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King MF, Wilson AM, López-García M, Proctor J, Peckham DG, Clifton IJ, Dancer SJ, Noakes CJ. Why is mock care not a good proxy for predicting hand contamination during patient care? J Hosp Infect 2020; 109:44-51. [PMID: 33271214 DOI: 10.1016/j.jhin.2020.11.016] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2020] [Revised: 11/19/2020] [Accepted: 11/19/2020] [Indexed: 01/12/2023]
Abstract
BACKGROUND Healthcare worker (HCW) behaviours, such as the sequence of their contacts with surfaces and hand hygiene moments, are important for understanding disease transmission. AIM To propose a method for recording sequences of HCW behaviours during mock vs actual procedures, and to evaluate differences for use in infection risk modelling and staff training. METHODS Procedures for three types of care were observed under mock and actual settings: intravenous (IV) drip care, observational care and doctors' rounds on a respiratory ward in a university teaching hospital. Contacts and hand hygiene behaviours were recorded in real-time using either a handheld tablet or video cameras. FINDINGS Actual patient care demonstrated 70% more surface contacts than mock care. It was also 2.4 min longer than mock care, but equal in terms of patient contacts. On average, doctors' rounds took 7.5 min (2.5 min for mock care), whilst auxiliary nurses took 4.9 min for observational care (2.4 min for mock care). Registered nurses took 3.2 min for mock IV care and 3.8 min for actual IV care; this translated into a 44% increase in contacts. In 51% of actual care episodes and 37% of mock care episodes, hand hygiene was performed before patient contact; in comparison, 15% of staff delivering actual care performed hand hygiene after patient contact on leaving the room vs 22% for mock care. The number of overall touches in the patient room was a modest predictor of hand hygiene. Using a model to predict hand contamination from surface contacts for Staphylococcus aureus, Escherichia coli and norovirus, mock care underestimated micro-organisms on hands by approximately 30%.
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Affiliation(s)
- M F King
- School of Civil Engineering, University of Leeds, Leeds, UK.
| | - A M Wilson
- Department of Community, Environment and Policy, University of Arizona, Tucson, AZ, USA
| | | | - J Proctor
- School of Civil Engineering, University of Leeds, Leeds, UK
| | - D G Peckham
- School of Civil Engineering, University of Leeds, Leeds, UK; Leeds Cystic Fibrosis Trust Strategic Research Centre, University of Leeds, Leeds, UK
| | - I J Clifton
- School of Civil Engineering, University of Leeds, Leeds, UK; Leeds Cystic Fibrosis Trust Strategic Research Centre, University of Leeds, Leeds, UK; Leeds Institute of Medical Research at St. James's, University of Leeds, Leeds, UK; Adult Cystic Fibrosis Unit, St. James's University Hospital, Leeds, UK
| | - S J Dancer
- School of Applied Sciences, Edinburgh Napier University, Edinburgh, UK; Department of Microbiology, Hairmyres Hospital, NHS Lanarkshire, Glasgow, UK
| | - C J Noakes
- School of Civil Engineering, University of Leeds, Leeds, UK
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2
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Spoletini G, Etherington C, Shaw N, Clifton IJ, Denton M, Whitaker P, Peckham DG. Use of ceftazidime/avibactam for the treatment of MDR Pseudomonas aeruginosa and Burkholderia cepacia complex infections in cystic fibrosis: a case series. J Antimicrob Chemother 2019; 74:1425-1429. [DOI: 10.1093/jac/dky558] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2018] [Revised: 12/05/2018] [Accepted: 12/06/2018] [Indexed: 12/26/2022] Open
Affiliation(s)
- G Spoletini
- The Leeds Regional Adult Cystic Fibrosis Centre, St James’s University Hospital, Leeds Teaching Hospital NHS Trust, Leeds, UK
- Leeds Institute of Medical Research, University of Leeds, Leeds, UK
| | - C Etherington
- The Leeds Regional Adult Cystic Fibrosis Centre, St James’s University Hospital, Leeds Teaching Hospital NHS Trust, Leeds, UK
| | - N Shaw
- The Leeds Regional Adult Cystic Fibrosis Centre, St James’s University Hospital, Leeds Teaching Hospital NHS Trust, Leeds, UK
| | - I J Clifton
- The Leeds Regional Adult Cystic Fibrosis Centre, St James’s University Hospital, Leeds Teaching Hospital NHS Trust, Leeds, UK
| | - M Denton
- The Leeds Regional Adult Cystic Fibrosis Centre, St James’s University Hospital, Leeds Teaching Hospital NHS Trust, Leeds, UK
- Department of Microbiology, Leeds General Infirmary, Leeds Teaching Hospital NHS Trust, Leeds, UK
| | - P Whitaker
- The Leeds Regional Adult Cystic Fibrosis Centre, St James’s University Hospital, Leeds Teaching Hospital NHS Trust, Leeds, UK
| | - D G Peckham
- The Leeds Regional Adult Cystic Fibrosis Centre, St James’s University Hospital, Leeds Teaching Hospital NHS Trust, Leeds, UK
- Leeds Institute of Medical Research, University of Leeds, Leeds, UK
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Hodgekiss C, Edwards A, Clifton IJ. P232 Communication and End of Life Care (EoLC) in People with Respiratory Disease. Thorax 2012. [DOI: 10.1136/thoraxjnl-2012-202678.293] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
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5
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Clifton IJ, Scarsbrook AF, Muers MF. No lung cancer at resection of PET positive lesions: an audit of the lung cancer multidisciplinary team. Eur Respir J 2009; 33:941-2. [PMID: 19336598 DOI: 10.1183/09031936.00176708] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
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6
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Hamed RB, Batchelar ET, Clifton IJ, Schofield CJ. Mechanisms and structures of crotonase superfamily enzymes – How nature controls enolate and oxyanion reactivity. Cell Mol Life Sci 2008; 65:2507-27. [DOI: 10.1007/s00018-008-8082-6] [Citation(s) in RCA: 93] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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7
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Duke EM, Hadfield A, Martin JL, Clifton IJ, Hajdu J, Johnson LN, Reid GP, Trentham DR, Bruce I, Fleet GW. Towards time-resolved diffraction studies with glycogen phosphorylase. Ciba Found Symp 2007; 161:75-86; discussion 86-90. [PMID: 1814698 DOI: 10.1002/9780470514146.ch6] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Laue diffraction with high intensity, broad-spectrum synchrotron radiation sources allows three-dimensional data sets on protein crystals to be recorded in seconds or milliseconds and opens the way for time-resolved studies on dynamic events in crystals. This chapter briefly reviews the field and describes progress towards time-resolved studies with glycogen phosphorylase. Methods for the synchronization of the start of reaction with the start of data collection have been developed for the phosphorolytic reaction of glycogen phosphorylase. The compound 3,5-dinitrophenylphosphate is photolabile, yielding Pi and the by-product, 3,5-dinitrophenol, which is non-reactive with the enzyme. Spectroscopic studies show that the compound has good quantum yield and that photolysis is rapid (greater than 1000 s-1). Release of the dinitrophenylate anion, following a pulse of light from a xenon flash lamp, has been monitored with a diode array spectrophotometer specially adapted for measurements on crystals. In a laboratory X-ray experiment with crystals of glycogen phosphorylase b, release of Pi and formation of the enzyme-product complex have been demonstrated. The way is now open for Laue diffraction studies on the catalytic reaction in the crystal.
