1
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Bazayeva M, Andreini C, Rosato A. A database overview of metal-coordination distances in metalloproteins. Acta Crystallogr D Struct Biol 2024; 80:362-376. [PMID: 38682667 PMCID: PMC11066882 DOI: 10.1107/s2059798324003152] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2023] [Accepted: 04/11/2024] [Indexed: 05/01/2024] Open
Abstract
Metalloproteins are ubiquitous in all living organisms and take part in a very wide range of biological processes. For this reason, their experimental characterization is crucial to obtain improved knowledge of their structure and biological functions. The three-dimensional structure represents highly relevant information since it provides insight into the interaction between the metal ion(s) and the protein fold. Such interactions determine the chemical reactivity of the bound metal. The available PDB structures can contain errors due to experimental factors such as poor resolution and radiation damage. A lack of use of distance restraints during the refinement and validation process also impacts the structure quality. Here, the aim was to obtain a thorough overview of the distribution of the distances between metal ions and their donor atoms through the statistical analysis of a data set based on more than 115 000 metal-binding sites in proteins. This analysis not only produced reference data that can be used by experimentalists to support the structure-determination process, for example as refinement restraints, but also resulted in an improved insight into how protein coordination occurs for different metals and the nature of their binding interactions. In particular, the features of carboxylate coordination were inspected, which is the only type of interaction that is commonly present for nearly all metals.
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Affiliation(s)
- Milana Bazayeva
- Department of Chemistry, University of Florence, Via della Lastruccia 3, 50019 Sesto Fiorentino, Italy
- Magnetic Resonance Center (CERM), University of Florence, Via Luigi Sacconi 6, 50019 Sesto Fiorentino, Italy
| | - Claudia Andreini
- Department of Chemistry, University of Florence, Via della Lastruccia 3, 50019 Sesto Fiorentino, Italy
- Magnetic Resonance Center (CERM), University of Florence, Via Luigi Sacconi 6, 50019 Sesto Fiorentino, Italy
- Consorzio Interuniversitario di Risonanze Magnetiche di Metallo Proteine, Via Luigi Sacconi 6, 50019 Sesto Fiorentino, Italy
| | - Antonio Rosato
- Department of Chemistry, University of Florence, Via della Lastruccia 3, 50019 Sesto Fiorentino, Italy
- Magnetic Resonance Center (CERM), University of Florence, Via Luigi Sacconi 6, 50019 Sesto Fiorentino, Italy
- Consorzio Interuniversitario di Risonanze Magnetiche di Metallo Proteine, Via Luigi Sacconi 6, 50019 Sesto Fiorentino, Italy
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2
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Makita H, Simon PS, Kern J, Yano J, Yachandra VK. Combining on-line spectroscopy with synchrotron and X-ray free electron laser crystallography. Curr Opin Struct Biol 2023; 80:102604. [PMID: 37148654 PMCID: PMC10793627 DOI: 10.1016/j.sbi.2023.102604] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2023] [Revised: 03/22/2023] [Accepted: 04/05/2023] [Indexed: 05/08/2023]
Abstract
With the recent advances in serial crystallography methods at both synchrotron and X-ray free electron laser sources, more details of intermediate or transient states of the catalytic reactions are being revealed structurally. These structural studies of reaction dynamics drive the need for on-line in crystallo spectroscopy methods to complement the crystallography experiment. The recent applications of combined spectroscopy and crystallography methods enable on-line determination of in crystallo reaction kinetics and structures of catalytic intermediates, sample integrity, and radiation-induced sample modifications, if any, as well as heterogeneity of crystals from different preparations or sample batches. This review describes different modes of spectroscopy that are combined with the crystallography experiment at both synchrotron and X-ray free-electron laser facilities, and the complementary information that each method can provide to facilitate the structural study of enzyme catalysis and protein dynamics.
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Affiliation(s)
- Hiroki Makita
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Philipp S Simon
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Jan Kern
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA.
| | - Junko Yano
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA.
| | - Vittal K Yachandra
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA.
