I03-Macromolecular Crystallography
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Samuel L.
Freeman
,
Vera
Skafar
,
Hanna
Kwon
,
Alistair J.
Fielding
,
Peter C. E.
Moody
,
Alejandra
Martínez
,
Federico
Issoglio
,
Lucas
Inchausti
,
Pablo
Smircich
,
Ari
Zeida
,
Lucía
Piacenza
,
Rafael
Radi
,
Emma L.
Raven
Diamond Proposal Number(s):
[23269]
Open Access
Abstract: The protozoan parasite Trypanosoma cruzi is the causative agent of American trypanosomiasis, otherwise known as Chagas disease. To survive in the host, the T. cruzi parasite needs antioxidant defence systems. One of these is a hybrid heme peroxidase, the T. cruzi ascorbate peroxidase-cytochrome c peroxidase enzyme (TcAPx-CcP). TcAPx-CcP has high sequence identity to members of the class I peroxidase family, notably ascorbate peroxidase (APX) and cytochrome c peroxidase (CcP), as well as a mitochondrial peroxidase from Leishmania major (LmP). The aim of this work was to solve the structure and examine the reactivity of the TcAPx-CcP enzyme. Low temperature electron paramagnetic resonance (EPR) spectra support the formation of an exchange-coupled [Fe(IV)=O Trp233•+] Compound I radical species, analogous to that used in CcP and LmP. We demonstrate that TcAPx-CcP is similar in overall structure to APX and CcP, but there are differences in the substrate binding regions. Furthermore, the electron transfer pathway from cytochrome c to the heme in CcP and LmP is preserved in the TcAPx-CcP structure. Integration of steady state kinetic experiments, molecular dynamic simulations, and bioinformatic analyses indicates that TcAPx-CcP preferentially oxidizes cytochrome c, but is still competent for oxididation of ascorbate. The results reveal that TcAPx-CcP is a credible cytochrome c peroxidase which can also bind and use ascorbate in host cells, where concentrations are in the millimolar range. Thus, kinetically and functionally TcAPx-CcP can be considered a hybrid peroxidase.
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Jun 2022
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I03-Macromolecular Crystallography
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Abstract: Campylobacter jejuni is a pathogenic bacteria that causes gastrointestinal disorders and is thus of great importance. Phosphorylating Glyceraldehyde 3-phosphate dehydrogenase (GAPDH) is a ubiquitous cellular enzyme that has a well-defined role in glycolysis and other pathways where it catalyses the oxidative phosphorylation of glyceraldehyde 3-phosphate (2-hydroxy-3-oxopropyl dihydrogen phosphate) to 1,3-Bisphosphoglycerate ((2-Hydroxy-3-phosphonooxy-propanoyloxy)phosphonic acid). The C. jejuni genome encodes a single GAPDH enzyme (CjGAPDH) which displays dual (NAD/NADP) coenzyme specificity. NAD-specific GAPDHs are given the EC classification of 1.2.1.12, whereas NADP-specific GAPDHs are classed as 1.2.1.13. GAPDH's with dual specificity are in the class 1.2.1.59. Here we present the X-ray crystal structure of this enzyme (at 2.25 Å), this comprises superimposed structures of NAD- and NADP- complexes showing the structural adaptation that allows this dual specificity, and we consider this in the context of the pathogen's metabolism. There are no previous reports of EC 1.2.1.59 structures that compare the binding of the two co-enzymes. Furthermore, we also report the structure (at 2.05 Å) of the enzyme complexed with the nucleoside ADP and consider this with respect to the reported “moonlighting” activities of GAPDH.
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Jun 2021
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Hanna
Kwon
,
Jaswir
Basran
,
Chinar
Pathak
,
Mahdi
Hussain
,
Samuel L.
Freeman
,
Alistair J.
Fielding
,
Anna J.
Bailey
,
Natalia
Stefanou
,
Hazel A.
Sparkes
,
Takehiko
Tosha
,
Keitaro
Yamashita
,
Kunio
Hirata
,
Hironori
Murakami
,
Go
Ueno
,
Hideo
Ago
,
Kensuke
Tono
,
Masaki
Yamamoto
,
Hitomi
Sawai
,
Yoshitsugu
Shiro
,
Hiroshi
Sugimoto
,
Emma
Raven
,
Peter C. E.