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Affiliation(s)
- E M Duke
- Laboratory of Molecular Biophysics, Oxford, UK
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8
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Clifton IJ, Morton AM, Peckham DG, Conway SP. An unusual cause of hypercalcaemia in a patient with cystic fibrosis. J Cyst Fibros 2007; 6:369-70. [PMID: 17267294 DOI: 10.1016/j.jcf.2006.12.004] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2006] [Revised: 10/16/2006] [Accepted: 12/14/2006] [Indexed: 11/19/2022]
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9
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Clifton IJ, Kastelik JA, Peckham DG, Hale A, Denton M, Etherington C, Conway SP. Ten years of viral and non-bacterial serology in adults with cystic fibrosis. Epidemiol Infect 2007; 136:128-34. [PMID: 17352838 PMCID: PMC2870771 DOI: 10.1017/s0950268807008278] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Viral infections are associated with pulmonary exacerbations in children with cystic fibrosis (CF), but few studies have addressed the frequency in adults. This paper investigates the frequency and impact of viral infections in adults with CF receiving intravenous antibiotics. Pre- and post-treatment spirometry, inflammatory markers and antibody titres against influenza A, influenza B, adenovirus, respiratory syncytial virus, Mycoplasma pneumoniae, Chlamydia psittaci, and Coxiella burnetti were analysed over a 10-year period. Non-bacterial infections were identified in 5.1% of 3156 courses of treatment. The annual incidence of admissions per patient associated with viral infection was 4.9%. The presence of viral infection in association with a pulmonary exacerbation did not adversely affect lung function or inflammatory markers in the short term. Adults with CF have a lower incidence of respiratory viral infections associated with pulmonary exacerbations requiring intravenous antibiotics compared to children and infants with CF.
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Affiliation(s)
- I J Clifton
- Regional Cystic Fibrosis Unit, Seacroft Hospital, Leeds, UK.
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10
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Ramachandran S, Clifton IJ, Collyns TA, Watson JP, Pearson SB. The treatment of spinal tuberculosis: a retrospective study. Int J Tuberc Lung Dis 2005; 9:541-4. [PMID: 15875926] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/02/2023] Open
Abstract
BACKGROUND There are conflicting guidelines and variations in clinical practice in the management of bone tuberculosis (TB), including spinal TB. A case who received 6 months of treatment in line with current British Thoracic Society (BTS) guidelines, and subsequently relapsed, prompted a survey of treatment and outcomes of spinal and other bone TB. METHODS A retrospective study examining the clinical features, treatment duration and outcome of patients presenting with spinal and other bone TB to the Leeds Teaching Hospitals National Health Service Trust, between 1998 and 2002. RESULTS Forty-two patients were identified. Notes from 34 patients with spinal TB and four patients with TB of other bones were reviewed. Of eight patients who received 6 months of therapy, five relapsed. Of 30 patients who received treatment for 9 months or longer, none relapsed (P < 0.05). CONCLUSION Six months of treatment, as currently recommended by the BTS, may be inadequate for bone TB, including spinal TB.
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Affiliation(s)
- S Ramachandran
- Department of Respiratory Medicine, Leeds General Infirmary, Leeds, United Kingdom
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11
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Clifton IJ, Morton AM, Ambrose NS, Peckham DG, Conway SP. Treatment of resistant distal intestinal obstruction syndrome with a modified antegrade continence enema procedure. J Cyst Fibros 2004; 3:273-5. [PMID: 15698947 DOI: 10.1016/j.jcf.2004.06.008] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2003] [Accepted: 06/18/2004] [Indexed: 11/22/2022]
Abstract
We report a case of a patient with CF who had a long history of recurrent distal intestinal obstruction syndrome. She had been treated with conventional treatment including gastrografin, n-acetyl cysteine, Klean prep and Picolax. She underwent a modified antegrade continence enema procedure. She currently irrigates her conduit every 2-3 days. She has had no further symptoms of distal intestinal obstruction syndrome.
