O molecule has H‐bonding interaction with another H2O molecule, the different spin states having similar energies for the Fea33+ sites, and whether the Fea33+ and CuB2+ sites are ferromagnetically or antiferromagnetically spin‐coupled.
Collapse
Affiliation(s)
- Wen-Ge Han Du
- The Scripps Research Institute, Integrative Structural and Computational Biology, UNITED STATES
| | | | - Louis Noodleman
- The Scripps Research Institute, Department of Integrative Structural and Computational Biology, Hz112, 10550 North Torrey Pines Road, 92037, La Jolla, UNITED STATES
| |
Collapse
|
3
|
Wu J, Chen SL. Key Piece in the Wolfe Cycle of Methanogenesis: The S–S Bond Dissociation Conducted by Noncubane [Fe4S4] Cluster-Dependent Heterodisulfide Reductase. ACS Catal 2022. [DOI: 10.1021/acscatal.1c06036] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Jue Wu
- Key Laboratory of Cluster Science of Ministry of Education, School of Chemistry and Chemical Engineering, Beijing Institute of Technology, Beijing 100081, China
| | - Shi-Lu Chen
- Key Laboratory of Cluster Science of Ministry of Education, School of Chemistry and Chemical Engineering, Beijing Institute of Technology, Beijing 100081, China
| |
Collapse
|
4
|
Theoretical Studies of Acetyl-CoA Synthase Catalytic Mechanism. Catalysts 2022. [DOI: 10.3390/catal12020195] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/10/2022] Open
Abstract
DFT calculations were performed for the A-cluster from the enzyme Acetyl-CoA synthase (ACS). The acid constants (pKa), reduction potentials, and pH-dependent reduction potential for the A-cluster with different oxidation states and ligands were calculated. Good agreement of the reduction potentials, dependent on pH in the experiment, was obtained. On the basis of the calculations, a mechanism for the methylation reaction involving two–electron reduction and protonation on the proximal nickel atom of the reduced A-cluster is proposed.
Collapse
|
5
|
Yu MJ, Chen SL. From Alkane to Alkene: The Inert Aliphatic C–H Bond Activation Presented by Binuclear Iron Stearoyl-CoA Desaturase with a Long di-Fe Distance of 6 Å. ACS Catal 2019. [DOI: 10.1021/acscatal.9b00456] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Affiliation(s)
- Ming-Jia Yu
- Key Laboratory of Cluster Science of Ministry of Education, School of Chemistry and Chemical Engineering, Beijing Institute of Technology, Beijing 100081, People’s Republic of China
| | - Shi-Lu Chen
- Key Laboratory of Cluster Science of Ministry of Education, School of Chemistry and Chemical Engineering, Beijing Institute of Technology, Beijing 100081, People’s Republic of China
| |
Collapse
|
6
|
Martinie RJ, Blaesi EJ, Bollinger JM, Krebs C, Finkelstein KD, Pollock CJ. Two-Color Valence-to-Core X-ray Emission Spectroscopy Tracks Cofactor Protonation State in a Class I Ribonucleotide Reductase. Angew Chem Int Ed Engl 2018; 57:12754-12758. [PMID: 30075052 PMCID: PMC6579043 DOI: 10.1002/anie.201807366] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2018] [Revised: 07/20/2018] [Indexed: 12/20/2022]
Abstract
Proton transfer reactions are of central importance to a wide variety of biochemical processes, though determining proton location and monitoring proton transfers in biological systems is often extremely challenging. Herein, we use two-color valence-to-core X-ray emission spectroscopy (VtC XES) to identify protonation events across three oxidation states of the O2 -activating, radical-initiating manganese-iron heterodinuclear cofactor in a class I-c ribonucleotide reductase. This is the first application of VtC XES to an enzyme intermediate and the first simultaneous measurement of two-color VtC spectra. In contrast to more conventional methods of assessing protonation state, VtC XES is a more direct probe applicable to a wide range of metalloenzyme systems. These data, coupled to insight provided by DFT calculations, allow the inorganic cores of the MnIV FeIV and MnIV FeIII states of the enzyme to be assigned as MnIV (μ-O)2 FeIV and MnIV (μ-O)(μ-OH)FeIII , respectively.