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3
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Rodrigues MJ, Giri N, Royant A, Zhang Y, Bolton R, Evans G, Ealick SE, Begley T, Tews I. Trapping and structural characterisation of a covalent intermediate in vitamin B6 biosynthesis catalysed by the Pdx1 PLP synthase. RSC Chem Biol 2022; 3:227-230. [PMID: 35360887 PMCID: PMC8827014 DOI: 10.1039/d1cb00160d] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2021] [Accepted: 10/25/2021] [Indexed: 12/01/2022] Open
Abstract
The Pdx1 enzyme catalyses condensation of two carbohydrates and ammonia to form pyridoxal 5-phosphate (PLP) via an imine relay mechanism of carbonyl intermediates. The I333 intermediate characterised here using structural, UV-vis absorption spectroscopy and mass spectrometry analyses rationalises stereoselective deprotonation and subsequent substrate assisted phosphate elimination, central to PLP biosynthesis. Explaining stereoselective deprotonation and phosphate elimination in PLP biosynthesis through crystal structure, UV-vis absorption spectroscopic and mass spectrometric characterisation of a chromophoric intermediate.![]()
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Affiliation(s)
- Matthew J. Rodrigues
- Biological Sciences, Institute for Life Sciences, University of Southampton, Southampton, SO17 1BJ, UK
- Diamond Light Source, Harwell Science and Innovation Campus, Didcot, OX11 0DE, UK
| | - Nitai Giri
- Department of Chemistry, Texas A&M University, College Station, TX 77843, USA
| | - Antoine Royant
- Université Grenoble Alpes, CNRS, CEA, Institut de Biologie Structurale (IBS), CS 10090, Grenoble Cedex 9 38044, France
- European Synchrotron Radiation Facility, CS 40220, Grenoble Cedex 9 38043, France
| | - Yang Zhang
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY 14853, USA
| | - Rachel Bolton
- Biological Sciences, Institute for Life Sciences, University of Southampton, Southampton, SO17 1BJ, UK
- Diamond Light Source, Harwell Science and Innovation Campus, Didcot, OX11 0DE, UK
| | - Gwyndaf Evans
- Diamond Light Source, Harwell Science and Innovation Campus, Didcot, OX11 0DE, UK
| | - Steve E. Ealick
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY 14853, USA
| | - Tadhg Begley
- Department of Chemistry, Texas A&M University, College Station, TX 77843, USA
| | - Ivo Tews
- Biological Sciences, Institute for Life Sciences, University of Southampton, Southampton, SO17 1BJ, UK
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4
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Hough MA, Owen RL. Serial synchrotron and XFEL crystallography for studies of metalloprotein catalysis. Curr Opin Struct Biol 2021; 71:232-238. [PMID: 34455163 PMCID: PMC8667872 DOI: 10.1016/j.sbi.2021.07.007] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2021] [Revised: 07/15/2021] [Accepted: 07/17/2021] [Indexed: 11/24/2022]
Abstract
An estimated half of all proteins contain a metal, with these being essential for a tremendous variety of biological functions. X-ray crystallography is the major method for obtaining structures at high resolution of these metalloproteins, but there are considerable challenges to obtain intact structures due to the effects of radiation damage. Serial crystallography offers the prospect of determining low-dose synchrotron or effectively damage free XFEL structures at room temperature and enables time-resolved or dose-resolved approaches. Complementary spectroscopic data can validate redox and or ligand states within metalloprotein crystals. In this opinion, we discuss developments in the application of serial crystallographic approaches to metalloproteins and comment on future directions.
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Affiliation(s)
- Michael A Hough
- School of Life Sciences, University of Essex, Wivenhoe Park, Colchester, CO4 3SQ, UK.
| | - Robin L Owen
- Diamond Light Source, Harwell Science and Innovation Campus, Didcot OX11 0DE, UK.
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5
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Sen K, Hough MA, Strange RW, Yong C, Keal TW. QM/MM Simulations of Protein Crystal Reactivity Guided by MSOX Crystallography: A Copper Nitrite Reductase Case Study. J Phys Chem B 2021; 125:9102-9114. [PMID: 34357776 DOI: 10.1021/acs.jpcb.1c03661] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The recently developed multiple structures from one crystal (MSOX) serial crystallography method can be used to provide multiple snapshots of the progress of enzymatic reactions taking place within a protein crystal. Such MSOX snapshots can be used as a reference for combined quantum mechanical/molecular mechanical (QM/MM) simulations of enzyme reactivity within the crystal. QM/MM calculations are used to identify details of reference states that cannot be directly observed by X-ray diffraction experiments, such as protonation and oxidation states. These reference states are then used as known fixed endpoints for the modeling of reaction paths. We investigate the mechanism of nitrite reduction in an Achromobacter cycloclastes copper nitrite reductase crystal using MSOX-guided QM/MM calculations, identifying the change in nitrite binding orientation with a change in copper oxidation state, and determining the reaction path to the final NO-bound MSOX structure. The results are compared with QM/MM simulations performed in a solvated environment.