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Affiliation(s)
- I J Clifton
- Regional Adult Cystic Fibrosis Unit, Seacroft Hospital, Leeds, UK
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12
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Wilmouth RC, Edman K, Neutze R, Wright PA, Clifton IJ, Schneider TR, Schofield CJ, Hajdu J. Snapshots of serine protease catalysis: unravelling the mechanism of deacylation. Acta Crystallogr A 2002. [DOI: 10.1107/s010876730208618x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
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13
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Wright PA, Wilmouth RC, Clifton IJ, Schofield CJ. Kinetic and crystallographic analysis of complexes formed between elastase and peptides from β-casein. ACTA ACUST UNITED AC 2001; 268:2969-74. [PMID: 11358514 DOI: 10.1046/j.1432-1327.2001.02186.x] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Human beta-casomorphin-7 (NH2-Tyr-Pro-Phe-Val-Glu-Pro-Ile-CO2H) is a naturally occurring peptide inhibitor of elastase that has been shown to form an acyl-enzyme complex stable enough for X-ray crystallographic analysis at pH 5. To investigate the importance of the N-terminal residues of the beta-casomorphin-7 peptide for the inhibition of elastase, kinetic and crystallographic analyses were undertaken to identify the minimum number of residues required for effective formation of a stable complex between truncated beta-casomorphin-7 peptides and porcine pancreatic elastase (PPE). The results clearly demonstrate that significant inhibition of PPE can be effected by simple tri-, tetra-and pentapeptides terminating in a carboxylic acid. These results also suggest that in vivo regulation of protease activity could be mediated via short peptides as well as by proteins. Crystallographic analysis of the complex formed between N-acetyl-Val-Glu-Pro-Ile-CO2H and PPE at pH 5 (to 1.67 A resolution) revealed an active site water molecule in an analogous position to that observed in the PPE/beta-casomorphin-7 structure supportive of its assignment as the 'hydrolytic water' in the deacylation step of serine protease catalysis.
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Affiliation(s)
- P A Wright
- The Dyson Perrins Laboratory and The Oxford Centre for Molecular Sciences, Oxford, UK
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14
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Ogle JM, Clifton IJ, Rutledge PJ, Elkins JM, Burzlaff NI, Adlington RM, Roach PL, Baldwin JE. Alternative oxidation by isopenicillin N synthase observed by X-ray diffraction. Chem Biol 2001; 8:1231-7. [PMID: 11755401 DOI: 10.1016/s1074-5521(01)00090-4] [Citation(s) in RCA: 42] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
BACKGROUND Isopenicillin N synthase (IPNS) catalyses formation of bicyclic isopenicillin N, precursor to all penicillin and cephalosporin antibiotics, from the linear tripeptide delta-(L-alpha-aminoadipoyl)-L-cysteinyl-D-valine. IPNS is a non-haem iron(II)-dependent enzyme which utilises the full oxidising potential of molecular oxygen in catalysing the bicyclisation reaction. The reaction mechanism is believed to involve initial formation of the beta-lactam ring (via a thioaldehyde intermediate) to give an iron(IV)-oxo species, which then mediates closure of the 5-membered thiazolidine ring. RESULTS Here we report experiments employing time-resolved crystallography to observe turnover of an isosteric substrate analogue designed to intercept the catalytic pathway at an early stage. Reaction in the crystalline enzyme-substrate complex was initiated by the application of high-pressure oxygen, and subsequent flash freezing allowed an oxygenated product to be trapped, bound at the iron centre. A mechanism for formation of the observed thiocarboxylate product is proposed. CONCLUSIONS In the absence of its natural reaction partner (the N-H proton of the L-cysteinyl-D-valine amide bond), the proposed hydroperoxide intermediate appears to attack the putative thioaldehyde species directly. These results shed light on the events preceding beta-lactam closure in the IPNS reaction cycle, and enhance our understanding of the mechanism for reaction of the enzyme with its natural substrate.
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Affiliation(s)
- J M Ogle
- The Dyson Perrins Laboratory, University of Oxford, UK
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15
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Clifton IJ, Hsueh LC, Baldwin JE, Harlos K, Schofield CJ. Structure of proline 3-hydroxylase. Evolution of the family of 2-oxoglutarate dependent oxygenases. Eur J Biochem 2001; 268:6625-36. [PMID: 11737217 DOI: 10.1046/j.0014-2956.2001.02617.x] [Citation(s) in RCA: 86] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Iron (II)/2-oxoglutarate (2-OG)-dependent oxygenases catalyse oxidative reactions in a range of metabolic processes including the hydroxylation of proline and lysine residues during the post-translational modification of collagen. 2-OG oxygenases commonly require ascorbate for full activity. In the vitamin C deficient disease, scurvy, reduced activity of 2-OG oxygenases results in impaired formation of collagen. Here we report the crystal structure of bacterial proline 3-hydroxylase from Streptomyces sp., an enzyme which hydroxylates proline at position 3, the first of a 2-OG oxygenase catalysing oxidation of a free alpha-amino acid. Structures were obtained for the enzyme in the absence of iron (to 2.3A resolution, R=20.2%, Rfree=25.3%) and that complexed to iron (II) (to 2.4A resolution, R=19.8%, Rfree=22.6%). The structure contains conserved motifs present in other 2-OG oxygenases including a 'jelly roll' beta strand core and residues binding iron and 2-oxoglutarate, consistent with divergent evolution within the extended family. The structure differs significantly from many other 2-OG oxygenases in possessing a discrete C-terminal helical domain. Analysis of the structure suggests a model for proline binding and a mechanism for uncoupling of proline and 2-OG turnover.
