Prof Emma Raven
|Professor of Biological Chemistry|
|BSc (Leicester), PhD (Newcastle upon Tyne)
|Tel : +44 (0)116 229 7047
|Email : firstname.lastname@example.org|
|Research Group : Chemical Biology
Our research in chemical biology focuses on using protein engineering techniques to examine catalytic activity and function in heme enzymes. The Biological Chemistry Group collaborates extensively within the Centre for Chemical Biology at Leicester.
- Substrate Binding and Catalytic Mechanism in Heme Peroxidases
- Covalent Heme Formation in Peroxidases
- Experimental Approach
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The initial step in the l-kynurenine pathway – which is the major pathway of l-tryptophan metabolism in biology – involves the oxidation of l-tryptophan to N-formylkynurenine. This is an O2-dependent process and is catalysed by one of two heme dioxygenase enzymes: tryptophan 2,3-dioxygenase (TDO) or indoleamine 2,3 dioxygenase (IDO).
The mechanism of tryptophan oxidation is of direct interest from a biomedical/pharmaceutical perspective because overexpression of certain dioxygenases is known in a number of tumour cells, which makes these dioxygenases very attractive targets for pharmacological intervention.
We are interested in the mechanism and structure of human dioxygenases, and we use various methodologies (spectroscopy, kinetics, crystallography) to tackle molecular-level questions about their biological function. We have an on-going collaboration (funded by the Wellcome Trust) with the University of Edinburgh on this project.
Substrate Binding and Catalytic Mechanism in Heme Peroxidases
(supported by BBSRC and The Wellcome Trust)
Heme peroxidases are an important class of iron-containing enzymes that catalyse the H2O2 -dependent oxidation of a variety of substrates. They contain an iron protoporphyrin IX group and are involved in a diverse range of biological functions, including antibacterial action and H2O2 detoxification.
The catalytic mechanism involves formation of a high-valent, ferryl heme intermediate followed by reduction of the oxidised heme by substrate.
The substrate specificity of these enzymes is very diverse and, although most peroxidases use small organic substrates, the chemical determinants that define the enzyme–substrate interaction are largely unknown.
Figure 1 shows the overlay of the structures ascorbate peroxidase (red) and cytochrome c peroxidase (green). The tyrosine residue of CcP overlays with the ascorbate group in APX, blocking the binding site. The binding site for cytochrome c binding is also shown.
We have recently made major progress in understanding substrate specificity in the heme peroxidases (collaborative work with Professor Peter Moody, Biochemistry).
First, we have determined the crystal structure of ascorbate peroxidase in complex with its physiological substrate, ascorbate (Figure 1).
This has revealed the location of the ascorbate binding site for the first time but has also made it possible to account for the different substrate specificities observed in other heme peroxidases ( e.g. cytochrome c peroxidase). We have also identified the binding interaction of ascorbate peroxidase with other, non-physiological substrates – these bind at a different location.
Figure 2 shows the structure of ascorbate peroxidate in complex with the aromatic substrate analogue salicylhydroxamic acid.
With BBSRC project grant and studentship support, we are now investigating how protein structure helps to define substrate specificity in both ascorbate peroxidase and cytochrome c peroxidase.
Heme peroxidases from mammalian sources (e.g. human) are distinguished from their plant and fungal counterparts by virtue of a covalently bound heme group. Figure 3 asks 'What is the mechanism of these covalent links in mammalian heme peroxideses?' This is instead of the more usual iron protoporphyrin IX group.
With funding from The Wellcome Trust, we are interested in examining how formation of these covalent links occurs. To do this, we use HPLC and mass spectrometry together with protein engineering, kinetics and X-ray crystallography. We have recently shown that autocatalytic formation of covalently-linked heme is possible in ascorbate peroxidase by placement of a methionine residue close to the heme.3 We are currently examining the mechanism of formation of this link.
We have also shown that radical formation at other positions in ascorbate peroxidase can, under certain conditions, lead to the formation of covalent heme-protein links through mechanisms that are analogous to those used in related heme enzymes.4 Collectively, this suggests that the strategic positioning of a suitable residue within a catalytically competent protein architecture is sufficient for heme cross-linking to occur. This provides a new slant on the way we think about these covalently-modified enzymes because it suggests that some proteins may need to be posed in an environment that specifically 'switches off' these radical processes.
The experimental approach adopted in our laboratory requires a multidisciplinary approach that includes chemical, biochemical, mechanistic, redox, spectroscopic and structural techniques. Much of this work is done within the Raven laboratory and with other groups at Leicester, for example with Professor Peter Moody, Biochemistry and with the Protein and Nucleic Acid Chemistry Laboratory, but we also collaborate within the UK and abroad with structural biologists, spectroscopists and other protein chemists. As a member of the Raven group, you can expect to be exposed to a number of different chemical, biochemical and molecular biological techniques and to interact with other scientists from other disciplines at a local, national and international level.
Kwon, H.; Basran, J.; Casadei, C. M.; Fielding, A. J. Schrader, T. E.; Ostermann, A.; Devos, J.; Aller, P.; Blakeley, M. P.; Moody, P. C. E.; Raven, E. L. Direct visualisation of a Fe(IV)-OH intermediate in a heme enzyme. Nature Comm. 2016, 7, Article number: 13445 (doi:10.1038/ncomms13445).