Moody
Open Access
Abstract: Oxygen activation in all heme enzymes requires the formation of high oxidation states of iron, usually referred to as ferryl heme. There are two known intermediates: Compound I and Compound II. The nature of the ferryl heme – and whether it is an Fe IV =O or Fe IV ‐OH species – is important for controlling reactivity across groups of heme enzymes. The most recent evidence for Compound I indicates that the ferryl heme is an unprotonated Fe IV =O species. For Compound II, the nature of the ferryl heme is not unambiguously established. Here, we report 1.06 Å and 1.50 Å crystal structures for Compound II intermediates in cytochrome c peroxidase (C c P) and ascorbate peroxidase (APX), collected using the X‐ray free electron laser at SACLA. The structures reveal differences between the two peroxidases. The iron‐oxygen bond length in C c P (1.76 Å) is notably shorter than in APX (1.87 Å). The results indicate that the ferryl species is finely tuned across Compound I and Compound II species in closely related peroxidase enzymes. We propose that this fine‐tuning is linked to the functional need for proton delivery to the heme.
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Apr 2021
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I03-Macromolecular Crystallography
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Mark J
Burton
,
Joel
Cresser-Brown
,
Morgan
Thomas
,
Nicola
Portolano
,
Jaswir
Basran
,
Samuel L.
Freeman
,
Hanna
Kwon
,
Andrew R.
Bottrill
,
Manuel J
Llansola-Portoles
,
Andrew A
Pascal
,
Rebekah
Jukes-Jones
,
Tatyana
Chernova
,
Ralf
Schmid
,
Noel W.
Davies
,
Nina M.
Storey
,
Pierre
Dorlet
,
Peter C. E.
Moody
,
John S
Mitcheson
,
Emma L.
Raven
Diamond Proposal Number(s):
[14692]
Abstract: The ether-à-go-go (EAG) family of voltage gated K+ channels are important regulators of neuronal and cardiac action potential firing (excitability) and have major roles in human diseases such as epilepsy, schizophrenia, cancer and sudden cardiac death. A defining feature of EAG (Kv10-12) channels is a highly conserved domain on the amino-terminus, known as the eag-domain, consisting of a PAS domain capped by a short sequence containing an amphipathic helix (Cap-domain). The PAS and Cap domains are both vital for the normal function of EAG channels. Using heme-affinity pull-down assays and proteomics of lysates from primary cortical neurons, we identified that an EAG channel, hERG3 (Kv11.3), binds to heme. In whole cell electrophysiology experiments, we identified that heme inhibits hERG3 channel activity. In addition, we expressed the Cap and PAS domain of hERG3 in E.coli and, using spectroscopy and kinetics, identified the PAS domain as the location for heme binding. The results identify heme as a regulator of hERG3 channel activity. These observations are discussed in the context of the emerging role for heme as a regulator of ion channel activity in cells.
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Jul 2020
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I02-Macromolecular Crystallography
I03-Macromolecular Crystallography
I04-1-Macromolecular Crystallography (fixed wavelength)
I04-Macromolecular Crystallography
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Diamond Proposal Number(s):
[14692, 10369, 8359, 6388, 310]
Abstract: Aerobic organisms have evolved to activate oxygen from the atmosphere, which allows them to catalyze the oxidation of different kinds of substrates. This activation of oxygen is achieved by a metal center (usually iron or copper) buried within a metalloprotein. In the case of iron-containing heme enzymes, the activation of oxygen is achieved by formation of transient iron-oxo (ferryl) intermediates; these intermediates are called Compound I and Compound II. The Compound I and II intermediates were first discovered in the 1930s in horseradish peroxidase, and it is now known that these same species are used across the family of heme enzymes, which include all of the peroxidases, the heme catalases, the P450s, cytochrome c oxidase, and NO synthase. Many years have passed since the first observations, but establishing the chemical nature of these transient ferryl species remains a fundamental question that is relevant to the reactivity, and therefore the usefulness, of these species in biology.