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Affiliation(s)
- Kakali Sen
- School of Life Sciences, University of Essex, Wivenhoe Park, Colchester, Essex CO4 3SQ, United Kingdom.,Scientific Computing Department, STFC Daresbury Laboratory, Keckwick Lane, Daresbury, Warrington, Cheshire WA4 4AD, United Kingdom
| | - Michael A Hough
- School of Life Sciences, University of Essex, Wivenhoe Park, Colchester, Essex CO4 3SQ, United Kingdom
| | - Richard W Strange
- School of Life Sciences, University of Essex, Wivenhoe Park, Colchester, Essex CO4 3SQ, United Kingdom
| | - Chin Yong
- Scientific Computing Department, STFC Daresbury Laboratory, Keckwick Lane, Daresbury, Warrington, Cheshire WA4 4AD, United Kingdom
| | - Thomas W Keal
- Scientific Computing Department, STFC Daresbury Laboratory, Keckwick Lane, Daresbury, Warrington, Cheshire WA4 4AD, United Kingdom
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Smulevich G. Solution and crystal phase resonance Raman spectroscopy: Valuable tools to unveil the structure and function of heme proteins. J PORPHYR PHTHALOCYA 2019. [DOI: 10.1142/s1088424619300088] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
In the present review, examples are provided illustrating the application of resonance Raman microscopy to heme protein single crystals to highlight the artifacts induced by the crystallization process or the conformational alteration induced by cooling. Moreover, the structural information determined from the RR spectra of heme proteins in solution and crystals is compared to that obtained from their X-ray structures to show how the combined spectroscopic/crystallographic approach is a powerful weapon in the structural biologist’s armamentarium.
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Affiliation(s)
- Giulietta Smulevich
- Dipartimento di Chimica “Ugo Schiff,” Università di Firenze, Via Della Lastruccia 3-13, 50019 Sesto Fiorentino(Fi), Italy
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7
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Standfuss J. Membrane protein dynamics studied by X-ray lasers – or why only time will tell. Curr Opin Struct Biol 2019; 57:63-71. [DOI: 10.1016/j.sbi.2019.02.001] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2018] [Revised: 02/04/2019] [Accepted: 02/04/2019] [Indexed: 01/05/2023]
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8
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Choosing the optimal spectroscopic toolkit to understand protein function. Biosci Rep 2017; 37:BSR20160378. [PMID: 28522552 PMCID: PMC5463260 DOI: 10.1042/bsr20160378] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2017] [Revised: 05/16/2017] [Accepted: 05/18/2017] [Indexed: 12/02/2022] Open
Abstract
Spectroscopy was one of the earliest methods used to study the properties and reactions of proteins, and remains one of the most powerful and widely used approaches to this day. A sometimes bewildering range of spectroscopies is now available, applicable to different sample states, timescales and indeed biological questions. This editorial describes some of the most relevant spectroscopic methods together with a selection of illustrative examples.
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9
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Kekilli D, Moreno-Chicano T, Chaplin AK, Horrell S, Dworkowski FSN, Worrall JAR, Strange RW, Hough MA. Photoreduction and validation of haem-ligand intermediate states in protein crystals by in situ single-crystal spectroscopy and diffraction. IUCRJ 2017; 4:263-270. [PMID: 28512573 PMCID: PMC5414400 DOI: 10.1107/s2052252517002159] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/16/2016] [Accepted: 02/09/2017] [Indexed: 05/24/2023]
Abstract
Powerful synergies are available from the combination of multiple methods to study proteins in the crystalline form. Spectroscopies which probe the same region of the crystal from which X-ray crystal structures are determined can give insights into redox, ligand and spin states to complement the information gained from the electron-density maps. The correct assignment of crystal structures to the correct protein redox and ligand states is essential to avoid the misinterpretation of structural data. This is a particular concern for haem proteins, which can occupy a wide range of redox states and are exquisitely sensitive to becoming reduced by solvated electrons generated from interactions of X-rays with water molecules in the crystal. Here, single-crystal spectroscopic fingerprinting has been applied to investigate the laser photoreduction of ferric haem in cytochrome c'. Furthermore, in situ X-ray-driven generation of haem intermediates in crystals of the dye-decolourizing-type peroxidase A (DtpA) from Streptomyces lividans is described.