Collapse
Affiliation(s)
- Ryan J Martinie
- Department of Chemistry, The Pennsylvania State University, 318 Chemistry Building, University Park, PA, 16802, USA
| | - Elizabeth J Blaesi
- Department of Chemistry, The Pennsylvania State University, 318 Chemistry Building, University Park, PA, 16802, USA
| | - J Martin Bollinger
- Department of Chemistry and Department of Biochemistry and Molecular Biology, The Pennsylvania State University, 318 Chemistry Building, University Park, PA, 16802, USA
| | - Carsten Krebs
- Department of Chemistry and Department of Biochemistry and Molecular Biology, The Pennsylvania State University, 318 Chemistry Building, University Park, PA, 16802, USA
| | - Kenneth D Finkelstein
- Cornell High Energy Synchrotron Source, Wilson Laboratory, Cornell University, Ithaca, NY, 14853, USA
| | - Christopher J Pollock
- Department of Chemistry, The Pennsylvania State University, 318 Chemistry Building, University Park, PA, 16802, USA
- Present address: Cornell High Energy Synchrotron Source, Wilson Laboratory, Cornell University, Ithaca, NY, 14853, USA
| |
Collapse
|
7
|
Martinie RJ, Blaesi EJ, Bollinger JM, Krebs C, Finkelstein KD, Pollock CJ. Two‐Color Valence‐to‐Core X‐ray Emission Spectroscopy Tracks Cofactor Protonation State in a Class I Ribonucleotide Reductase. Angew Chem Int Ed Engl 2018. [DOI: 10.1002/ange.201807366] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Ryan J. Martinie
- Department of Chemistry The Pennsylvania State University 318 Chemistry Building University Park PA 16802 USA
| | - Elizabeth J. Blaesi
- Department of Chemistry The Pennsylvania State University 318 Chemistry Building University Park PA 16802 USA
| | - J. Martin Bollinger
- Department of Chemistry and Department of Biochemistry and Molecular Biology The Pennsylvania State University 318 Chemistry Building University Park PA 16802 USA
| | - Carsten Krebs
- Department of Chemistry and Department of Biochemistry and Molecular Biology The Pennsylvania State University 318 Chemistry Building University Park PA 16802 USA
| | - Kenneth D. Finkelstein
- Cornell High Energy Synchrotron Source, Wilson Laboratory Cornell University Ithaca NY 14853 USA
| | - Christopher J. Pollock
- Department of Chemistry The Pennsylvania State University 318 Chemistry Building University Park PA 16802 USA
- Present address: Cornell High Energy Synchrotron Source Wilson Laboratory Cornell University Ithaca NY 14853 USA
| |
Collapse
|
8
|
Ree N, Andersen CL, Kilde MD, Hammerich O, Nielsen MB, Mikkelsen KV. The quest for determining one-electron redox potentials of azulene-1-carbonitriles by calculation. Phys Chem Chem Phys 2018; 20:7438-7446. [PMID: 29484319 DOI: 10.1039/c7cp08687c] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
Electrochemical processes drive many chemical and biochemical reactions. Theoretical methods to accurately predict redox potentials are therefore crucial for understanding these reactions and designing new chemical species with desired properties. We have investigated a theoretical methodology using electronic structure methods based on density functional theory and continuum solvation models. These methods have been validated with linear correlation plots comparing theoretical and experimental results for the redox properties of a series of azulene derivatives. The results showed excellent correlations despite only minor structural variations of the azulenes, which support this rather simple theoretical methodology for determining redox potentials of organic molecules. Furthermore, we have estimated the absolute redox potential of the ferrocene/ferrocenium redox couple to be 4.8 ± 0.1 V in dichloromethane, which is slightly lower than previous estimates.
Collapse
Affiliation(s)
- Nicolai Ree
- Department of Chemistry, University of Copenhagen, Universitetsparken 5, 2100 Copenhagen Ø, Denmark.
| | | | | | | | | | | |
Collapse
|
9
|
Ryzhkova EP. Alternative enzymes as a special strategy for the adaptation of procaryotic organisms (Review). APPL BIOCHEM MICRO+ 2017. [DOI: 10.1134/s0003683817050131] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
|
10
|
Martinie RJ, Blaesi EJ, Krebs C, Bollinger JM, Silakov A, Pollock CJ. Evidence for a Di-μ-oxo Diamond Core in the Mn(IV)/Fe(IV) Activation Intermediate of Ribonucleotide Reductase from Chlamydia trachomatis. J Am Chem Soc 2017; 139:1950-1957. [PMID: 28075562 DOI: 10.1021/jacs.6b11563] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
High-valent iron and manganese complexes effect some of the most challenging biochemical reactions known, including hydrocarbon and water oxidations associated with the global carbon cycle and oxygenic photosynthesis, respectively. Their extreme reactivity presents an impediment to structural characterization, but their biological importance and potential chemical utility have, nevertheless, motivated extensive efforts toward that end. Several such intermediates accumulate during activation of class I ribonucleotide reductase (RNR) β subunits, which self-assemble dimetal cofactors with stable one-electron oxidants that serve to initiate the enzyme's free-radical mechanism. In the class I-c β subunit from Chlamydia trachomatis, a heterodinuclear Mn(II)/Fe(II) complex reacts with dioxygen to form a Mn(IV)/Fe(IV) intermediate, which undergoes reduction of the iron site to produce the active Mn(IV)/Fe(III) cofactor. Herein, we assess the structure of the Mn(IV)/Fe(IV) activation intermediate using Fe- and Mn-edge extended X-ray absorption fine structure (EXAFS) analysis and multifrequency pulse electron paramagnetic resonance (EPR) spectroscopy. The EXAFS results reveal a metal-metal vector of 2.74-2.75 Å and an intense light-atom (C/N/O) scattering interaction 1.8 Å from the Fe. Pulse EPR data reveal an exchangeable deuterium hyperfine coupling of strength |T| = 0.7 MHz, but no stronger couplings. The results suggest that the intermediate possesses a di-μ-oxo diamond core structure with a terminal hydroxide ligand to the Mn(IV).
Collapse
Affiliation(s)
- Ryan J Martinie
- Department of Chemistry and ‡Department of Biochemistry and Molecular Biology, The Pennsylvania State University , University Park, Pennsylvania 16802, United States
| | - Elizabeth J Blaesi
- Department of Chemistry and ‡Department of Biochemistry and Molecular Biology, The Pennsylvania State University , University Park, Pennsylvania 16802, United States
| | - Carsten Krebs
- Department of Chemistry and ‡Department of Biochemistry and Molecular Biology, The Pennsylvania State University , University Park, Pennsylvania 16802, United States
| | - J Martin Bollinger
- Department of Chemistry and ‡Department of Biochemistry and Molecular Biology, The Pennsylvania State University , University Park, Pennsylvania 16802, United States
| | - Alexey Silakov
- Department of Chemistry and ‡Department of Biochemistry and Molecular Biology, The Pennsylvania State University , University Park, Pennsylvania 16802, United States
| | - Christopher J Pollock
- Department of Chemistry and ‡Department of Biochemistry and Molecular Biology, The Pennsylvania State University , University Park, Pennsylvania 16802, United States
| |
Collapse
|
11
|
Sproviero EM. Geometrical properties of the manganese(iv)/iron(iii) cofactor of Chlamydia trachomatis ribonucleotide reductase unveiled by simulations of XAS spectra. Dalton Trans 2017; 46:4724-4736. [DOI: 10.1039/c6dt03893j] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
A combination of EXAFS simulations and DFT calculations, including a novel protocol to evaluate Debye–Waller factors, provide insights into the structure of the Mn(iv)/Fe(iii) cofactor ofCtR2.