This Account summarizes experiments that were conceived and conducted at Leicester and presents our ideas on the chemical nature, stability, and reactivity of these ferryl heme species. We begin by briefly summarizing the early milestones in the field, from the 1940s and 1950s. We present comparisons between the nature and reactivity of the ferryl species in horseradish peroxidase, cytochrome c peroxidase, and ascorbate peroxidase; and we consider different modes of electron delivery to ferryl heme, from different substrates in different peroxidases.
We address the question of whether the ferryl heme is best formulated as an (unprotonated) FeIV═O or as a (protonated) FeIV–OH species. A range of spectroscopic approaches (EXAFS, resonance Raman, Mossbauer, and EPR) have been used over many decades to examine this question, and in the last ten years, X-ray crystallography has also been employed. We describe how information from all of these studies has blended together to create an overall picture, and how the recent application of neutron crystallography has directly identified protonation states and has helped to clarify the precise nature of the ferryl heme in cytochrome c peroxidase and ascorbate peroxidase. We draw comparisons between the Compound I and Compound II species that we have observed in peroxidases with those found in other heme systems, notably the P450s, highlighting possible commonality across these heme ferryl systems. The identification of proton locations from neutron structures of these ferryl species opens the door for understanding the proton translocations that need to occur during O–O bond cleavage.
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Jan 2018
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I02-Macromolecular Crystallography
I03-Macromolecular Crystallography
I04-1-Macromolecular Crystallography (fixed wavelength)
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Diamond Proposal Number(s):
[14692, 10369, 8359]
Open Access
Abstract: The multiprotein complex C1 initiates the classical pathway of complement activation on binding to antibody–antigen complexes, pathogen surfaces, apoptotic cells, and polyanionic structures. It is formed from the recognition subcomponent C1q and a tetramer of proteases C1r2C1s2 as a Ca2+-dependent complex. Here we have determined the structure of a complex between the CUB1-EGF-CUB2 fragments of C1r and C1s to reveal the C1r–C1s interaction that forms the core of C1. Both fragments are L-shaped and interlock to form a compact antiparallel heterodimer with a Ca2+ from each subcomponent at the interface. Contacts, involving all three domains of each protease, are more extensive than those of C1r or C1s homodimers, explaining why heterocomplexes form preferentially. The available structural and biophysical data support a model of C1r2C1s2 in which two C1r-C1s dimers are linked via the catalytic domains of C1r. They are incompatible with a recent model in which the N-terminal domains of C1r and C1s form a fixed tetramer. On binding to C1q, the proteases become more compact, with the C1r-C1s dimers at the center and the six collagenous stems of C1q arranged around the perimeter. Activation is likely driven by separation of the C1r-C1s dimer pairs when C1q binds to a surface. Considerable flexibility in C1s likely facilitates C1 complex formation, activation of C1s by C1r, and binding and activation of downstream substrates C4 and C4b-bound C2 to initiate the reaction cascade.
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Jan 2018
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I04-Macromolecular Crystallography
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Hanna
Kwon
,
Jaswir
Basran
,
Cecilia M.
Casadei
,
Alistair J.
Fielding
,
Tobias E.
Schrader
,
Andreas
Ostermann
,
Juliette M.
Devos
,
Pierre
Aller
,
Matthew P.
Blakeley
,
P. C. E.
Moody
,
Emma L.
Raven
Diamond Proposal Number(s):
[10369]
Open Access
Abstract: Catalytic heme enzymes carry out a wide range of oxidations in biology. They have in common a mechanism that requires formation of highly oxidized ferryl intermediates. It is these ferryl intermediates that provide the catalytic engine to drive the biological activity. Unravelling the nature of the ferryl species is of fundamental and widespread importance. The essential question is whether the ferryl is best described as a Fe(IV)=O or a Fe(IV)–OH species, but previous spectroscopic and X-ray crystallographic studies have not been able to unambiguously differentiate between the two species. Here we use a different approach. We report a neutron crystal structure of the ferryl intermediate in Compound II of a heme peroxidase; the structure allows the protonation states of the ferryl heme to be directly observed. This, together with pre-steady state kinetic analyses, electron paramagnetic resonance spectroscopy and single crystal X-ray fluorescence, identifies a Fe(IV)–OH species as the reactive intermediate. The structure establishes a precedent for the formation of Fe(IV)–OH in a peroxidase.