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Affiliation(s)
- Demet Kekilli
- School of Biological Sciences, University of Essex, Wivenhoe Park, Colchester CO4 3SQ, England
| | - Tadeo Moreno-Chicano
- School of Biological Sciences, University of Essex, Wivenhoe Park, Colchester CO4 3SQ, England
| | - Amanda K. Chaplin
- School of Biological Sciences, University of Essex, Wivenhoe Park, Colchester CO4 3SQ, England
| | - Sam Horrell
- School of Biological Sciences, University of Essex, Wivenhoe Park, Colchester CO4 3SQ, England
| | | | - Jonathan A. R. Worrall
- School of Biological Sciences, University of Essex, Wivenhoe Park, Colchester CO4 3SQ, England
| | - Richard W. Strange
- School of Biological Sciences, University of Essex, Wivenhoe Park, Colchester CO4 3SQ, England
| | - Michael A. Hough
- School of Biological Sciences, University of Essex, Wivenhoe Park, Colchester CO4 3SQ, England
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10
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McCombs NL, Moreno-Chicano T, Carey LM, Franzen S, Hough MA, Ghiladi RA. Interaction of Azole-Based Environmental Pollutants with the Coelomic Hemoglobin from Amphitrite ornata: A Molecular Basis for Toxicity. Biochemistry 2017; 56:2294-2303. [PMID: 28387506 DOI: 10.1021/acs.biochem.7b00041] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The toxicities of azole pollutants that have widespread agricultural and industrial uses are either poorly understood or unknown, particularly with respect to how infaunal organisms are impacted by this class of persistent organic pollutant. To identify a molecular basis by which azole compounds may have unforeseen toxicity on marine annelids, we examine here their impact on the multifunctional dehaloperoxidase (DHP) hemoglobin from the terebellid polychaete Amphitrite ornata. Ultraviolet-visible and resonance Raman spectroscopic studies showed an increase in the six-coordinate low-spin heme population in DHP isoenzyme B upon binding of imidazole, benzotriazole, and benzimidazole (Kd values of 52, 82, and 110 μM, respectively), suggestive of their direct binding to the heme-Fe. Accordingly, atomic-resolution X-ray crystal structures, supported by computational studies, of the DHP B complexes of benzotriazole (1.14 Å), benzimidazole (1.08 Å), imidazole (1.08 Å), and indazole (1.12 Å) revealed two ligand binding motifs, one with direct ligand binding to the heme-Fe, and another in which the ligand binds in the hydrophobic distal pocket without coordinating the heme-Fe. Taken together, the results demonstrate a new mechanism by which azole pollutants can potentially disrupt hemoglobin function, thereby improving our understanding of their impact on infaunal organisms in marine and aquatic environments.