Collapse
Affiliation(s)
- Eduardo M. Sproviero
- Department of Chemistry and Biochemistry
- University of the Sciences in Philadelphia
- Philadelphia
- USA
| |
Collapse
|
12
|
Liao RZ, Siegbahn PEM. Phosphate Hydrolysis by the Fe2–Ca3-Dependent Alkaline Phosphatase PhoX: Mechanistic Insights from DFT calculations. Inorg Chem 2015; 54:11941-7. [DOI: 10.1021/acs.inorgchem.5b02268] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Rong-Zhen Liao
- Key Laboratory of Material Chemistry for
Energy Conversion and Storage, Ministry of Education, School of Chemistry
and Chemical Engineering, Huazhong University of Science and Technology, Wuhan 430074, China
| | - Per E. M. Siegbahn
- Department
of Organic Chemistry, Arrhenius Laboratory, Stockholm University, SE-10691 Stockholm, Sweden
| |
Collapse
|
13
|
Han Du WG, Noodleman L. Broken Symmetry DFT Calculations/Analysis for Oxidized and Reduced Dinuclear Center in Cytochrome c Oxidase: Relating Structures, Protonation States, Energies, and Mössbauer Properties in ba3 Thermus thermophilus. Inorg Chem 2015; 54:7272-90. [PMID: 26192749 PMCID: PMC4525772 DOI: 10.1021/acs.inorgchem.5b00700] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2015] [Indexed: 12/22/2022]
Abstract
The Fea3(3+)···CuB(2+) dinuclear center (DNC) structure of the as-isolated oxidized ba3 cytochrome c oxidase (CcO) from Thermus thermophilus (Tt) is still not fully understood. When the proteins are initially crystallized in the oxidized state, they typically become radiolyticly reduced through X-ray irradiation. Several X-ray crystal structures of reduced ba3 CcO from Tt are available. However, depending on whether the crystals were prepared in a lipidic cubic phase environment or in detergent micelles, and whether the CcO's were chemically or radiolyticly reduced, the X-ray diffraction analysis of the crystals showed different Fea3(2+)···CuB(+) DNC structures. On the other hand, Mössbauer spectroscopic experiments on reduced and oxidized ba3 CcOs from Tt (Zimmermann et al., Proc. Natl. Acad. Sci. USA 1988, 85, 5779-5783) revealed multiple (57)Fea3(2+) and (57)Fea3(3+) components. Moreover, one of the (57)Fea3(3+) components observed at 4.2 K transformed from a proposed "low-spin" state to a different high-spin species when the temperature was increased above 190 K, whereas the other high-spin (57)Fea3(3+) component remained unchanged. In the current Article, in order to understand the heterogeneities of the DNC in both Mössbauer spectra and X-ray crystal structures, the spin crossover of one of the (57)Fea3(3+) components, and how the coordination and spin states of the Fea3(3+/2+) and Cu(2+/1+) sites relate to the heterogeneity of the DNC structures, we have applied density functional OLYP calculations to the DNC clusters established based on the different X-ray crystal structures of ba3 CcO from Tt. As a result, specific oxidized and reduced DNC structures related to the observed Mössbauer spectra and to spectral changes with temperature have been proposed. Our calculations also show that, in certain intermediate states, the His233 and His283 ligand side chains may dissociate from the CuB(+) site, and they may become potential proton loading sites during the catalytic cycle.
Collapse
Affiliation(s)
- Wen-Ge Han Du
- Department of Integrative Structural and Computational
Biology, CB213, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037, United States
| | - Louis Noodleman
- Department of Integrative Structural and Computational
Biology, CB213, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037, United States
| |
Collapse
|
14
|
Gouré E, Carboni M, Dubourdeaux P, Clémancey M, Balasubramanian R, Lebrun C, Bayle PA, Maldivi P, Blondin G, Latour JM. Cis/trans isomerizations in diiron complexes involving aniline or anilide ligands. Inorg Chem 2014; 53:10060-9. [PMID: 25254906 DOI: 10.1021/ic501793v] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
We have recently reported a deprotonation-induced valence inversion within a phenoxido-bridged mixed-valent diiron(II,III) complex. The initial aniline coordinated to the Fe(II) site reacts with triethylamine, and the resulting complex contains an anilide ligand coordinated to the Fe(III) ion. The behavior of these complexes in acetonitrile is indeed more intricate. Owing to the very distinctive spectroscopic signatures of the complexes, the conjunction of NMR, Mössbauer, and UV-visible absorption spectroscopies allows one to evidence two isomerization reactions, one involving the aniline linked to Fe(II) and the other the anilide on Fe(III). Theoretical calculations sustain this conclusion. Aniline in the cis position versus the bridging phenoxide is shown to be the most stable isomer while the anilide trans to the phenoxido bridge is favored. The trans isomer of the aniline complex is more acidic than the cis one by 1 pKa unit. Isomerization of the anilide complex is 10 times faster than the analogous isomerization of the aniline complex. Both reactions are proposed to proceed through a unique mechanism. This is the first time that such isomerization reactions are evidenced in dinuclear complexes.