Nnamchi, C. I.; Parkin, G.; Efimov, I.; Basran, J.; Kwon, H.; Svistunekno, D. A.; Agirre, J.; Okolo, B. N.; Moneke, A.; Nwanguma, B. C.; Moody, P. C. E.; Raven, E. L. Structural characterisation of a heme peroxidase from Sorghum. J. Biol. Inorg. Chem. 2016, 21, 63-70.
Yuan, X.; Rietzschel, N.; Kwon, H.; Da Dilva, A. B. W. N.; Hanna, D.; Phillips, J.; Raven, E. L.; Reddi, A. R.; Hamza, I. Regulation of intracellular heme trafficking revealed by subcellular reporters. Proc. Natl. Acad. Sci. 2016, 113, E5144-5152.
Burton, M. J.; Kapetanaki, S. M.; Chernova, T.; Jamieson, A. G.; Dorlet, P.; Santolini, J.; Moody, P. C. E.; Mitcheson, J. S.; Davies, N. W.; Schmid, R.; Raven, E. L.; Storey, N. M. A heme-binding domain controls regulation of ATP-dependent potassium channels. Proc. Natl. Acad. Sci. 2016, 113, 3785. Published as a companion paper (back-to-back) with another heme paper from Prof Saito’s laboratory in Japan.
Booth, E. S.; Basran, J.; Lee, M.; Handa, S.; Raven, E. L. Substrate Oxidation by Indoleamine 2,3-Dioxygenase: Evidence for a Common Reaction Mechanism. J. Biol. Chem. 2015, 290, 30924-30930.
- Casadei, C. M.; Gumiero, A.; Clive L. Metcalfe; Murphy, E. J.; Basran, J.; Concilio, M. G.; Teixeira, S. C. M.; Schrader, T. E.; Fielding, A. J.; Ostermann, A.; Blakeley, M. P.; Raven, E. L.; Moody, P. C. E. Science, 2014, 345, 193-197. ‘Neutron cryo-crystallography captures the protonation state of ferryl heme in a peroxidase.’ This paper was selected for F1000Prime, as being of special significance in its field: F1000Prime link.
- Jenner, M.; Ellis, J.; Huang, W.-C.; Raven, E. L.; Roberts, G. C. R.; Oldham, N. J. Angew. Chemie. Int Ed, 2011, 50, 8291-8294. ‘Detection of Open and Closed Conformations of NADPH-Cytochrome P450 Reductase by Electrospray Ionisation-Ion Mobility-Mass Spectrometry’.
- Efimov, I.; Badyal, S. K.; Metcalfe, C. L.; Macdonald, I. K.; Gumiero, A.; Raven, E. L.; Moody, P. C. E. J. Am. Chem. Soc. 2011, 133, 15376-15383.
‘Proton delivery to ferryl heme in a heme peroxidase: enzymatic use of the Grotthuss mechanism.’
- Basran, J.; Efimov, I.; Chauhan, N.; Thackray, S. J.; Krupa, J.; Eaton, G.; Griffith, G. A.; Mowat, C. G.; Handa, S.; Raven, E. L. J. Am. Chem. Soc. 2011, 133, 16251-16257.
‘The mechanism of formation of N-formylkynurenine by heme deoxygenates.’
- Murphy, E. J.; Metcalfe, C. L.; Nnamchi, C.; Moody, P. C. E.; Raven, E. L. FEBS Journal, 2012, 279,1632-1639.
‘Crystal structures of guaiacol and phenol bound to a heme peroxidase.’
- Efimov, I.; Basran, J.; Chauhan, N.; Sun, X.; Chapman, S. K.; Mowat, C. G.; Raven, E. L. J. Am. Chem. Soc. 2012, 134, 3034-3041.
‘The mechanism of substrate inhibition in indoleamine 2,3-dioxygenase.’
- Chauhan, N.; Basran, J.; Rafice, S.; Efimov, I.; Millett, E. S.; Mowat, C. G.; Moody, P. C. E.; Handa, S.; Raven, E. L. FEBS. J. 2012, 279, 4501-4509.
‘How is the distal pocket of a heme protein optimized for binding of tryptophan?’
- Huang, W.-C.; Ellis, J. E.; Moody, P. C. E; Raven, E. L.; Roberts, G. C. R. Structure, 2013, 21, 1-9.
‘Redox-linked domain movements in the catalytic cycle of cytochrome P450 reductase.’
- Efimov, I.; Parkin, G.; Millett, E. S.; Glenday, J.; Chan, C. K.; Weedon, H.; Randhawa, H.; Basran, J. Raven, E. L. FEBS Lett. 2014, 588, 701-704.
‘A simple method for the determination of reduction potentials in heme proteins.’
- Gumiero, A.; Metcalfe, C. L.; Pearson, A. R.; Raven, E. L.; Moody, P. C. E. J. Biol. Chem. 2011, 286, 1260-1268. ‘The nature of the ferryl heme in Compounds I and II.’
