1
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Fowler NJ, Albalwi MF, Lee S, Hounslow AM, Williamson MP. Improved methodology for protein NMR structure calculation using hydrogen bond restraints and ANSURR validation: The SH2 domain of SH2B1. Structure 2023; 31:975-986.e3. [PMID: 37311460 DOI: 10.1016/j.str.2023.05.012] [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: 03/10/2023] [Revised: 05/02/2023] [Accepted: 05/18/2023] [Indexed: 06/15/2023]
Abstract
Protein structures calculated using NMR data are less accurate and less well-defined than they could be. Here we use the program ANSURR to show that this deficiency is at least in part due to a lack of hydrogen bond restraints. We describe a protocol to introduce hydrogen bond restraints into the structure calculation of the SH2 domain from SH2B1 in a systematic and transparent way and show that the structures generated are more accurate and better defined as a result. We also show that ANSURR can be used as a guide to know when the structure calculation is good enough to stop.
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Affiliation(s)
- Nicholas J Fowler
- School of Biosciences, University of Sheffield, S10 2TN Sheffield, UK.
| | - Marym F Albalwi
- School of Biosciences, University of Sheffield, S10 2TN Sheffield, UK
| | - Subin Lee
- School of Biosciences, University of Sheffield, S10 2TN Sheffield, UK
| | - Andrea M Hounslow
- School of Biosciences, University of Sheffield, S10 2TN Sheffield, UK
| | - Mike P Williamson
- School of Biosciences, University of Sheffield, S10 2TN Sheffield, UK.
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2
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L P Hosszu L, Sangar D, Batchelor M, Risse E, Hounslow AM, Collinge J, Waltho JP, Bieschke J. Loss of residues 119 - 136, including the first β-strand of human prion protein, generates an aggregation-competent partially "open" form. J Mol Biol 2023:168158. [PMID: 37244570 DOI: 10.1016/j.jmb.2023.168158] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2022] [Revised: 05/18/2023] [Accepted: 05/19/2023] [Indexed: 05/29/2023]
Abstract
In prion replication, the cellular form of prion protein (PrPC) must undergo a full conformational transition to its disease-associated fibrillar form. Transmembrane forms of PrP have been implicated in this structural conversion. The cooperative unfolding of a structural core in PrPC presents a substantial energy barrier to prion formation, with membrane insertion and detachment of parts of PrP presenting a plausible route to its reduction. Here, we examined the removal of residues 119 - 136 of PrP, a region which includes the first β-strand and a substantial portion of the conserved hydrophobic region of PrP, a region which associates with the ER membrane, on the structure, stability and self-association of the folded domain of PrPC. We see an "open" native-like conformer with increased solvent exposure which fibrilises more readily than the native state. These data suggest a stepwise folding transition, which is initiated by the conformational switch to this "open" form of PrPC.
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Affiliation(s)
- Laszlo L P Hosszu
- MRC Prion Unit at UCL, UCL Institute of Prion Diseases, 33 Cleveland Street, London, W1W 7FF, UK
| | - Daljit Sangar
- MRC Prion Unit at UCL, UCL Institute of Prion Diseases, 33 Cleveland Street, London, W1W 7FF, UK
| | - Mark Batchelor
- MRC Prion Unit at UCL, UCL Institute of Prion Diseases, 33 Cleveland Street, London, W1W 7FF, UK
| | - Emmanuel Risse
- MRC Prion Unit at UCL, UCL Institute of Prion Diseases, 33 Cleveland Street, London, W1W 7FF, UK
| | - Andrea M Hounslow
- Department of Molecular Biology and Biotechnology, University of Sheffield, Firth Court, Western Bank, Sheffield S10 2TN, UK
| | - John Collinge
- MRC Prion Unit at UCL, UCL Institute of Prion Diseases, 33 Cleveland Street, London, W1W 7FF, UK
| | - Jonathan P Waltho
- Department of Molecular Biology and Biotechnology, University of Sheffield, Firth Court, Western Bank, Sheffield S10 2TN, UK; Manchester Institute of Biotechnology, University of Manchester, 131 Princess Street, Manchester, M1 7DN, UK
| | - Jan Bieschke
- MRC Prion Unit at UCL, UCL Institute of Prion Diseases, 33 Cleveland Street, London, W1W 7FF, UK.
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3
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Davis JL, Hounslow AM, Baxter NJ, Mesnage S, Williamson MP. 1H, 13C, and 15N resonance assignments of a conserved putative cell wall binding domain from Enterococcus faecalis. BIOMOLECULAR NMR ASSIGNMENTS 2022; 16:247-251. [PMID: 35665899 PMCID: PMC9510096 DOI: 10.1007/s12104-022-10087-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/26/2021] [Accepted: 04/29/2022] [Indexed: 06/15/2023]
Abstract
Enterococcus faecalis is a major causative agent of hospital acquired infections. The ability of E. faecalis to evade the host immune system is essential during pathogenesis, which has been shown to be dependent on the complete separation of daughter cells by peptidoglycan hydrolases. AtlE is a peptidoglycan hydrolase which is predicted to bind to the cell wall of E. faecalis, via six C-terminal repeat sequences. Here, we report the near complete assignment of one of these six repeats, as well as the predicted backbone structure and dynamics. This data will provide a platform for future NMR studies to explore the ligand recognition motif of AtlE and help to uncover its potential role in E. faecalis virulence.