Collapse
Affiliation(s)
- Eric Gouré
- CEA, iRTSV/LCBM, pmb , F-38000 Grenoble, France
| | | | | | | | | | | | | | | | | | | |
Collapse
|
15
|
Marenich AV, Ho J, Coote ML, Cramer CJ, Truhlar DG. Computational electrochemistry: prediction of liquid-phase reduction potentials. Phys Chem Chem Phys 2014; 16:15068-106. [PMID: 24958074 DOI: 10.1039/c4cp01572j] [Citation(s) in RCA: 314] [Impact Index Per Article: 31.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
This article reviews recent developments and applications in the area of computational electrochemistry. Our focus is on predicting the reduction potentials of electron transfer and other electrochemical reactions and half-reactions in both aqueous and nonaqueous solutions. Topics covered include various computational protocols that combine quantum mechanical electronic structure methods (such as density functional theory) with implicit-solvent models, explicit-solvent protocols that employ Monte Carlo or molecular dynamics simulations (for example, Car-Parrinello molecular dynamics using the grand canonical ensemble formalism), and the Marcus theory of electronic charge transfer. We also review computational approaches based on empirical relationships between molecular and electronic structure and electron transfer reactivity. The scope of the implicit-solvent protocols is emphasized, and the present status of the theory and future directions are outlined.
Collapse
Affiliation(s)
- Aleksandr V Marenich
- Department of Chemistry, Chemical Theory Center, and Supercomputing Institute, University of Minnesota, 207 Pleasant Street S.E., Minneapolis, MN 55455-0431, USA.
| | | | | | | | | |
Collapse
|
16
|
Luber S, Leung S, Herrmann C, Du WH, Noodleman L, Batista VS. EXAFS simulation refinement based on broken-symmetry DFT geometries for the Mn(IV)-Fe(III) center of class I RNR from Chlamydia trachomatis. Dalton Trans 2014; 43:576-83. [PMID: 24129440 PMCID: PMC3855085 DOI: 10.1039/c3dt51563j] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Ribonucleotide reductases (RNRs) catalyze the reduction of ribonucleotides into deoxyribonucleotides necessary for DNA biosynthesis. Unlike the conventional class Ia RNRs which use a diiron cofactor in their subunit R2, the active site of the RNR-R2 from Chlamydia trachomatis (Ct) contains a Mn/Fe cofactor. The detailed structure of the Mn/Fe core has yet to be established. In this paper we evaluate six different structural models of the Ct RNR active site in the Mn(iv)/Fe(iii) state by using Mössbauer parameter calculations and simulations of Mn/Fe extended X-ray absorption fine structure (EXAFS) spectroscopy, and we identify a structure similar to a previously proposed DFT-optimized model that shows quantitative agreement with both EXAFS and Mössbauer spectroscopic data.
Collapse
Affiliation(s)
- Sandra Luber
- Department of Chemistry, Yale University, P.O. Box 208107, New Haven, CT 06520, USA
| | - Sophie Leung
- Department of Chemistry, Yale University, P.O. Box 208107, New Haven, CT 06520, USA
| | - Carmen Herrmann
- Department of Chemistry, Yale University, P.O. Box 208107, New Haven, CT 06520, USA
| | - Wenge Han Du
- Department of Integrative Structural and Computational Biology, TPC15, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA
| | - Louis Noodleman
- Department of Integrative Structural and Computational Biology, TPC15, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA
| | - Victor S. Batista
- Department of Chemistry, Yale University, P.O. Box 208107, New Haven, CT 06520, USA
| |
Collapse
|
17
|
Du WGH, Noodleman L. Density functional study for the bridged dinuclear center based on a high-resolution X-ray crystal structure of ba3 cytochrome c oxidase from Thermus thermophilus. Inorg Chem 2013; 52:14072-88. [PMID: 24262070 DOI: 10.1021/ic401858s] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Strong electron density for a peroxide type dioxygen species bridging the Fea3 and CuB dinuclear center (DNC) was observed in the high-resolution (1.8 Å) X-ray crystal structures (PDB entries 3S8G and 3S8F) of ba3 cytochrome c oxidase (CcO) from Thermus thermophilus. The crystals represent the as-isolated X-ray photoreduced CcO structures. The bridging peroxide was proposed to arise from the recombination of two radiation-produced HO(•) radicals formed either very near to or even in the space between the two metals of the DNC. It is unclear whether this peroxide species is in the O2(2-), O2(•)(-), HO2(-), or the H2O2 form and what is the detailed electronic structure and binding geometry including the DNC. In order to answer what form of this dioxygen species was observed in the DNC of the 1.8 Å X-ray CcO crystal structure (3S8G), we have applied broken-symmetry density functional theory (BS-DFT) geometric and energetic calculations (using OLYP potential) on large DNC cluster models with different Fea3-CuB oxidation and spin states and with O2(2-), O2(•)(-), HO2(-), or H2O2 in the bridging position. By comparing the DFT optimized geometries with the X-ray crystal structure (3S8G), we propose that the bridging peroxide is HO2(-). The X-ray crystal structure is likely to represent the superposition of the Fea3(2+)-(HO2(-))-CuB(+) DNC's in different states (Fe(2+) in low spin (LS), intermediate spin (IS), or high spin (HS)) with the majority species having the proton of the HO2(-) residing on the oxygen atom (O1) which is closer to the Fea3(2+) site in the Fea3(2+)-(HO-O)(-)-CuB(+) conformation. Our calculations show that the side chain of Tyr237 is likely trapped in the deprotonated Tyr237(-) anion form in the 3S8G X-ray crystal structure.