Gumiero, A.; Murphy, E. J.; Metcalfe, C. L.; Moody, P. C. E.; Raven, E. L. Arch. Biochem. Biophys. 2010, 500, 13-20. Special issue of peroxidase chemistry. ‘An analysis of substrate binding interactions in the heme peroxidase enzymes: a structural perspective.’
Davydov, R.; Chauhan, N.; Thackray, S. J.; Anderson, J. L.; Papadopoulou, N.; Mowat, C.; Chapman, S. K.; Raven, E. L.; Hoffman, B. M. J. Amer. Chem. Soc., 2010, 132, 5494-5500.
‘Probing the ternary complexes of indoleamine and tryptophan 2,3-dioxygenases by cryoreduction EPR and ENDOR spectroscopy.’
Raven, E. L.; Robinson, N., Nat. Prod. Rep., 2010, 27, 635-636. Metals in cells themed issue.
Ortiz de Montellano, P. M.; Raven, E. L., Nat. Prod. Rep. 2007, 24, 499. The chemistry and biochemistry of heme proteins. .
Pipirou, Z.; Bottrill, A. R.; Metcalfe, C. M.; Mistry, S. C.; Badyal, S. K.; Rawlings, B. J.; Raven, E. L. Biochemistry 2007, 46, 2174-2180. ‘Autocatalytic Formation of a Covalent Link between Tryptophan 41 and the Heme in Ascorbate Peroxidase.’
Efimov, I.; Papadopoulou, N. D.; McLean, K. J.; Badyal, S. K.; Macdonald, I. K.; Munro, A. W.; Moody, P. C. E.; Raven, E. L. Biochemistry 2007, 46, 8017-8023. ‘The Redox Properties of Ascorbate Peroxidase.’
Metcalfe, C. L.; Daltrop, O.; Ferguson, S. J.; Raven, E. L. Biochem. J. 2007, 408, 355-361. ‘Tuning the formation of a covalent heme-protein link by selection of reductive or oxidative conditions as exemplified by ascorbate peroxidase.’
Pipirou, Z.; Bottrill, A. R.; Svistunenko, D. A.; Efimov, I.; Basran, J.; Mistry, S. C.; Cooper, C. E.; Raven, E. L. Biochemistry 2007, 46, 13269-13278. ’The reactivity of heme in biological systems: autocatalytic formation of both tyrosine-heme and tryptophan-heme covalent links in a single protein architecture.’
Metcalfe, C. L.; Macdonald, I. K.; Murphy, E. J.; Brown, K. A.; Raven, E. L.; Moody, P. C. E. J. Biol. Chem. 2008, J. Biol. Chem. 283, 6193-6200. ‘The tuberculosis prodrug isoniazid bound to activating peroxidases.’
Badyal, S. K.; Metcalfe, C. L.; Basran, J.; Efimov, I.; Moody, P. C. E.; Raven, E. L. Biochemistry 2008, 47, 4403-4409. ‘Iron oxidation state as a molecular trigger controlling active site structure in a heme peroxidase.’
Chauhan, N.; Basran, J.; Efimov, I.; Svistunenko, D. A.; Seward, H. E.; Peter C. E. Moody, Raven, E. L. Biochemistry 2008, 47, 4752-4760. Back to back with below. ‘The role of serine 167 in human indoleamine 2,3-dioxygenase: a comparison with tryptophan 2,3-dioxygenase.’
Basran, J.; Rafice, S.; Chauhan, N.; Efimov, I.; Cheesman, M. R.; Ghamsari, L.; Raven, E. L. Biochemistry 2008, 47, 4761-4769. Back to back with above. ‘A kinetic, spectroscopic and redox study of human tryptophan 2,3, dioxygenase.’
Murphy, E. J.; Metcalfe, C. L.; Basran, J.; Moody, P. C. E.; Raven, E. L. Biochemistry 2008, 47, 13933-13941.
‘Engineering the substrate specificity and reactivity of a heme protein: creation of an ascorbate binding site in cytochrome c peroxidase’.
Chauhan, N.; Thackray, S. J.; Rafice, S. A.; Eaton, G.; Lee, M.; Efimov, I.; Basran, J.; Jenkins, P. R.; Mowat, C. G.; Chapman, S. K.; Raven, E. L. J. Amer. Chem. Soc., 2009, 131, 4186-4187.
‘Reassessment of the Reaction Mechanism in the Heme Dioxygenases.’
Pipirou, Z.; Guallar, V.; Basran, J.; Metcalfe, C. L.; Murphy, E. J.; Bottrill, A. R.; Mistry, S. C.; Raven, E. L. Biochemistry, 2009, 48, 3593-3599.
‘Peroxide-dependent Formation of a Covalent Link between Trp51 and the Heme in Cytochrome c Peroxidase.’
- Badyal, S. K.; Eaton, G.; Mistry, S.; Pipirou, Z.; Basran, J.; Metcalfe, C. L.; Gumiero, A.; Handa, S.; Moody, P. C. E.; Raven, E. L. Biochemistry 2009, 48, 4738-4746.
‘Evidence for Heme Oxygenase Activity in a Heme Peroxidase’.