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Affiliation(s)
- Jessica L Davis
- School of Biosciences, University of Sheffield, Firth Court, Western Bank, S10 2TN, Sheffield, UK
| | - Andrea M Hounslow
- School of Biosciences, University of Sheffield, Firth Court, Western Bank, S10 2TN, Sheffield, UK
| | - Nicola J Baxter
- School of Biosciences, University of Sheffield, Firth Court, Western Bank, S10 2TN, Sheffield, UK
| | - Stéphane Mesnage
- School of Biosciences, University of Sheffield, Firth Court, Western Bank, S10 2TN, Sheffield, UK
| | - Mike P Williamson
- School of Biosciences, University of Sheffield, Firth Court, Western Bank, S10 2TN, Sheffield, UK.
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4
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Robertson AJ, Cruz-Navarrete FA, Wood HP, Vekaria N, Hounslow AM, Bisson C, Cliff MJ, Baxter NJ, Waltho JP. An Enzyme with High Catalytic Proficiency Utilizes Distal Site Substrate Binding Energy to Stabilize the Closed State but at the Expense of Substrate Inhibition. ACS Catal 2022; 12:3149-3164. [PMID: 35692864 PMCID: PMC9171722 DOI: 10.1021/acscatal.1c05524] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2021] [Revised: 02/10/2022] [Indexed: 02/05/2023]
Abstract
Understanding the factors that underpin the enormous catalytic proficiencies of enzymes is fundamental to catalysis and enzyme design. Enzymes are, in part, able to achieve high catalytic proficiencies by utilizing the binding energy derived from nonreacting portions of the substrate. In particular, enzymes with substrates containing a nonreacting phosphodianion group coordinated in a distal site have been suggested to exploit this binding energy primarily to facilitate a conformational change from an open inactive form to a closed active form, rather than to either induce ground state destabilization or stabilize the transition state. However, detailed structural evidence for the model is limited. Here, we use β-phosphoglucomutase (βPGM) to investigate the relationship between binding a phosphodianion group in a distal site, the adoption of a closed enzyme form, and catalytic proficiency. βPGM catalyzes the isomerization of β-glucose 1-phosphate to glucose 6-phosphate via phosphoryl transfer reactions in the proximal site, while coordinating a phosphodianion group of the substrate(s) in a distal site. βPGM has one of the largest catalytic proficiencies measured and undergoes significant domain closure during its catalytic cycle. We find that side chain substitution at the distal site results in decreased substrate binding that destabilizes the closed active form but is not sufficient to preclude the adoption of a fully closed, near-transition state conformation. Furthermore, we reveal that binding of a phosphodianion group in the distal site stimulates domain closure even in the absence of a transferring phosphoryl group in the proximal site, explaining the previously reported β-glucose 1-phosphate inhibition. Finally, our results support a trend whereby enzymes with high catalytic proficiencies involving phosphorylated substrates exhibit a greater requirement to stabilize the closed active form.
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Affiliation(s)
- Angus J. Robertson
- School of Biosciences, The University of Sheffield, Sheffield, S10 2TN, United Kingdom
| | | | - Henry P. Wood
- School of Biosciences, The University of Sheffield, Sheffield, S10 2TN, United Kingdom
| | - Nikita Vekaria
- Manchester Institute of Biotechnology and Department of Chemistry, The University of Manchester, Manchester, M1 7DN, United Kingdom
| | - Andrea M. Hounslow
- School of Biosciences, The University of Sheffield, Sheffield, S10 2TN, United Kingdom
| | - Claudine Bisson
- School of Biosciences, The University of Sheffield, Sheffield, S10 2TN, United Kingdom
| | - Matthew J. Cliff
- Manchester Institute of Biotechnology and Department of Chemistry, The University of Manchester, Manchester, M1 7DN, United Kingdom
| | - Nicola J. Baxter
- School of Biosciences, The University of Sheffield, Sheffield, S10 2TN, United Kingdom
- Manchester Institute of Biotechnology and Department of Chemistry, The University of Manchester, Manchester, M1 7DN, United Kingdom
| | - Jonathan P. Waltho
- School of Biosciences, The University of Sheffield, Sheffield, S10 2TN, United Kingdom
- Manchester Institute of Biotechnology and Department of Chemistry, The University of Manchester, Manchester, M1 7DN, United Kingdom
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5
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Molecular mechanism of glycolytic flux control intrinsic to human phosphoglycerate kinase. Proc Natl Acad Sci U S A 2021; 118:2112986118. [PMID: 34893542 DOI: 10.1073/pnas.2112986118] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/02/2021] [Indexed: 01/17/2023] Open
Abstract