Collapse
Affiliation(s)
- Wen-Ge Han Du
- Department of Integrative Structural and Computational Biology, TPC15, The Scripps Research Institute , 10550 North Torrey Pines Road, La Jolla, California 92037, United States
| | | |
Collapse
|
18
|
Tereniak SJ, Carlson RK, Clouston LJ, Young VG, Bill E, Maurice R, Chen YS, Kim HJ, Gagliardi L, Lu CC. Role of the Metal in the Bonding and Properties of Bimetallic Complexes Involving Manganese, Iron, and Cobalt. J Am Chem Soc 2013; 136:1842-55. [DOI: 10.1021/ja409016w] [Citation(s) in RCA: 78] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Affiliation(s)
- Stephen J. Tereniak
- Department
of Chemistry, University of Minnesota, 207 Pleasant Street SE, Minneapolis, Minnesota 55455-0431, United States
| | - Rebecca K. Carlson
- Department
of Chemistry, University of Minnesota, 207 Pleasant Street SE, Minneapolis, Minnesota 55455-0431, United States
- Supercomputing
Institute and Chemical Theory Center, University of Minnesota, Minneapolis, Minnesota 55455, United States
| | - Laura J. Clouston
- Department
of Chemistry, University of Minnesota, 207 Pleasant Street SE, Minneapolis, Minnesota 55455-0431, United States
| | - Victor G. Young
- Department
of Chemistry, University of Minnesota, 207 Pleasant Street SE, Minneapolis, Minnesota 55455-0431, United States
| | - Eckhard Bill
- Max Planck Institut für Chemische Energiekonversion, Stiftstraße 34-36, 45470 Mülheim an der Ruhr, Germany
| | - Rémi Maurice
- Department
of Chemistry, University of Minnesota, 207 Pleasant Street SE, Minneapolis, Minnesota 55455-0431, United States
- Supercomputing
Institute and Chemical Theory Center, University of Minnesota, Minneapolis, Minnesota 55455, United States
| | - Yu-Sheng Chen
- ChemMatCARS, University of Chicago, Argonne, Illinois 60439, United States
| | - Hyun Jung Kim
- Department
of Chemistry, University of Minnesota, 207 Pleasant Street SE, Minneapolis, Minnesota 55455-0431, United States
- Supercomputing
Institute and Chemical Theory Center, University of Minnesota, Minneapolis, Minnesota 55455, United States
| | - Laura Gagliardi
- Department
of Chemistry, University of Minnesota, 207 Pleasant Street SE, Minneapolis, Minnesota 55455-0431, United States
- Supercomputing
Institute and Chemical Theory Center, University of Minnesota, Minneapolis, Minnesota 55455, United States
| | - Connie C. Lu
- Department
of Chemistry, University of Minnesota, 207 Pleasant Street SE, Minneapolis, Minnesota 55455-0431, United States
| |
Collapse
|
19
|
Chmielowska A, Lodowski P, Jaworska M. Redox Potentials and Protonation of the A-Cluster from Acetyl-CoA Synthase. A Density Functional Theory Study. J Phys Chem A 2013; 117:12484-96. [DOI: 10.1021/jp402616e] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Affiliation(s)
| | - Piotr Lodowski
- Institute
of Chemistry, University of Silesia, Szkolna 9, 40-006 Katowice, Poland
| | - Maria Jaworska
- Institute
of Chemistry, University of Silesia, Szkolna 9, 40-006 Katowice, Poland
| |
Collapse
|
20
|
Direct observation of structurally encoded metal discrimination and ether bond formation in a heterodinuclear metalloprotein. Proc Natl Acad Sci U S A 2013; 110:17189-94. [PMID: 24101498 DOI: 10.1073/pnas.1304368110] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023] Open
Abstract
Although metallocofactors are ubiquitous in enzyme catalysis, how metal binding specificity arises remains poorly understood, especially in the case of metals with similar primary ligand preferences such as manganese and iron. The biochemical selection of manganese over iron presents a particularly intricate problem because manganese is generally present in cells at a lower concentration than iron, while also having a lower predicted complex stability according to the Irving-Williams series (Mn(II) < Fe(II) < Ni(II) < Co(II) < Cu(II) > Zn(II)). Here we show that a heterodinuclear Mn/Fe cofactor with the same primary protein ligands in both metal sites self-assembles from Mn(II) and Fe(II) in vitro, thus diverging from the Irving-Williams series without requiring auxiliary factors such as metallochaperones. Crystallographic, spectroscopic, and computational data demonstrate that one of the two metal sites preferentially binds Fe(II) over Mn(II) as expected, whereas the other site is nonspecific, binding equal amounts of both metals in the absence of oxygen. Oxygen exposure results in further accumulation of the Mn/Fe cofactor, indicating that cofactor assembly is at least a two-step process governed by both the intrinsic metal specificity of the protein scaffold and additional effects exerted during oxygen binding or activation. We further show that the mixed-metal cofactor catalyzes a two-electron oxidation of the protein scaffold, yielding a tyrosine-valine ether cross-link. Theoretical modeling of the reaction by density functional theory suggests a multistep mechanism including a valyl radical intermediate.