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Affiliation(s)
- I J Clifton
- The Dyson Perrins Laboratory and the Oxford Centre for Molecular Sciences, Oxford, UK
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16
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Mukherji M, Chien W, Kershaw NJ, Clifton IJ, Schofield CJ, Wierzbicki AS, Lloyd MD. Structure-function analysis of phytanoyl-CoA 2-hydroxylase mutations causing Refsum's disease. Hum Mol Genet 2001; 10:1971-82. [PMID: 11555634 DOI: 10.1093/hmg/10.18.1971] [Citation(s) in RCA: 59] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Refsum's disease is a neurological syndrome characterized by adult-onset retinitis pigmentosa, anosmia, sensory neuropathy and phytanic acidaemia. Many cases are caused by mutations in peroxisomal oxygenase phytanoyl-CoA 2-hydroxylase (PAHX) which catalyses the initial alpha-oxidation step in the degradation of phytanic acid. Both pro and mature forms of recombinant PAHX were produced in Escherichia coli, highly purified, and shown to have a requirement for iron(II) as a co-factor and 2-oxoglutarate as a co-substrate. Sequence analysis in the light of crystallographic data for other members of the 2-oxoglutarate-dependent oxygenase super-family led to secondary structural predictions for PAHX, which were tested by site-directed mutagenesis. The H175A and D177A mutants did not catalyse hydroxylation of phytanoyl-CoA, consistent with their assigned role as iron(II) binding ligands. The clinically observed P29S, Q176K, G204S, N269H, R275Q and R275W mutants were assayed for both 2-oxoglutarate and phytanoyl-CoA oxidation. The P29S mutant was fully active, implying that the mutation resulted in defective targeting of the protein to peroxisomes. Mutation of Arg-275 resulted in impaired 2-oxoglutarate binding. The Q176K, G204S and N269H mutations caused partial uncoupling of 2-oxoglutarate conversion from phytanoyl-CoA oxidation. The results demonstrate that the diagnosis of Refsum's disease should not solely rely upon PAHX assays for 2-oxoglutarate or phytanoyl-CoA oxidation.
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Affiliation(s)
- M Mukherji
- The Oxford Centre for Molecular Science and The Dyson Perrins Laboratory, South Parks Road, Oxford OX1 3QY, UK
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17
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Wilmouth RC, Edman K, Neutze R, Wright PA, Clifton IJ, Schneider TR, Schofield CJ, Hajdu J. X-ray snapshots of serine protease catalysis reveal a tetrahedral intermediate. Nat Struct Biol 2001; 8:689-94. [PMID: 11473259 DOI: 10.1038/90401] [Citation(s) in RCA: 89] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
Studies on the catalytic mechanism and inhibition of serine proteases are widely used as paradigms for teaching enzyme catalysis. Ground-breaking work on the structures of chymotrypsin and subtilisin led to the idea of a conserved catalytic triad formed by the active site Ser, His and Asp residues. An oxyanion hole, consisting of the peptide amide of the active site serine and a neighbouring glycine, was identified, and hydrogen bonding in the oxyanion hole was suggested to stabilize the two proposed tetrahedral intermediates on the catalytic pathway. Here we show electron density changes consistent with the formation of a tetrahedral intermediate during the hydrolysis of an acyl-enzyme complex formed between a natural heptapeptide and elastase. No electron density for an enzyme-product complex was observed. The structures also suggest a mechanism for the synchronization of hydrolysis and peptide release triggered by the conversion of the sp2 hybridized carbonyl carbon to an sp3 carbon in the tetrahedral intermediate. This affects the location of the peptide in the active site cleft, triggering the collapse of a hydrogen bonding network between the peptide and the beta-sheet of the active site.
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Affiliation(s)
- R C Wilmouth
- The Dyson Perrins Laboratory and Oxford Centre for Molecular Sciences, University of Oxford, South Parks Road, Oxford OX1 3QY, UK
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18
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Lee HJ, Lloyd MD, Clifton IJ, Harlos K, Dubus A, Baldwin JE, Frere JM, Schofield CJ. Alteration of the co-substrate selectivity of deacetoxycephalosporin C synthase. The role of arginine 258. J Biol Chem 2001; 276:18290-5. [PMID: 11279000 DOI: 10.1074/jbc.m100085200] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Deacetoxycephalosporin C synthase is an iron(II) 2-oxoglutaratedependent oxygenase that catalyzes the oxidative ring-expansion of penicillin N to deacetoxycephalosporin C. The wild-type enzyme is only able to efficiently utilize 2-oxoglutarate and 2-oxoadipate as a 2-oxoacid co-substrate. Mutation of arginine 258, the side chain of which forms an electrostatic interaction with the 5-carboxylate of the 2-oxoglutarate co-substrate, to a glutamine residue reduced activity to about 5% of the wild-type enzyme with 2-oxoglutarate. However, other aliphatic 2-oxoacids, which were not co-substrates for the wild-type enzyme, were utilized by the R258Q mutant. These 2-oxoacids "rescued" catalytic activity to the level observed for the wild-type enzyme as judged by penicillin N and G conversion. These co-substrates underwent oxidative decarboxylation as observed for 2-oxoglutarate in the normal reaction with the wild-type enzyme. Crystal structures of the iron(II)- 2-oxo-3-methylbutanoate (1.5 A), and iron(II)-2-oxo-4-methylpentanoate (1.6 A) enzyme complexes were obtained, which reveal the molecular basis for this "chemical co-substrate rescue" and help to rationalize the co-substrate selectivity of 2-oxoglutaratedependent oxygenases.