Glycolysis plays a fundamental role in energy production and metabolic homeostasis. The intracellular [adenosine triphosphate]/[adenosine diphosphate] ([ATP]/[ADP]) ratio controls glycolytic flux; however, the regulatory mechanism underlying reactions catalyzed by individual glycolytic enzymes enabling flux adaptation remains incompletely understood. Phosphoglycerate kinase (PGK) catalyzes the reversible phosphotransfer reaction, which directly produces ATP in a near-equilibrium step of glycolysis. Despite extensive studies on the transcriptional regulation of PGK expression, the mechanism in response to changes in the [ATP]/[ADP] ratio remains obscure. Here, we report a protein-level regulation of human PGK (hPGK) by utilizing the switching ligand-binding cooperativities between adenine nucleotides and 3-phosphoglycerate (3PG). This was revealed by nuclear magnetic resonance (NMR) spectroscopy at physiological salt concentrations. MgADP and 3PG bind to hPGK with negative cooperativity, whereas MgAMPPNP (a nonhydrolyzable ATP analog) and 3PG bind to hPGK with positive cooperativity. These opposite cooperativities enable a shift between different ligand-bound states depending on the intracellular [ATP]/[ADP] ratio. Based on these findings, we present an atomic-scale description of the reaction scheme for hPGK under physiological conditions. Our results indicate that hPGK intrinsically modulates its function via ligand-binding cooperativities that are finely tuned to respond to changes in the [ATP]/[ADP] ratio. The alteration of ligand-binding cooperativities could be one of the self-regulatory mechanisms for enzymes in bidirectional pathways, which enables rapid adaptation to changes in the intracellular environment.
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6
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Allomorphy as a mechanism of post-translational control of enzyme activity. Nat Commun 2020; 11:5538. [PMID: 33139716 PMCID: PMC7608592 DOI: 10.1038/s41467-020-19215-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2020] [Accepted: 09/23/2020] [Indexed: 11/08/2022] Open
Abstract
Enzyme regulation is vital for metabolic adaptability in living systems. Fine control of enzyme activity is often delivered through post-translational mechanisms, such as allostery or allokairy. β-phosphoglucomutase (βPGM) from Lactococcus lactis is a phosphoryl transfer enzyme required for complete catabolism of trehalose and maltose, through the isomerisation of β-glucose 1-phosphate to glucose 6-phosphate via β-glucose 1,6-bisphosphate. Surprisingly for a gatekeeper of glycolysis, no fine control mechanism of βPGM has yet been reported. Herein, we describe allomorphy, a post-translational control mechanism of enzyme activity. In βPGM, isomerisation of the K145-P146 peptide bond results in the population of two conformers that have different activities owing to repositioning of the K145 sidechain. In vivo phosphorylating agents, such as fructose 1,6-bisphosphate, generate phosphorylated forms of both conformers, leading to a lag phase in activity until the more active phosphorylated conformer dominates. In contrast, the reaction intermediate β-glucose 1,6-bisphosphate, whose concentration depends on the β-glucose 1-phosphate concentration, couples the conformational switch and the phosphorylation step, resulting in the rapid generation of the more active phosphorylated conformer. In enabling different behaviours for different allomorphic activators, allomorphy allows an organism to maximise its responsiveness to environmental changes while minimising the diversion of valuable metabolites. β-phosphoglucomutase (βPGM) from Lactococcus lactis is a phosphoryl transfer enzyme required for catabolism of trehalose and maltose. Coupled analyses of multiple βPGM structures and enzymatic activity lead to the proposal of allomorphy — a post-translational mechanism controlling enzyme activity.
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7
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Cruz-Navarrete FA, Baxter NJ, Wood HP, Hounslow AM, Waltho JP. 1H, 15N and 13C backbone resonance assignments of the P146A variant of β-phosphoglucomutase from Lactococcus lactis in its substrate-free form. BIOMOLECULAR NMR ASSIGNMENTS 2019; 13:349-356. [PMID: 31396843 PMCID: PMC6713671 DOI: 10.1007/s12104-019-09904-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/24/2019] [Accepted: 07/20/2019] [Indexed: 06/10/2023]
Abstract
β-Phosphoglucomutase (βPGM) is a magnesium-dependent phosphoryl transfer enzyme that catalyses the reversible isomerisation of β-glucose 1-phosphate and glucose 6-phosphate, via two phosphoryl transfer steps and a β-glucose 1,6-bisphosphate intermediate. Substrate-free βPGM is an essential component of the catalytic cycle and an understanding of its dynamics would present significant insights into βPGM functionality, and enzyme catalysed phosphoryl transfer in general. Previously, 30 residues around the active site of substrate-free βPGMWT were identified as undergoing extensive millisecond dynamics and were unassignable. Here we report 1H, 15N and 13C backbone resonance assignments of the P146A variant (βPGMP146A) in its substrate-free form, where the K145-A146 peptide bond adopts a trans conformation in contrast to all crystal structures of βPGMWT, where the K145-P146 peptide bond is cis. In βPGMP146A millisecond dynamics are suppressed for all but 17 residues, allowing 92% of backbone resonances to be assigned. Secondary structure predictions using TALOS-N reflect βPGM crystal structures, and a chemical shift comparison between substrate-free βPGMP146A and βPGMWT confirms that the solution conformations are very similar, except for the D137-A147 loop. Hence, the isomerisation state of the 145-146 peptide bond has little effect on structure but the cis conformation triggers millisecond dynamics in the hinge (V12-T16), the nucleophile (D8) and residues that coordinate the transferring phosphate group (D8 and S114-S116), and the D137-A147 loop (V141-A142 and K145). These millisecond dynamics occur in addition to those for residues involved in coordinating the catalytic MgII ion and the L44-L53 loop responsible for substrate discrimination.