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Affiliation(s)
- Nikolette L McCombs
- Department of Chemistry, North Carolina State University , Raleigh, North Carolina 27695-8204, United States
| | - Tadeo Moreno-Chicano
- School of Biological Sciences, University of Essex , Wivenhoe Park, Colchester, Essex CO4 3SQ, U.K
| | - Leiah M Carey
- Department of Chemistry, North Carolina State University , Raleigh, North Carolina 27695-8204, United States
| | - Stefan Franzen
- Department of Chemistry, North Carolina State University , Raleigh, North Carolina 27695-8204, United States
| | - Michael A Hough
- School of Biological Sciences, University of Essex , Wivenhoe Park, Colchester, Essex CO4 3SQ, U.K
| | - Reza A Ghiladi
- Department of Chemistry, North Carolina State University , Raleigh, North Carolina 27695-8204, United States
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11
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Kekilli D, Petersen CA, Pixton DA, Ghafoor DD, Abdullah GH, Dworkowski FSN, Wilson MT, Heyes DJ, Hardman SJO, Murphy LM, Strange RW, Scrutton NS, Andrew CR, Hough MA. Engineering proximal vs. distal heme-NO coordination via dinitrosyl dynamics: implications for NO sensor design. Chem Sci 2017; 8:1986-1994. [PMID: 28451315 PMCID: PMC5390784 DOI: 10.1039/c6sc04190f] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2016] [Accepted: 11/08/2016] [Indexed: 01/18/2023] Open
Abstract
Proximal vs. distal heme-NO coordination is a novel strategy for selective gas response in heme-based NO-sensors. In the case of Alcaligenes xylosoxidans cytochrome c' (AXCP), formation of a transient distal 6cNO complex is followed by scission of the trans Fe-His bond and conversion to a proximal 5cNO product via a putative dinitrosyl species. Here we show that replacement of the AXCP distal Leu16 residue with smaller or similar sized residues (Ala, Val or Ile) traps the distal 6cNO complex, whereas Leu or Phe residues lead to a proximal 5cNO product with a transient or non-detectable distal 6cNO precursor. Crystallographic, spectroscopic, and kinetic measurements of 6cNO AXCP complexes show that increased distal steric hindrance leads to distortion of the Fe-N-O angle and flipping of the heme 7-propionate. However, it is the kinetic parameters of the distal NO ligand that determine whether 6cNO or proximal 5cNO end products are formed. Our data support a 'balance of affinities' mechanism in which proximal 5cNO coordination depends on relatively rapid release of the distal NO from the dinitrosyl precursor. This mechanism, which is applicable to other proteins that form transient dinitrosyls, represents a novel strategy for 5cNO formation that does not rely on an inherently weak Fe-His bond. Our data suggest a general means of engineering selective gas response into biologically-derived gas sensors in synthetic biology.
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Affiliation(s)
- Demet Kekilli
- School of Biological Sciences , University of Essex , Wivenhoe Park , Colchester , Essex CO4 3SQ , UK .
| | - Christine A Petersen
- Department of Chemistry and Biochemistry , Eastern Oregon University , La Grande , Oregon 97850 , USA .
| | - David A Pixton
- Department of Chemistry and Biochemistry , Eastern Oregon University , La Grande , Oregon 97850 , USA .
| | - Dlzar D Ghafoor
- Faculty of Science and Education Science , University of Sulaimani , Sulaymaniyah , Iraq
| | | | | | - Michael T Wilson
- School of Biological Sciences , University of Essex , Wivenhoe Park , Colchester , Essex CO4 3SQ , UK .
| | - Derren J Heyes
- Manchester Institute of Biotechnology , 131 Princess Street , Manchester M1 7DN , UK
| | - Samantha J O Hardman
- Manchester Institute of Biotechnology , 131 Princess Street , Manchester M1 7DN , UK
| | - Loretta M Murphy
- School of Chemistry , Bangor University , Bangor , Gwynedd , Wales LL57 2UW , UK
| | - Richard W Strange
- School of Biological Sciences , University of Essex , Wivenhoe Park , Colchester , Essex CO4 3SQ , UK .
- Molecular Biophysics Group , Institute of Integrative Biology , Faculty of Health and Life Sciences , University of Liverpool , Liverpool , L69 7ZB , UK
| | - Nigel S Scrutton
- Manchester Institute of Biotechnology , 131 Princess Street , Manchester M1 7DN , UK
| | - Colin R Andrew
- Department of Chemistry and Biochemistry , Eastern Oregon University , La Grande , Oregon 97850 , USA .
| | - Michael A Hough
- School of Biological Sciences , University of Essex , Wivenhoe Park , Colchester , Essex CO4 3SQ , UK .
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12
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Kwon H, Smith O, Raven EL, Moody PCE. Combining X-ray and neutron crystallography with spectroscopy. Acta Crystallogr D Struct Biol 2017; 73:141-147. [PMID: 28177310 PMCID: PMC5297917 DOI: 10.1107/s2059798316016314] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2016] [Accepted: 10/13/2016] [Indexed: 12/03/2022] Open
Abstract
X-ray protein crystallography has, through the determination of the three-dimensional structures of enzymes and their complexes, been essential to the understanding of biological chemistry. However, as X-rays are scattered by electrons, the technique has difficulty locating the presence and position of H atoms (and cannot locate H+ ions), knowledge of which is often crucially important for the understanding of enzyme mechanism. Furthermore, X-ray irradiation, through photoelectronic effects, will perturb the redox state in the crystal. By using single-crystal spectrophotometry, reactions taking place in the crystal can be monitored, either to trap intermediates or follow photoreduction during X-ray data collection. By using neutron crystallography, the positions of H atoms can be located, as it is the nuclei rather than the electrons that scatter neutrons, and the scattering length is not determined by the atomic number. Combining the two techniques allows much greater insight into both reaction mechanism and X-ray-induced photoreduction.