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Affiliation(s)
- H J Lee
- Oxford Centre for Molecular Sciences and the Dyson Perrins Laboratory, South Parks Road, Oxford OX1 3QY, United Kingdom
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Lee HJ, Lloyd MD, Harlos K, Clifton IJ, Baldwin JE, Schofield CJ. Kinetic and crystallographic studies on deacetoxycephalosporin C synthase (DAOCS). J Mol Biol 2001; 308:937-48. [PMID: 11352583 DOI: 10.1006/jmbi.2001.4649] [Citation(s) in RCA: 83] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Deacetoxycephalosporin C synthase (DAOCS) is an iron(II) and 2-oxoglutarate-dependent oxygenase that catalyzes the conversion of penicillin N to deacetoxycephalosporin C, the committed step in the biosynthesis of cephalosporin antibiotics. The crystal structure of DAOCS revealed that the C terminus of one molecule is inserted into the active site of its neighbor in a cyclical fashion within a trimeric unit. This arrangement has hindered the generation of crystalline enzyme-substrate complexes. Therefore, we constructed a series of DAOCS mutants with modified C termini. Oxidation of 2-oxoglutarate was significantly uncoupled from oxidation of the penicillin substrate in certain truncated mutants. The extent of uncoupling varied with the number of residues deleted and the penicillin substrate used. Crystal structures were determined for the DeltaR306 mutant complexed with iron(II) and 2-oxoglutarate (to 2.10 A) and the DeltaR306A mutant complexed with iron(II), succinate and unhydrated carbon dioxide (to 1.96 A). The latter may mimic a product complex, and supports proposals for a metal-bound CO(2) intermediate during catalysis.
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Affiliation(s)
- H J Lee
- The Oxford Centre for Molecular Sciences and The Dyson Perrins Laboratory, South Parks Road, Oxford, OX1 3QY, UK
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20
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Affiliation(s)
- R C Wilmouth
- The Oxford Centre for Molecular Sciences and The Dyson Perrins Laboratory, University of Oxford, United Kingdom
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21
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Wright PA, Wilmouth RC, Clifton IJ, Schofield CJ. 'pH-jump' crystallographic analyses of gamma-lactam-porcine pancreatic elastase complexes. Biochem J 2000; 351 Pt 2:335-40. [PMID: 11023818 PMCID: PMC1221368] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/17/2023]
Abstract
beta-Lactams inhibit a range of enzymes via acylation of nucleophilic serine residues. Certain gamma-lactam analogues of monocyclic beta-lactams have also been shown to be reversible inhibitors of porcine pancreatic elastase (PPE), forming acyl-enzyme complexes that are stable with respect to hydrolysis. Crystallographic analysis at pH 5 of an acyl-enzyme complex formed with PPE and one of these inhibitors revealed the ester carbonyl located in the oxyanion hole in a similar conformation to that observed in the structure of a complex formed between a heptapeptide (beta-casomorphin-7) and PPE. Only weak electron density was observed for the His-57 side chain in its 'native' conformation. Instead, the His-57 side chain predominantly adopted a conformation rotated approx. 90 degrees from its normal position. PPE-gamma-lactam crystals were subjected to 'pH-jumps' by placing the crystals in a buffer of increased pH prior to freezing for data collection. The results indicate that the conformation of the gamma-lactam-derived acyl-enzyme species in the PPE active site is dependent on pH, a result having implications for the analysis of other serine protease-inhibitor structures at non-catalytic pH values. The results help to define the stereoelectronic relationship between the ester of the acyl-enzyme complex, the side chain of His-57 and the incoming nucleophile during the reversible (de)acylation steps, implying it is closely analogous to the hydrolytic deacylation step during catalytic peptide hydrolysis.
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Affiliation(s)
- P A Wright
- The Oxford Centre for Molecular Sciences and The Dyson Perrins Laboratory, South Parks Road, Oxford OX1 3QY, UK
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22
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Burzlaff NI, Rutledge PJ, Clifton IJ, Hensgens CM, Pickford M, Adlington RM, Roach PL, Baldwin JE. The reaction cycle of isopenicillin N synthase observed by X-ray diffraction. Nature 1999; 401:721-4. [PMID: 10537113 DOI: 10.1038/44400] [Citation(s) in RCA: 157] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Isopenicillin N synthase (IPNS), a non-haem iron-dependent oxidase, catalyses the biosynthesis of isopenicillin N (IPN), the precursor of all penicillins and cephalosporins. The key steps in this reaction are the two iron-dioxygen-mediated ring closures of the tripeptide delta-(L-alpha-aminoadipoyl)-L-cysteinyl-D-valine (ACV). It has been proposed that the four-membered beta-lactam ring forms initially, associated with a highly oxidized iron(iv)-oxo (ferryl) moiety, which subsequently mediates closure of the five-membered thiazolidine ring. Here we describe observation of the IPNS reaction in crystals by X-ray crystallography. IPNS Fe2+ substrate crystals were grown anaerobically, exposed to high pressures of oxygen to promote reaction and frozen, and their structures were elucidated by X-ray diffraction. Using the natural substrate ACV, this resulted in the IPNS x Fe2+ x IPN product complex. With the substrate analogue, delta-(L-alpha-aminoadipoyl)-L-cysteinyl-L-S-methylcysteine (ACmC) in the crystal, the reaction cycle was interrupted at the monocyclic stage. These mono- and bicyclic structures support our hypothesis of a two-stage reaction sequence leading to penicillin. Furthermore, the formation of a monocyclic sulphoxide product from ACmC is most simply explained by the interception of a high-valency iron-oxo species.
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Affiliation(s)
- N I Burzlaff
- The Dyson Perrins Laboratory and the Oxford Centre for Molecular Sciences, University of Oxford, UK
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23
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Wilmouth RC, Westwood NJ, Anderson K, Brownlee W, Claridge TD, Clifton IJ, Pritchard GJ, Aplin RT, Schofield CJ. Inhibition of elastase by N-sulfonylaryl beta-lactams: anatomy of a stable acyl-enzyme complex. Biochemistry 1998; 37:17506-13. [PMID: 9860865 DOI: 10.1021/bi9816249] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
beta-Lactam inhibitors of transpeptidase enzymes involved in cell wall biosynthesis remain among the most important therapeutic agents in clinical use. beta-Lactams have more recently been developed as inhibitors of serine proteases including elastase. All therapeutically useful beta-lactam inhibitors operate via mechanisms resulting in the formation of hydrolytically stable acyl-enzyme complexes. Presently, it is difficult to predict which beta-lactams will form stable acyl-enzyme complexes with serine enzymes. Further, the factors that result in the seemingly special nature of beta-lactams versus other acylating agents are unclear-if indeed they exist. Here we present the 1.6 A resolution crystal structure of a stable acyl-enzyme complex formed between porcine pancreatic elastase and a representative monocyclic beta-lactam, which forms a simple acyl-enzyme. The structure shows that the ester carbonyl is not located within the oxyanion hole and the "hydrolytic" water is displaced. Combined with additional kinetic and mass spectrometric data, the structure allows the rationalization of the low degree of hydrolytic lability observed for the beta-lactam-derived acyl-enzyme complex.