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Affiliation(s)
- F Aaron Cruz-Navarrete
- Department of Molecular Biology and Biotechnology, Krebs Institute for Biomolecular Research, The University of Sheffield, Firth Court, Western Bank, Sheffield, S10 2TN, UK
| | - Nicola J Baxter
- Department of Molecular Biology and Biotechnology, Krebs Institute for Biomolecular Research, The University of Sheffield, Firth Court, Western Bank, Sheffield, S10 2TN, UK
- Manchester Institute of Biotechnology and School of Chemistry, The University of Manchester, 131 Princess Street, Manchester, M1 7DN, UK
| | - Henry P Wood
- Department of Molecular Biology and Biotechnology, Krebs Institute for Biomolecular Research, The University of Sheffield, Firth Court, Western Bank, Sheffield, S10 2TN, UK
| | - Andrea M Hounslow
- Department of Molecular Biology and Biotechnology, Krebs Institute for Biomolecular Research, The University of Sheffield, Firth Court, Western Bank, Sheffield, S10 2TN, UK
| | - Jonathan P Waltho
- Department of Molecular Biology and Biotechnology, Krebs Institute for Biomolecular Research, The University of Sheffield, Firth Court, Western Bank, Sheffield, S10 2TN, UK.
- Manchester Institute of Biotechnology and School of Chemistry, The University of Manchester, 131 Princess Street, Manchester, M1 7DN, UK.
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8
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Bennet IA, Finger LD, Baxter NJ, Ambrose B, Hounslow AM, Thompson MJ, Exell JC, Shahari NNBM, Craggs TD, Waltho JP, Grasby JA. Regional conformational flexibility couples substrate specificity and scissile phosphate diester selectivity in human flap endonuclease 1. Nucleic Acids Res 2019; 46:5618-5633. [PMID: 29718417 PMCID: PMC6009646 DOI: 10.1093/nar/gky293] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2017] [Accepted: 04/09/2018] [Indexed: 02/07/2023] Open
Abstract
Human flap endonuclease-1 (hFEN1) catalyzes the divalent metal ion-dependent removal of single-stranded DNA protrusions known as flaps during DNA replication and repair. Substrate selectivity involves passage of the 5'-terminus/flap through the arch and recognition of a single nucleotide 3'-flap by the α2-α3 loop. Using NMR spectroscopy, we show that the solution conformation of free and DNA-bound hFEN1 are consistent with crystal structures; however, parts of the arch region and α2-α3 loop are disordered without substrate. Disorder within the arch explains how 5'-flaps can pass under it. NMR and single-molecule FRET data show a shift in the conformational ensemble in the arch and loop region upon addition of DNA. Furthermore, the addition of divalent metal ions to the active site of the hFEN1-DNA substrate complex demonstrates that active site changes are propagated via DNA-mediated allostery to regions key to substrate differentiation. The hFEN1-DNA complex also shows evidence of millisecond timescale motions in the arch region that may be required for DNA to enter the active site. Thus, hFEN1 regional conformational flexibility spanning a range of dynamic timescales is crucial to reach the catalytically relevant ensemble.