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Affiliation(s)
- Hanna Kwon
- Henry Wellcome Laboratories for Structural Biology, Leicester Institute for Structural and Chemical Biology and Department of Molecular and Cell Biology, University of Leicester, Lancaster Road, Leicester LE1 7RH, England
| | - Oliver Smith
- Henry Wellcome Laboratories for Structural Biology, Leicester Institute for Structural and Chemical Biology and Department of Molecular and Cell Biology, University of Leicester, Lancaster Road, Leicester LE1 7RH, England
| | - Emma Lloyd Raven
- Leicester Institute for Structural and Chemical Biology and Department of Chemistry, University of Leicester, University Road, Leicester LE1 7RH, England
| | - Peter C. E. Moody
- Henry Wellcome Laboratories for Structural Biology, Leicester Institute for Structural and Chemical Biology and Department of Molecular and Cell Biology, University of Leicester, Lancaster Road, Leicester LE1 7RH, England
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13
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Ghafoor DD, Kekilli D, Abdullah GH, Dworkowski FSN, Hassan HG, Wilson MT, Strange RW, Hough MA. Hydrogen bonding of the dissociated histidine ligand is not required for formation of a proximal NO adduct in cytochrome c'. J Biol Inorg Chem 2015; 20:949-56. [PMID: 26100643 DOI: 10.1007/s00775-015-1278-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2015] [Accepted: 06/04/2015] [Indexed: 11/28/2022]
Abstract
Cytochromes c', that occur in methanotrophic, denitrifying and photosynthetic bacteria, form unusual proximal penta-coordinate NO complexes via a hexa-coordinate distal NO intermediate. Their NO binding properties are similar to those of the eukaryotic NO sensor, soluble guanylate cyclase, for which they provide a valuable structural model. Previous studies suggested that hydrogen bonding between the displaced proximal histidine (His120) ligand (following its dissociation from heme due to trans effects from the distally bound NO) and a conserved aspartate residue (Asp121) could play a key role in allowing proximal NO binding to occur. We have characterized three variants of Alcaligenes xylosoxidans cytochrome c' (AXCP) where Asp121 has been replaced by Ala, Ile and Gln, respectively. In all variants, hydrogen bonding between residue 121 and His120 is abolished yet 5-coordinate proximal NO species are still formed. Our data therefore demonstrate that the His120-Asp121 bond is not essential for proximal NO binding although it likely provides an energy minimum for the displaced His ligand. All variants have altered proximal pocket structure relative to native AXCP.
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Affiliation(s)
- Dlzar D Ghafoor
- Faculty of Science and Education Science, University of Sulaimani, Sulaymaniyah, Iraq
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14
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Hough MA, Andrew CR. Cytochromes c': Structure, Reactivity and Relevance to Haem-Based Gas Sensing. Adv Microb Physiol 2015; 67:1-84. [PMID: 26616515 DOI: 10.1016/bs.ampbs.2015.08.001] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Cytochromes c' are a group of class IIa cytochromes with pentacoordinate haem centres and are found in photosynthetic, denitrifying and methanotrophic bacteria. Their function remains unclear, although roles in nitric oxide (NO) trafficking during denitrification or in cellular defence against nitrosoative stress have been proposed. Cytochromes c' are typically dimeric with each c-type haem-containing monomer folding as a four-α-helix bundle. Their hydrophobic and crowded distal sites impose severe restrictions on the binding of distal ligands, including diatomic gases. By contrast, NO binds to the proximal haem face in a similar manner to that of the eukaryotic NO sensor, soluble guanylate cyclase and bacterial analogues. In this review, we focus on how structural features of cytochromes c' influence haem spectroscopy and reactivity with NO, CO and O2. We also discuss the relevance of cytochrome c' to understanding the mechanisms of gas binding to haem-based sensor proteins.
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