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Affiliation(s)
- R C Wilmouth
- The Oxford Centre for Molecular Sciences, The Dyson Perrins Laboratory, Oxford, United Kingdom
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24
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Roach PL, Clifton IJ, Hensgens CM, Shibata N, Schofield CJ, Hajdu J, Baldwin JE. Structure of isopenicillin N synthase complexed with substrate and the mechanism of penicillin formation. Nature 1997; 387:827-30. [PMID: 9194566 DOI: 10.1038/42990] [Citation(s) in RCA: 322] [Impact Index Per Article: 11.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
The biosynthesis of penicillin and cephalosporin antibiotics in microorganisms requires the formation of the bicyclic nucleus of penicillin. Isopenicillin N synthase (IPNS), a non-haem iron-dependent oxidase, catalyses the reaction of a tripeptide, delta-(L-alpha-aminoadipoyl)-L-cysteinyl-D-valine (ACV), and dioxygen to form isopenicillin N and two water molecules. Mechanistic studies suggest the reaction is initiated by ligation of the substrate thiolate to the iron centre, and proceeds through an enzyme-bound monocyclic intermediate. Here we report the crystal structure of IPNS complexed to ferrous iron and ACV, determined to 1.3 A resolution. Based on the structure, we propose a mechanism for penicillin formation that involves ligation of ACV to the iron centre, creating a vacant iron coordination site into which dioxygen can bind. Subsequently, iron-dioxygen and iron-oxo species remove the requisite hydrogens from ACV without the direct assistance of protein residues. The crystal structure of the complex with the dioxygen analogue, NO and ACV bound to the active-site iron supports this hypothesis.
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Affiliation(s)
- P L Roach
- The Dyson Perrins Laboratory, University of Oxford, UK
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25
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Wilmouth RC, Clifton IJ, Robinson CV, Roach PL, Aplin RT, Westwood NJ, Hajdu J, Schofield CJ. Structure of a specific acyl-enzyme complex formed between beta-casomorphin-7 and porcine pancreatic elastase. Nat Struct Biol 1997; 4:456-62. [PMID: 9187653 DOI: 10.1038/nsb0697-456] [Citation(s) in RCA: 44] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
Mass spectrometric screening reveals that an unmodified natural heptapeptide--human beta-casomorphin-7, an internal sequence of human beta-casein that possesses opioid-like activity--reacts with porcine pancreatic elastase to form an unusually stable acyl-enzyme complex at low pH. X-ray crystallographic analysis (to 1.9 A resolution) at pH 5 shows continuous electron density linking the C-terminal isoleucine of beta-casomorphin-7 to Ser 195 through an ester bond. The structure reveals a well defined water molecule (Wat 317), equidistant between the carbon of the ester carbonyl and N epsilon 2 of His 57. Deprotonation of Wat 317 will produce a hydroxide ion positioned to attack the ester carbonyl through the favoured Bürgi-Dunitz trajectory.
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26
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Barlow JN, Baldwin JE, Clifton IJ, Gibson E, Hensgens CM, Hajdu J, Hara T, Hassan A, John P, Lloyd MD, Roach PL, Prescott A, Robinson JK, Zhang ZH, Schofield CJ. Studies on non-haem ferrous-dependent oxygenases and oxidases. Biochem Soc Trans 1997; 25:86-90. [PMID: 9056849 DOI: 10.1042/bst0250086] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
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27
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Roach PL, Clifton IJ, Hensgens CM, Shibata N, Long AJ, Strange RW, Hasnain SS, Schofield CJ, Baldwin JE, Hajdu J. Anaerobic crystallisation of an isopenicillin N synthase.Fe(II).substrate complex demonstrated by X-ray studies. Eur J Biochem 1996; 242:736-40. [PMID: 9022704 DOI: 10.1111/j.1432-1033.1996.0736r.x] [Citation(s) in RCA: 49] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
Isopenicillin N synthase (IPNS) was cocrystallised with ferrous sulphate and its substrate, delta-(L-alpha-aminoadipoyl)-L-cysteinyl-D-valine (Aad-Cys-Val). Vital to the successful procedure was the maintenance of a rigorously anaerobic environment. Hanging-drop vapour-diffusion crystallisation experiments, using lithium sulphate as the precipitant produced three crystal forms. Form I crystals, with a plate habit, diffracted X-rays to at least 0.11-nm resolution at the European Synchrotron Radiation Facility and belong to the space group P2(1)2(1)2(1), with unit-cell dimensions a = 4.68, b = 7.15, c = 10.10 nm. Their asymmetric unit contains a single IPNS.Fe(II).Aad-Cys-Val complex with a solvent content of 38.5%. Form II crystals, with a hexagonal habit, diffract X-rays to at least 0.21 nm resolution at the European Synchrotron Radiation Facility and belong to the space group P3(1)21, with unit-cell dimensions a = 10.10, b = 10.10, c = 11.567 nm. Their asymmetric unit also contains a single IPNS.Fe(II).Aad-Cys-Val complex with a solvent content of 69.5%. Form III crystals, needles, do not show well-ordered diffraction. Although all three forms were initially produced in crystallisation experiments under identical conditions, appropriate micro and streak seeding allows selective crystallisation of form I or form II crystals. Extended X-ray-absorption fine-structure studies on a crystalline slurry of the form I crystals demonstrate the presence of an Fe-S(Aad-Cys-Val) bond length of 0.234 +/- 0.003 nm.