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Affiliation(s)
- Ian A Bennet
- Centre for Chemical Biology, Department of Chemistry, Krebs Institute for Biomolecular Research, The University of Sheffield, Sheffield S3 7HF, UK
| | - L David Finger
- Centre for Chemical Biology, Department of Chemistry, Krebs Institute for Biomolecular Research, The University of Sheffield, Sheffield S3 7HF, UK
| | - Nicola J Baxter
- Department of Molecular Biology and Biotechnology, Krebs Institute for Biomolecular Research, The University of Sheffield, Sheffield S10 2TN, UK.,Manchester Institute of Biotechnology, School of Chemistry, The University of Manchester, Manchester M1 7DN, UK
| | - Benjamin Ambrose
- Centre for Chemical Biology, Department of Chemistry, Krebs Institute for Biomolecular Research, The University of Sheffield, Sheffield S3 7HF, UK
| | - Andrea M Hounslow
- Department of Molecular Biology and Biotechnology, Krebs Institute for Biomolecular Research, The University of Sheffield, Sheffield S10 2TN, UK
| | - Mark J Thompson
- Centre for Chemical Biology, Department of Chemistry, Krebs Institute for Biomolecular Research, The University of Sheffield, Sheffield S3 7HF, UK
| | - Jack C Exell
- Centre for Chemical Biology, Department of Chemistry, Krebs Institute for Biomolecular Research, The University of Sheffield, Sheffield S3 7HF, UK
| | - Nur Nazihah B Md Shahari
- Centre for Chemical Biology, Department of Chemistry, Krebs Institute for Biomolecular Research, The University of Sheffield, Sheffield S3 7HF, UK
| | - Timothy D Craggs
- Centre for Chemical Biology, Department of Chemistry, Krebs Institute for Biomolecular Research, The University of Sheffield, Sheffield S3 7HF, UK
| | - Jonathan P Waltho
- Department of Molecular Biology and Biotechnology, Krebs Institute for Biomolecular Research, The University of Sheffield, Sheffield S10 2TN, UK.,Manchester Institute of Biotechnology, School of Chemistry, The University of Manchester, Manchester M1 7DN, UK
| | - Jane A Grasby
- Centre for Chemical Biology, Department of Chemistry, Krebs Institute for Biomolecular Research, The University of Sheffield, Sheffield S3 7HF, UK
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9
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Johnson LA, Robertson AJ, Baxter NJ, Trevitt CR, Bisson C, Jin Y, Wood HP, Hounslow AM, Cliff MJ, Blackburn GM, Bowler MW, Waltho JP. van der Waals Contact between Nucleophile and Transferring Phosphorus Is Insufficient To Achieve Enzyme Transition-State Architecture. ACS Catal 2018. [DOI: 10.1021/acscatal.8b01612] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Luke A. Johnson
- Krebs Institute for Biomolecular Research, Department of Molecular Biology and Biotechnology, The University of Sheffield, Sheffield S10 2TN, United Kingdom
| | - Angus J. Robertson
- Krebs Institute for Biomolecular Research, Department of Molecular Biology and Biotechnology, The University of Sheffield, Sheffield S10 2TN, United Kingdom
| | - Nicola J. Baxter
- Krebs Institute for Biomolecular Research, Department of Molecular Biology and Biotechnology, The University of Sheffield, Sheffield S10 2TN, United Kingdom
- Manchester Institute of Biotechnology and School of Chemistry, The University of Manchester, Manchester M1 7DN, United Kingdom
| | - Clare R. Trevitt
- Krebs Institute for Biomolecular Research, Department of Molecular Biology and Biotechnology, The University of Sheffield, Sheffield S10 2TN, United Kingdom
| | - Claudine Bisson
- Krebs Institute for Biomolecular Research, Department of Molecular Biology and Biotechnology, The University of Sheffield, Sheffield S10 2TN, United Kingdom
| | - Yi Jin
- Krebs Institute for Biomolecular Research, Department of Molecular Biology and Biotechnology, The University of Sheffield, Sheffield S10 2TN, United Kingdom
| | - Henry P. Wood
- Krebs Institute for Biomolecular Research, Department of Molecular Biology and Biotechnology, The University of Sheffield, Sheffield S10 2TN, United Kingdom
| | - Andrea M. Hounslow
- Krebs Institute for Biomolecular Research, Department of Molecular Biology and Biotechnology, The University of Sheffield, Sheffield S10 2TN, United Kingdom
| | - Matthew J. Cliff
- Manchester Institute of Biotechnology and School of Chemistry, The University of Manchester, Manchester M1 7DN, United Kingdom
| | - G. Michael Blackburn
- Krebs Institute for Biomolecular Research, Department of Molecular Biology and Biotechnology, The University of Sheffield, Sheffield S10 2TN, United Kingdom
| | - Matthew W. Bowler
- European Molecular Biology Laboratory, Grenoble Outstation, 71 Avenue des Martyrs, CS 90181, F-38042 Grenoble, France
| | - Jonathan P. Waltho
- Krebs Institute for Biomolecular Research, Department of Molecular Biology and Biotechnology, The University of Sheffield, Sheffield S10 2TN, United Kingdom
- Manchester Institute of Biotechnology and School of Chemistry, The University of Manchester, Manchester M1 7DN, United Kingdom
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10
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Serimbetov Z, Baxter NJ, Cliff MJ, Waltho JP. 1H, 15N, 13C backbone resonance assignments of human phosphoglycerate kinase in a transition state analogue complex with ADP, 3-phosphoglycerate and magnesium trifluoride. BIOMOLECULAR NMR ASSIGNMENTS 2017; 11:251-256. [PMID: 28866776 PMCID: PMC5594045 DOI: 10.1007/s12104-017-9758-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/30/2017] [Accepted: 08/05/2017] [Indexed: 06/07/2023]
Abstract
Human phosphoglycerate kinase (PGK) is an energy generating glycolytic enzyme that catalyses the transfer of a phosphoryl group from 1,3-bisphosphoglycerate (BPG) to ADP producing 3-phosphoglycerate (3PG) and ATP. PGK is composed of two α/β Rossmann-fold domains linked by a central α-helix and the active site is located in the cleft formed between the N-domain which binds BPG or 3PG, and the C-domain which binds the nucleotides ADP or ATP. Domain closure is required to bring the two substrates into close proximity for phosphoryl transfer to occur, however previous structural studies involving a range of native substrates and substrate analogues only yielded open or partly closed PGK complexes. X-ray crystallography using magnesium trifluoride (MgF3-) as a isoelectronic and near-isosteric mimic of the transferring phosphoryl group (PO3-), together with 3PG and ADP has been successful in trapping human PGK in a fully closed transition state analogue (TSA) complex. In this work we report the 1H, 15N and 13C backbone resonance assignments of human PGK in the solution conformation of the fully closed PGK:3PG:MgF3:ADP TSA complex. Assignments were obtained by heteronuclear multidimensional NMR spectroscopy. In total, 97% of all backbone resonances were assigned in the complex, with 385 out of a possible 399 residues assigned in the 1H-15N TROSY spectrum. Prediction of solution secondary structure from a chemical shift analysis using the TALOS-N webserver is in good agreement with the published X-ray crystal structure of this complex.