Collapse
|
21
|
Dassama LMK, Krebs C, Bollinger JM, Rosenzweig AC, Boal AK. Structural basis for assembly of the Mn(IV)/Fe(III) cofactor in the class Ic ribonucleotide reductase from Chlamydia trachomatis. Biochemistry 2013; 52:6424-36. [PMID: 23924396 DOI: 10.1021/bi400819x] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
The class Ic ribonucleotide reductase (RNR) from Chlamydia trachomatis (Ct) employs a Mn(IV)/Fe(III) cofactor in each monomer of its β2 subunit to initiate nucleotide reduction. The cofactor forms by reaction of Mn(II)/Fe(II)-β2 with O2. Previously, in vitro cofactor assembly from apo β2 and divalent metal ions produced a mixture of two forms, with Mn at site 1 (Mn(IV)/Fe(III)) or site 2 (Fe(III)/Mn(IV)), of which the more active Mn(IV)/Fe(III) product predominates. Here we have addressed the basis for metal site selectivity by determining X-ray crystal structures of apo, Mn(II), and Mn(II)/Fe(II) complexes of Ct β2. A structure obtained anaerobically with equimolar Mn(II), Fe(II), and apoprotein reveals exclusive incorporation of Mn(II) at site 1 and Fe(II) at site 2, in contrast to the more modest site selectivity achieved previously. Site specificity is controlled thermodynamically by the apoprotein structure, as only minor adjustments of ligands occur upon metal binding. Additional structures imply that, by itself, Mn(II) binds in either site. Together, the structures are consistent with a model for in vitro cofactor assembly in which Fe(II) specificity for site 2 drives assembly of the appropriately configured heterobimetallic center, provided that Fe(II) is substoichiometric. This model suggests that use of a Mn(IV)/Fe(III) cofactor in vivo could be an adaptation to Fe(II) limitation. A 1.8 Å resolution model of the Mn(II)/Fe(II)-β2 complex reveals additional structural determinants for activation of the cofactor, including a proposed site for side-on (η(2)) addition of O2 to Fe(II) and a short (3.2 Å) Mn(II)-Fe(II) interionic distance, promoting formation of the Mn(IV)/Fe(IV) activation intermediate.
Collapse
Affiliation(s)
- Laura M K Dassama
- Department of Chemistry and Department of Biochemistry and Molecular Biology, The Pennsylvania State University , University Park, Pennsylvania 16802, United States
| | | | | | | | | |
Collapse
|
22
|
Sigfridsson KGV, Chernev P, Leidel N, Popović-Bijelić A, Gräslund A, Haumann M. Rapid X-ray photoreduction of dimetal-oxygen cofactors in ribonucleotide reductase. J Biol Chem 2013; 288:9648-9661. [PMID: 23400774 DOI: 10.1074/jbc.m112.438796] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Prototypic dinuclear metal cofactors with varying metallation constitute a class of O2-activating catalysts in numerous enzymes such as ribonucleotide reductase. Reliable structures are required to unravel the reaction mechanisms. However, protein crystallography data may be compromised by x-ray photoreduction (XRP). We studied XPR of Fe(III)Fe(III) and Mn(III)Fe(III) sites in the R2 subunit of Chlamydia trachomatis ribonucleotide reductase using x-ray absorption spectroscopy. Rapid and biphasic x-ray photoreduction kinetics at 20 and 80 K for both cofactor types suggested sequential formation of (III,II) and (II,II) species and similar redox potentials of iron and manganese sites. Comparing with typical x-ray doses in crystallography implies that (II,II) states are reached in <1 s in such studies. First-sphere metal coordination and metal-metal distances differed after chemical reduction at room temperature and after XPR at cryogenic temperatures, as corroborated by model structures from density functional theory calculations. The inter-metal distances in the XPR-induced (II,II) states, however, are similar to R2 crystal structures. Therefore, crystal data of initially oxidized R2-type proteins mostly contain photoreduced (II,II) cofactors, which deviate from the native structures functional in O2 activation, explaining observed variable metal ligation motifs. This situation may be remedied by novel femtosecond free electron-laser protein crystallography techniques.
Collapse
Affiliation(s)
| | - Petko Chernev
- Free University Berlin, Institute of Experimental Physics, 14195 Berlin, Germany
| | - Nils Leidel
- Free University Berlin, Institute of Experimental Physics, 14195 Berlin, Germany
| | - Ana Popović-Bijelić
- Department of Biochemistry and Biophysics, Stockholm University, 10691 Stockholm, Sweden
| | - Astrid Gräslund
- Department of Biochemistry and Biophysics, Stockholm University, 10691 Stockholm, Sweden
| | - Michael Haumann
- Free University Berlin, Institute of Experimental Physics, 14195 Berlin, Germany.
| |
Collapse
|
23
|
Dassama LMK, Boal AK, Krebs C, Rosenzweig AC, Bollinger JM. Evidence that the β subunit of Chlamydia trachomatis ribonucleotide reductase is active with the manganese ion of its manganese(IV)/iron(III) cofactor in site 1. J Am Chem Soc 2012; 134:2520-3. [PMID: 22242660 DOI: 10.1021/ja211314p] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
The reaction of a class I ribonucleotide reductase (RNR) begins when a cofactor in the β subunit oxidizes a cysteine residue ~35 Å away in the α subunit, generating a thiyl radical. In the class Ic enzyme from Chlamydia trachomatis (Ct), the cysteine oxidant is the Mn(IV) ion of a Mn(IV)/Fe(III) cluster, which assembles in a reaction between O(2) and the Mn(II)/Fe(II) complex of β. The heterodinuclear nature of the cofactor raises the question of which site, 1 or 2, contains the Mn(IV) ion. Because site 1 is closer to the conserved location of the cysteine-oxidizing tyrosyl radical of class Ia and Ib RNRs, we suggested that the Mn(IV) ion most likely resides in this site (i.e., (1)Mn(IV)/(2)Fe(III)), but a subsequent computational study favored its occupation of site 2 ((1)Fe(III)/(2)Mn(IV)). In this work, we have sought to resolve the location of the Mn(IV) ion in Ct RNR-β by correlating X-ray crystallographic anomalous scattering intensities with catalytic activity for samples of the protein reconstituted in vitro by two different procedures. In samples containing primarily Mn(IV)/Fe(III) clusters, Mn preferentially occupies site 1, but some anomalous scattering from site 2 is observed, implying that both (1)Mn(II)/(2)Fe(II) and (1)Fe(II)/(2)Mn(II) complexes are competent to react with O(2) to produce the corresponding oxidized states. However, with diminished Mn(II) loading in the reconstitution, there is no evidence for Mn occupancy of site 2, and the greater activity of these "low-Mn" samples on a per-Mn basis implies that the (1)Mn(IV)/(2)Fe(III)-β is at least the more active of the two oxidized forms and may be the only active form.