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Nov 2016
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I04-1-Macromolecular Crystallography (fixed wavelength)
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Umakhanth
Venkatraman Girija
,
Christopher
Furze
,
Alex
Gingras
,
Takayuki
Yoshizaki
,
Katsuki
Ohtani
,
Jamie E
Marshall
,
A Katrine
Wallis
,
Wilhelm J
Schwaeble
,
Mohammed
El-Mezgueldi
,
Daniel A
Mitchell
,
Peter
Moody
,
Nobutaka
Wakamiya
,
Russell
Wallis
Diamond Proposal Number(s):
[8359]
Open Access
Abstract: Collectin-K1 (CL-K1, or CL-11) is a multifunctional Ca2+-dependent lectin with roles in innate immunity, apoptosis and embryogenesis. It binds to carbohydrates on pathogens to activate the lectin pathway of complement and together with its associated serine protease MASP-3 serves as a guidance cue for neural crest development. High serum levels are associated with disseminated intravascular coagulation, where spontaneous clotting can lead to multiple organ failure. Autosomal mutations in the CL-K1 or MASP-3 genes cause a developmental disorder called 3MC (Carnevale, Mingarelli, Malpuech and Michels) syndrome, characterised by facial, genital, renal and limb abnormalities. One of these mutations (Gly204Ser in the CL-K1 gene) is associated with undetectable levels of protein in the serum of affected individuals.
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Dec 2015
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I03-Macromolecular Crystallography
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Chukwudi I.
Nnamchi
,
Gary
Parkin
,
Igor
Efimov
,
Jaswir
Basran
,
Hanna
Kwon
,
Dimitri A.
Svistunenko
,
Jon
Agirre
,
Bartholomew N.
Okolo
,
Anene
Moneke
,
Bennett C.
Nwanguma
,
Peter
Moody
,
Emma L.
Raven
Diamond Proposal Number(s):
[6388]
Open Access
Abstract: A cationic class III peroxidase from Sorghum
bicolor was purified to homogeneity. The enzyme contains
a high-spin heme, as evidenced by UV–visible spectroscopy
and EPR. Steady state oxidation of guaiacol was
demonstrated and the enzyme was shown to have higher
activity in the presence of calcium ions. A FeIII/FeII reduction
potential of −266 mV vs NHE was determined.
Stopped-flow experiments with H2O2 showed formation
of a typical peroxidase Compound I species, which converts
to Compound II in the presence of calcium. A crystal
structure of the enzyme is reported, the first for a sorghum
peroxidase. The structure reveals an active site that
is analogous to those for other class I heme peroxidase, and
a substrate binding site (assigned as arising from binding of indole-3-acetic acid) at the γ-heme edge. Metal binding
sites are observed in the structure on the distal (assigned
as a Na+ ion) and proximal (assigned as a Ca2+) sides of
the heme, which is consistent with the Ca2+-dependence of
the steady state and pre-steady state kinetics. It is probably
the case that the structural integrity (and, thus, the catalytic
activity) of the sorghum enzyme is dependent on metal ion
incorporation at these positions.
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Dec 2015
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I02-Macromolecular Crystallography
I03-Macromolecular Crystallography
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Diamond Proposal Number(s):
[6388]
Abstract: The Parkinsonism-associated protein DJ-1 has been suggested to activate the Cu–Zn superoxide dismutase (SOD1) by providing its copper cofactor. The structural and chemical means by which DJ-1 could support this function is unknown. In this study, we characterize the molecular interaction of DJ-1 with Cu(I). Mass spectrometric analysis indicates binding of one Cu(I) ion per DJ-1 homodimer. The crystal structure of DJ-1 bound to Cu(I) confirms metal coordination through a docking accessible biscysteinate site formed by juxtaposed cysteine residues at the homodimer interface. Spectroscopy in crystallo validates the identity and oxidation state of the bound metal. The measured subfemtomolar dissociation constant (Kd = 6.41 × 10–16 M) of DJ-1 for Cu(I) supports the physiological retention of the metal ion. Our results highlight the requirement of a stable homodimer for copper binding by DJ-1. Parkinsonism-linked mutations that weaken homodimer interactions will compromise this capability.
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Oct 2013
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