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Affiliation(s)
- Zhalgas Serimbetov
- Manchester Institute of Biotechnology and School of Chemistry, The University of Manchester, 131 Princess Street, Manchester, M1 7DN, UK
| | - Nicola J Baxter
- Manchester Institute of Biotechnology and School of Chemistry, The University of Manchester, 131 Princess Street, Manchester, M1 7DN, UK.
- Krebs Institute for Biomolecular Research, Department of Molecular Biology and Biotechnology, The University of Sheffield, Firth Court, Western Bank, Sheffield, S10 2TN, UK.
| | - Matthew J Cliff
- Manchester Institute of Biotechnology and School of Chemistry, The University of Manchester, 131 Princess Street, Manchester, M1 7DN, UK.
| | - Jonathan P Waltho
- Manchester Institute of Biotechnology and School of Chemistry, The University of Manchester, 131 Princess Street, Manchester, M1 7DN, UK.
- Krebs Institute for Biomolecular Research, Department of Molecular Biology and Biotechnology, The University of Sheffield, Firth Court, Western Bank, Sheffield, S10 2TN, UK.
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11
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Czarnota S, Baxter NJ, Cliff MJ, Waltho JP, Scrutton NS, Hay S. 1H, 15N, 13C backbone resonance assignments of human soluble catechol O-methyltransferase in complex with S-adenosyl-L-methionine and 3,5-dinitrocatechol. BIOMOLECULAR NMR ASSIGNMENTS 2017; 11:57-61. [PMID: 27981425 PMCID: PMC5343089 DOI: 10.1007/s12104-016-9720-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/23/2016] [Accepted: 11/30/2016] [Indexed: 06/06/2023]
Abstract
Catechol O-methyltransferase (COMT) is an enzyme that plays a major role in catechol neurotransmitter deactivation. Inhibition of COMT can increase neurotransmitter levels, which provides a means of treatment for Parkinson's disease, schizophrenia and depression. COMT exists as two isozymes: a soluble cytoplasmic form (S-COMT), expressed in the liver and kidneys and a membrane-bound form (MB-COMT), found mostly in the brain. Here we report the backbone 1H, 15N and 13C chemical shift assignments of S-COMT in complex with S-adenosyl-L-methionine, 3,5-dinitrocatechol and Mg2+. Assignments were obtained by heteronuclear multidimensional NMR spectroscopy. In total, 97 % of all backbone resonances were assigned in the complex, with 205 out of a possible 215 residues assigned in the 1H-15N TROSY spectrum. Prediction of solution secondary structure from a chemical shift analysis using the TALOS+ webserver is in good agreement with published X-ray crystal structures.
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Affiliation(s)
- Sylwia Czarnota
- Manchester Institute of Biotechnology and School of Chemistry, The University of Manchester, 131 Princess Street, Manchester, M1 7DN, UK
| | - Nicola J Baxter
- Manchester Institute of Biotechnology and School of Chemistry, The University of Manchester, 131 Princess Street, Manchester, M1 7DN, UK.
- Department of Molecular Biology and Biotechnology, Krebs Institute for Biomolecular Research, The University of Sheffield, Firth Court, Western Bank, Sheffield, S10 2TN, UK.
| | - Matthew J Cliff
- Manchester Institute of Biotechnology and School of Chemistry, The University of Manchester, 131 Princess Street, Manchester, M1 7DN, UK
| | - Jonathan P Waltho
- Manchester Institute of Biotechnology and School of Chemistry, The University of Manchester, 131 Princess Street, Manchester, M1 7DN, UK
- Department of Molecular Biology and Biotechnology, Krebs Institute for Biomolecular Research, The University of Sheffield, Firth Court, Western Bank, Sheffield, S10 2TN, UK
| | - Nigel S Scrutton
- Manchester Institute of Biotechnology and School of Chemistry, The University of Manchester, 131 Princess Street, Manchester, M1 7DN, UK
| | - Sam Hay
- Manchester Institute of Biotechnology and School of Chemistry, The University of Manchester, 131 Princess Street, Manchester, M1 7DN, UK.