Collapse
Affiliation(s)
- Laura M K Dassama
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, Pennsylvania 16802, USA
| | | | | | | | | |
Collapse
|
24
|
Leidel N, Popović-Bijelić A, Havelius KGV, Chernev P, Voevodskaya N, Gräslund A, Haumann M. High-valent [MnFe] and [FeFe] cofactors in ribonucleotide reductases. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2012; 1817:430-44. [PMID: 22222354 DOI: 10.1016/j.bbabio.2011.12.008] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/05/2011] [Revised: 12/13/2011] [Accepted: 12/16/2011] [Indexed: 11/30/2022]
Abstract
Ribonucleotide reductases (RNRs) are essential for DNA synthesis in most organisms. In class-Ic RNR from Chlamydia trachomatis (Ct), a MnFe cofactor in subunit R2 forms the site required for enzyme activity, instead of an FeFe cofactor plus a redox-active tyrosine in class-Ia RNRs, for example in mouse (Mus musculus, Mm). For R2 proteins from Ct and Mm, either grown in the presence of, or reconstituted with Mn and Fe ions, structural and electronic properties of higher valence MnFe and FeFe sites were determined by X-ray absorption spectroscopy and complementary techniques, in combination with bond-valence-sum and density functional theory calculations. At least ten different cofactor species could be tentatively distinguished. In Ct R2, two different Mn(IV)Fe(III) site configurations were assigned either L(4)Mn(IV)(μO)(2)Fe(III)L(4) (metal-metal distance of ~2.75Å, L = ligand) prevailing in metal-grown R2, or L(4)Mn(IV)(μO)(μOH)Fe(III)L(4) (~2.90Å) dominating in metal-reconstituted R2. Specific spectroscopic features were attributed to an Fe(IV)Fe(III) site (~2.55Å) with a L(4)Fe(IV)(μO)(2)Fe(III)L(3) core structure. Several Mn,Fe(III)Fe(III) (~2.9-3.1Å) and Mn,Fe(III)Fe(II) species (~3.3-3.4Å) likely showed 5-coordinated Mn(III) or Fe(III). Rapid X-ray photoreduction of iron and shorter metal-metal distances in the high-valent states suggested radiation-induced modifications in most crystal structures of R2. The actual configuration of the MnFe and FeFe cofactors seems to depend on assembly sequences, bound metal type, valence state, and previous catalytic activity involving subunit R1. In Ct R2, the protonation of a bridging oxide in the Mn(IV)(μO)(μOH)Fe(III) core may be important for preventing premature site reduction and initiation of the radical chemistry in R1.
Collapse
Affiliation(s)
- Nils Leidel
- Institut für Experimentalphysik, Freie Universität Berlin, 14195 Berlin, Germany
| | | | | | | | | | | | | |
Collapse
|
25
|
Jayapal P, Rajaraman G. On the controversy of metal ion composition on amine oxygenase (AurF): a computational investigation. Phys Chem Chem Phys 2012; 14:9050-3. [DOI: 10.1039/c2cp40874k] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
|
26
|
Roos K, Siegbahn PEM. A comparison of two-electron chemistry performed by the manganese and iron heterodimer and homodimers. J Biol Inorg Chem 2011; 17:363-73. [DOI: 10.1007/s00775-011-0858-8] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2011] [Accepted: 11/02/2011] [Indexed: 10/15/2022]
|
27
|
Han WG, Sandala GM, Giammona DA, Bashford D, Noodleman L. Mössbauer properties of the diferric cluster and the differential iron(II)-binding affinity of the iron sites in protein R2 of class Ia Escherichia coli ribonucleotide reductase: a DFT/electrostatics study. Dalton Trans 2011; 40:11164-75. [PMID: 21837345 PMCID: PMC3604995 DOI: 10.1039/c1dt10950b] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
The R2 subunit of class-Ia ribonucleotide reductase (RNR) from Escherichia coli (E. coli) contains a diiron active site. Starting from the apo-protein and Fe(II) in solution at low Fe(II)/apoR2 ratios, mononuclear Fe(II) binding is observed indicating possible different Fe(II) binding affinities for the two alternative sites. Further, based on their Mössbauer spectroscopy and two-iron-isotope reaction experiments, Bollinger et al. (J. Am. Chem. Soc., 1997, 119, 5976-5977) proposed that the site Fe1, which bonds to Asp84, should be associated with the higher observed (57)Fe Mössbauer quadrupole splitting (2.41 mm s(-1)) and lower isomer shift (0.45 mm s(-1)) in the Fe(III)Fe(III) state, site Fe2, which is further from Tyr122, should have a greater affinity for Fe(II) binding than site Fe1, and Fe(IV) in the intermediate X state should reside at site Fe2. In this paper, using density functional theory (DFT) incorporated with the conductor-like screening (COSMO) solvation model and with the finite-difference Poisson-Boltzmann self-consistent reaction field (PB-SCRF) methodologies, we have demonstrated that the observed large quadrupole splitting for the diferric state R2 does come from site Fe1(III) and it is mainly caused by the binding position of the carboxylate group of the Asp84 sidechain. Further, a series of active site clusters with mononuclear Fe(II) binding at either site Fe1 or Fe2 have been studied, which show that with a single dielectric medium outside the active site quantum region, there is no energetic preference for Fe(II) binding at one site over another. However, when including the explicit extended protein environment in the PB-SCRF model, the reaction field favors the Fe(II) binding at site Fe2 rather than at site Fe1 by ~9 kcal mol(-1). Therefore our calculations support the proposal of the previous Mössbauer spectroscopy and two-iron-isotope reaction experiments by Bollinger et al.