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Affiliation(s)
- P L Roach
- Dyson Perrins Laboratory, University of Oxford, UK
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28
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Schiffer CA, Clifton IJ, Davisson VJ, Santi DV, Stroud RM. Crystal structure of human thymidylate synthase: a structural mechanism for guiding substrates into the active site. Biochemistry 1995; 34:16279-87. [PMID: 8845352 DOI: 10.1021/bi00050a007] [Citation(s) in RCA: 85] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
The crystal structure of human thymidylate synthase, a target for anti-cancer drugs, is determined to 3.0 A resolution and refined to a crystallographic residual of 17.8%. The structure implicates the enzyme in a mechanism for facilitating the docking of substrates into the active site. This mechanism involves a twist of approximately 180 degrees of the active site loop, pivoted around the neighboring residues 184 and 204, and implicates ordering of external, eukaryote specific loops along with the well-characterized closure of the active site upon substrate binding. The highly conserved, but eukaryote-specific insertion of twelve residues 90-101 (h117-128), and of eight residues between 156 and 157 (h146-h153) are known to be alpha-helical in other eukaryotes, and lie close together on the outside of the protein in regions of disordered electron density in this crystal form. Two cysteines [cys 202 (h199) and 213 (h210)] are close enough to form a disulfide bond within each subunit, and a third cysteine [cys 183 (h180)] is positioned to form a disulfide bond with the active site cysteine [cys 198 (h195)] in its unliganded conformation. The amino terminal 27 residues, unique to human TS, contains 8 proline residues, is also in a region of disordered electron density, and is likely to be flexible prior to substrate binding. The drug resistance mutation, Y6H, confers a 4-fold reduction in FdUMP affinity and 8-fold reduction in kcat for the dUMP reaction. Though indirectly connected to the active site, the structure suggests a mechanism of resistance that possibly involves a change in structure. This structure offers a unique opportunity for structure-based drug design aimed at the unliganded form of the human enzyme.
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Affiliation(s)
- C A Schiffer
- Department of Biochemistry and Biophysics, University of California, San Francisco 94143-0448, USA
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Campbell JW, Clifton IJ, Harding MM, Hao Q. The Laue Data Module (LDM) – a software development for Laue X-ray diffraction data processing. J Appl Crystallogr 1995. [DOI: 10.1107/s0021889895005164] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
The Laue Data Module (LDM) has been defined and implemented in Fortran as the basis for new developments in the processing of Laue X-ray diffraction data. It provides a program-independent way of handling, storing and accessing the parameters required in the initial stages of Laue data processing. The program-independent Laue Reflection List (LRL) and associated functions have also been developed. The way in which these two developments may be used in application programs and as the basis for developing further program-independent Laue-data processing functions is described.
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30
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Roach PL, Clifton IJ, Fülöp V, Harlos K, Barton GJ, Hajdu J, Andersson I, Schofield CJ, Baldwin JE. Crystal structure of isopenicillin N synthase is the first from a new structural family of enzymes. Nature 1995; 375:700-4. [PMID: 7791906 DOI: 10.1038/375700a0] [Citation(s) in RCA: 329] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
Penicillin antibiotics are all produced from fermentation-derived penicillins because their chemical synthesis is not commercially viable. The key step in penicillin biosynthesis, in which both the beta-lactam and thiazolidine rings of the nucleus are created, is mediated by isopenicillin N synthase (IPNS), which binds ferrous iron and uses dioxygen as a cosubstrate. In a unique enzymatic step, with no chemical precedent, IPNS catalyses the transfer of four hydrogen atoms from its tripeptide substrate to dioxygen forming, in a single reaction, the complete bicyclic nucleus of the penicillins. We now report the structure of IPNS complexed with manganese, which reveals the active site is unusually buried within a 'jelly-roll' motif and lined by hydrophobic residues, and suggest how this structure permits the process of penicillin formation. Sequence analyses indicate IPNS, 1-aminocyclopropane-1-carboxylic acid oxidase and many of the 2-oxo-acid-dependent oxygenases contain a conserved jelly-roll motif, forming a new structural family of enzymes.
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Affiliation(s)
- P L Roach
- Dyson Perrins Laboratory, University of Oxford, UK
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31
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Roach PL, Schofield CJ, Baldwin JE, Clifton IJ, Hajdu J. Crystallization and preliminary X-ray diffraction studies on recombinant isopenicillin N synthase from Aspergillus nidulans. Protein Sci 1995; 4:1007-9. [PMID: 7663335 PMCID: PMC2143123 DOI: 10.1002/pro.5560040521] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
Recombinant Aspergillus nidulans isopenicillin N synthase was purified from an Escherichia coli expression system. The apoenzyme in the presence of saturating concentrations of MnCl2 could be crystallized by either macro- or microseeding, using the hanging drop vapor diffusion technique with polyethylene glycol 8000 as precipitant. The crystals (0.5-1.0 mm overall dimensions) diffract X-rays to at least 2.0 A resolution at synchrotrons and belong to space group P212121 with unit cell dimensions of a = 59.2 A, b = 127.0 A, and c = 139.6 A. The asymmetric unit contains one dimer, and the solvent content of the crystals is 60%. The crystals are radiation sensitive.