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12
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Xu Y, Ong ACM, Williamson MP, Hounslow AM. Backbone assignment and secondary structure of the PLAT domain of human polycystin-1. BIOMOLECULAR NMR ASSIGNMENTS 2015; 9:369-373. [PMID: 25943267 DOI: 10.1007/s12104-015-9612-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/27/2015] [Accepted: 04/27/2015] [Indexed: 06/04/2023]
Abstract
Polycystin-1 is a large transmembrane protein mutated in the common genetic disorder autosomal dominant polycystic kidney disease. One of the predicted intracellular domains of polycystin-1 is PLAT (Polycystin-1, Lipoxygenase and Alpha Toxin), which consists of 116 amino acids and is anchored to the membrane by linkers at both ends. It is predicted to have a large number of hydrophobic residues on the surface. Assignment of the NMR spectrum was hampered by considerable line broadening, and hence a programme of site-directed mutagenesis and searching for suitable solution conditions was undertaken. The optimum construct required fusion of the GB1 domain at the N-terminus and a His tag at the C-terminus, and proved to have several additional amino acids at both ends beyond the canonical domain boundaries, as well as mutation of W3128 to alanine. Optimum solubility required 500 mM sodium chloride, and usable spectra could only be obtained by perdeuteration. Backbone assignment was made using standard triple resonance spectra and is 88 % complete. The chemical shifts obtained suggest that a loop consisting of residues 3223-3228 is mobile in solution, and that the protein is similar in structure to a prediction produced by Swiss-Model based on the structure of a homologous protein.
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Affiliation(s)
- Yaoxian Xu
- Department of Molecular Biology and Biotechnology, University of Sheffield, Firth Court, Western Bank, Sheffield, S10 2TN, UK
- Kidney Genetics Group, Academic Unit of Nephrology, Department of Infection and Immunity, University of Sheffield Medical School, Sheffield, S10 2RX, UK
| | - Albert C M Ong
- Kidney Genetics Group, Academic Unit of Nephrology, Department of Infection and Immunity, University of Sheffield Medical School, Sheffield, S10 2RX, UK.
| | - Mike P Williamson
- Department of Molecular Biology and Biotechnology, University of Sheffield, Firth Court, Western Bank, Sheffield, S10 2TN, UK.
| | - Andrea M Hounslow
- Department of Molecular Biology and Biotechnology, University of Sheffield, Firth Court, Western Bank, Sheffield, S10 2TN, UK
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13
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Xu Y, Streets AJ, Hounslow AM, Tran U, Jean-Alphonse F, Needham AJ, Vilardaga JP, Wessely O, Williamson MP, Ong ACM. The Polycystin-1, Lipoxygenase, and α-Toxin Domain Regulates Polycystin-1 Trafficking. J Am Soc Nephrol 2015; 27:1159-73. [PMID: 26311459 DOI: 10.1681/asn.2014111074] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2014] [Accepted: 07/21/2015] [Indexed: 12/24/2022] Open
Abstract
Mutations in polycystin-1 (PC1) give rise to autosomal dominant polycystic kidney disease, an important and common cause of kidney failure. Despite its medical importance, the function of PC1 remains poorly understood. Here, we investigated the role of the intracellular polycystin-1, lipoxygenase, and α-toxin (PLAT) signature domain of PC1 using nuclear magnetic resonance, biochemical, cellular, and in vivo functional approaches. We found that the PLAT domain targets PC1 to the plasma membrane in polarized epithelial cells by a mechanism involving the selective binding of the PLAT domain to phosphatidylserine and L-α-phosphatidylinositol-4-phosphate (PI4P) enriched in the plasma membrane. This process is regulated by protein kinase A phosphorylation of the PLAT domain, which reduces PI4P binding and recruits β-arrestins and the clathrin adaptor AP2 to trigger PC1 internalization. Our results reveal a physiological role for the PC1-PLAT domain in renal epithelial cells and suggest that phosphorylation-dependent internalization of PC1 is closely linked to its function in renal development and homeostasis.