Collapse
Affiliation(s)
- Wen-Ge Han
- Department of Molecular Biology, TPC15, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037
| | - Gregory M. Sandala
- Department of Molecular Biology, TPC15, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037
| | - Debra Ann Giammona
- Structural Biology, St. Jude Children’s Research Hospital, 262 Danny Thomas Place, Memphis, TN 38105
| | - Donald Bashford
- Structural Biology, St. Jude Children’s Research Hospital, 262 Danny Thomas Place, Memphis, TN 38105
| | - Louis Noodleman
- Department of Molecular Biology, TPC15, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037
| |
Collapse
|
28
|
Bhave DP, Han WG, Pazicni S, Penner-Hahn JE, Carroll KS, Noodleman L. Geometric and electrostatic study of the [4Fe-4S] cluster of adenosine-5'-phosphosulfate reductase from broken symmetry density functional calculations and extended X-ray absorption fine structure spectroscopy. Inorg Chem 2011; 50:6610-25. [PMID: 21678934 DOI: 10.1021/ic200446c] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Adenosine-5'-phosphosulfate reductase (APSR) is an iron-sulfur protein that catalyzes the reduction of adenosine-5'-phosphosulfate (APS) to sulfite. APSR coordinates to a [4Fe-4S] cluster via a conserved CC-X(~80)-CXXC motif, and the cluster is essential for catalysis. Despite extensive functional, structural, and spectroscopic studies, the exact role of the iron-sulfur cluster in APS reduction remains unknown. To gain an understanding into the role of the cluster, density functional theory (DFT) analysis and extended X-ray fine structure spectroscopy (EXAFS) have been performed to reveal insights into the coordination, geometry, and electrostatics of the [4Fe-4S] cluster. X-ray absorption near-edge structure (XANES) data confirms that the cluster is in the [4Fe-4S](2+) state in both native and substrate-bound APSR while EXAFS data recorded at ~0.1 Å resolution indicates that there is no significant change in the structure of the [4Fe-4S] cluster between the native and substrate-bound forms of the protein. On the other hand, DFT calculations provide an insight into the subtle differences between the geometry of the cluster in the native and APS-bound forms of APSR. A comparison between models with and without the tandem cysteine pair coordination of the cluster suggests a role for the unique coordination in facilitating a compact geometric structure and "fine-tuning" the electronic structure to prevent reduction of the cluster. Further, calculations using models in which residue Lys144 is mutated to Ala confirm the finding that Lys144 serves as a crucial link in the interactions involving the [4Fe-4S] cluster and APS.
Collapse
Affiliation(s)
- Devayani P Bhave
- Chemical Biology Graduate Program, University of Michigan, Ann Arbor, Michigan 48109-2216, USA
| | | | | | | | | | | |
Collapse
|
29
|
Oxygen cleavage with manganese and iron in ribonucleotide reductase from Chlamydia trachomatis. J Biol Inorg Chem 2011; 16:553-65. [PMID: 21258828 DOI: 10.1007/s00775-011-0755-1] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2010] [Accepted: 01/04/2011] [Indexed: 10/18/2022]
Abstract
The oxygen cleavage in Chlamydia trachomatis ribonucleotide reductase (RNR) has been studied using B3LYP* hybrid density functional theory. Class Ic C. trachomatis RNR lacks the radical-bearing tyrosine, crucial for activity in conventional class I (subclass a and b) RNR. Instead of the Fe(III)Fe(III)-Tyr(rad) active state, C. trachomatis RNR has a mixed Mn(IV)Fe(III) metal center in subunit II (R2). A mixed MnFe metal center has never been observed as a radical cofactor before. The active state is generated by reductive oxygen cleavage at the metal site. On the basis of calculated barriers for oxygen cleavage in C. trachomatis R2 and R2 from Escherichia coli with a diiron, a mixed manganese-iron, and a dimanganese center, conclusions can be drawn about the effect of changing metals in R2. The oxygen cleavage is found to be governed by two factors: the redox potentials of the metals and the relative stability of the different peroxides. Mn(IV) has higher stability than Fe(IV), and the barrier is therefore lower with a mixed metal center than with a diiron center. With a dimanganese center, an asymmetric peroxide is more stable than the symmetric peroxide, and the barrier therefore becomes too high. Calculated proton-coupled redox potentials are compared to identify three possible R2 active states, the Fe(III)Fe(III)-Tyr(rad) state, the Mn(IV)Fe(III) state, and the Mn(IV)Mn(IV) state. A tentative energy profile of the thermodynamics of the radical transfer from R2 to subunit I is constructed to illustrate how the stability of the active states can be understood from a thermodynamical point of view.
Collapse
|
30
|
Högbom M. Metal use in ribonucleotide reductase R2, di-iron, di-manganese and heterodinuclear—an intricate bioinorganic workaround to use different metals for the same reaction. Metallomics 2011; 3:110-20. [DOI: 10.1039/c0mt00095g] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
|
31
|
|