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Affiliation(s)
- P L Roach
- Dyson Perrins Laboratory, University of Oxford, United Kingdom
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Fülöp V, Phizackerley RP, Soltis SM, Clifton IJ, Wakatsuki S, Erman J, Hajdu J, Edwards SL. Laue diffraction study on the structure of cytochrome c peroxidase compound I. Structure 1994; 2:201-8. [PMID: 8069633 DOI: 10.1016/s0969-2126(00)00021-6] [Citation(s) in RCA: 103] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
BACKGROUND Cytochrome c peroxidase from yeast is a soluble haem-containing protein found in the mitochondrial electron transport chain where it probably protects against toxic peroxides. The aim of this study was to obtain a reliable structure for the doubly oxidized transient intermediate (termed compound I) in the reaction of cytochrome c peroxidase with hydrogen peroxide. This intermediate contains a semistable free radical on Trp191, and an oxyferryl haem group. RESULTS Compound I was produced in crystals of yeast cytochrome c peroxidase by reacting the crystalline enzyme with hydrogen peroxide in a flow cell. The reaction was monitored by microspectrophotometry and Laue crystallography in separate experiments. A nearly complete conversion to compound I was achieved within two minutes of the addition of hydrogen peroxide, and the concentration of the intermediate remained at similar levels for an additional half an hour. The structure of the intermediate was determined by Laue diffraction. The refined Laue structure for compound I shows clear structural changes at the peroxide-binding site but no significant changes at the radical site. The photographs were processed with a new software package (LEAP), overcoming many of the former problems encountered in extracting structural information from Laue exposures. CONCLUSIONS The geometry of the haem environment in this protein allows structural changes to be extremely small, similar in magnitude to those observed for the Fe2+/Fe3+ transition in cytochrome c. The results suggest that these molecules have evolved to transfer electrons with a minimal need for structural adjustment.
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Affiliation(s)
- V Fülöp
- Oxford Centre for Molecular Sciences, UK
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Campbell JW, Clifton IJ, Greenhough TJ, Hajdu J, Harrison SC, Liddington RC, Shrive AK. Calcium binding sites in tomato bushy stunt virus visualized by Laue crystallography. J Mol Biol 1990; 214:627-32. [PMID: 2388260 DOI: 10.1016/0022-2836(90)90278-t] [Citation(s) in RCA: 19] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
We have collected Laue diffraction data from crystals of tomato bushy stunt virus using the full white X-ray spectrum from the wiggler magnet of the Synchrotron Radiation Source at Daresbury, U.K. A single 24 second exposure of a crystal soaked in EDTA yielded a data set that was 90% complete between 6 and 3.5 A resolution. A large proportion of the data could be measured using an overlap deconvolution routine to separate spatially overlapping reflections in the dense Laue photograph. Reflections with I greater than 2 sigma I (40% of the data set) were subjected to wavelength normalization. A difference Fourier map between these reflections and a monochromatic native set showed, after icosahedral averaging, the three pairs of Ca2+ binding sites related by quasi-symmetry and the movement of a liganding loop in the protein at the A/C subunit interface. The extent and quality of the data obtained from a single Laue photograph of this virus were thus sufficient to detect clearly such small structural alterations. In a second experiment, a Laue photograph was taken from a crystal that was soaked first in EDTA and then in GdCl3. A difference Fourier map between this Laue data set and the Laue data set from the EDTA-soaked crystal showed clearly the Gd3+ sites in the capsid, demonstrating that the Laue technique is a reliable and efficient means for data collection with virus crystals.
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Shrive AK, Clifton IJ, Hajdu J, Greenhough TJ. Laue film integration and deconvolution of spatially overlapping reflections. J Appl Crystallogr 1990. [DOI: 10.1107/s0021889890000346] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
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36
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Helliwell JR, Habash J, Cruickshank DWJ, Harding MM, Greenhough TJ, Campbell JW, Clifton IJ, Elder M, Machin PA, Papiz MZ, Zurek S. The recording and analysis of synchrotron X-radiation Laue diffraction photographs. J Appl Crystallogr 1989. [DOI: 10.1107/s0021889889006564] [Citation(s) in RCA: 137] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
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Hajdu J, Greenhough TJ, Clifton IJ, Campbell JW, Shrive AK, Harrison SC, Liddington RC. Laue crystallography: application to virus crystals. Basic Life Sci 1989; 51:331-9. [PMID: 2818434 DOI: 10.1007/978-1-4684-8041-2_30] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Affiliation(s)
- J Hajdu
- Laboratory of Molecular Biophysics, Oxford University, U.K
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38
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Hajdu J, Machin PA, Campbell JW, Greenhough TJ, Clifton IJ, Zurek S, Gover S, Johnson LN, Elder M. Millisecond X-ray diffraction and the first electron density map from Laue photographs of a protein crystal. Nature 1987; 329:178-81. [PMID: 3114644 DOI: 10.1038/329178a0] [Citation(s) in RCA: 68] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
Attempts to use X-ray crystallography to extract three-dimensional information on transient phenomena in crystals have been hampered primarily by long data collection times. Here we report on the first difference Fourier map obtained from Laue diffraction photographs of a protein crystal, glycogen phosphorylase b. Data collection time was 3 s using the high-intensity white X-radiation generated on the wiggler magnet of the Daresbury Synchrotron Radiation Source (SRS), but data acquisition in the millisecond-submillisecond range is possible. The method presented here uses a simple difference technique and was designed to analyse structural changes relative to a known starting structure. The combination of this approach with cine techniques allows the recording of three-dimensional motion pictures at atomic resolution and opens up new areas in structural biology and chemistry.
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Clifton IJ, Cruickshank DWJ, Diakun G, Elder M, Habash J, Helliwell JR, Liddington RC, Machin PA, Papiz MZ. Synchrotron X-radiation protein crystallography: CEA film absorption factor as a function of wavelength 0.3≤λ≤2Å. J Appl Crystallogr 1985. [DOI: 10.1107/s0021889885010354] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
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