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Affiliation(s)
- Yaoxian Xu
- Kidney Genetics Group, Academic Nephrology Unit, University of Sheffield Medical School, Sheffield, United Kingdom; Department of Molecular Biology and Biotechnology, University of Sheffield, Sheffield, United Kingdom
| | - Andrew J Streets
- Kidney Genetics Group, Academic Nephrology Unit, University of Sheffield Medical School, Sheffield, United Kingdom
| | - Andrea M Hounslow
- Department of Molecular Biology and Biotechnology, University of Sheffield, Sheffield, United Kingdom
| | - Uyen Tran
- Department of Cellular and Molecular Medicine, Cleveland Clinic Foundation, Cleveland, Ohio; and
| | - Frederic Jean-Alphonse
- Laboratory of GPCR Biology, Department of Pharmacology and Chemical Biology, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania
| | - Andrew J Needham
- Kidney Genetics Group, Academic Nephrology Unit, University of Sheffield Medical School, Sheffield, United Kingdom
| | - Jean-Pierre Vilardaga
- Laboratory of GPCR Biology, Department of Pharmacology and Chemical Biology, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania
| | - Oliver Wessely
- Department of Cellular and Molecular Medicine, Cleveland Clinic Foundation, Cleveland, Ohio; and
| | - Michael P Williamson
- Department of Molecular Biology and Biotechnology, University of Sheffield, Sheffield, United Kingdom
| | - Albert C M Ong
- Kidney Genetics Group, Academic Nephrology Unit, University of Sheffield Medical School, Sheffield, United Kingdom;
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14
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Trevitt CR, Hosszu LLP, Batchelor M, Panico S, Terry C, Nicoll AJ, Risse E, Taylor WA, Sandberg MK, Al-Doujaily H, Linehan JM, Saibil HR, Scott DJ, Collinge J, Waltho JP, Clarke AR. N-terminal domain of prion protein directs its oligomeric association. J Biol Chem 2014; 289:25497-508. [PMID: 25074940 PMCID: PMC4162156 DOI: 10.1074/jbc.m114.566588] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The self-association of prion protein (PrP) is a critical step in the pathology of prion diseases. It is increasingly recognized that small non-fibrillar β-sheet-rich oligomers of PrP may be of crucial importance in the prion disease process. Here, we characterize the structure of a well defined β-sheet-rich oligomer, containing ∼12 PrP molecules, and often enclosing a central cavity, formed using full-length recombinant PrP. The N-terminal region of prion protein (residues 23-90) is required for the formation of this distinct oligomer; a truncated form comprising residues 91-231 forms a broad distribution of aggregated species. No infectivity or toxicity was found using cell and animal model systems. This study demonstrates that examination of the full repertoire of conformers and assembly states that can be accessed by PrP under specific experimental conditions should ideally be done using the full-length protein.
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Affiliation(s)
- Clare R Trevitt
- From the Department of Neurodegenerative Disease, MRC Prion Unit, UCL Institute of Neurology, Queen Square, London WC1N 3BG
| | - Laszlo L P Hosszu
- From the Department of Neurodegenerative Disease, MRC Prion Unit, UCL Institute of Neurology, Queen Square, London WC1N 3BG
| | - Mark Batchelor
- From the Department of Neurodegenerative Disease, MRC Prion Unit, UCL Institute of Neurology, Queen Square, London WC1N 3BG
| | - Silvia Panico
- the Institute of Structural and Molecular Biology, Birkbeck College, Malet Street, London WC1E 7HX
| | - Cassandra Terry
- From the Department of Neurodegenerative Disease, MRC Prion Unit, UCL Institute of Neurology, Queen Square, London WC1N 3BG
| | - Andrew J Nicoll
- From the Department of Neurodegenerative Disease, MRC Prion Unit, UCL Institute of Neurology, Queen Square, London WC1N 3BG
| | - Emmanuel Risse
- From the Department of Neurodegenerative Disease, MRC Prion Unit, UCL Institute of Neurology, Queen Square, London WC1N 3BG
| | - William A Taylor
- From the Department of Neurodegenerative Disease, MRC Prion Unit, UCL Institute of Neurology, Queen Square, London WC1N 3BG
| | - Malin K Sandberg
- From the Department of Neurodegenerative Disease, MRC Prion Unit, UCL Institute of Neurology, Queen Square, London WC1N 3BG
| | - Huda Al-Doujaily
- From the Department of Neurodegenerative Disease, MRC Prion Unit, UCL Institute of Neurology, Queen Square, London WC1N 3BG
| | - Jacqueline M Linehan
- From the Department of Neurodegenerative Disease, MRC Prion Unit, UCL Institute of Neurology, Queen Square, London WC1N 3BG
| | - Helen R Saibil
- the Institute of Structural and Molecular Biology, Birkbeck College, Malet Street, London WC1E 7HX
| | - David J Scott
- the National Centre for Macromolecular Hydrodynamics, School of Biosciences, University of Nottingham, Sutton Bonington Campus, Leicestershire, LE12 5RD, the ISIS Spallation Neutron and Muon Source and Research Complex at Harwell, Rutherford Appleton Laboratory, Oxfordshire, OX11 0FA, and
| | - John Collinge
- From the Department of Neurodegenerative Disease, MRC Prion Unit, UCL Institute of Neurology, Queen Square, London WC1N 3BG
| | - Jonathan P Waltho
- the Department of Molecular Biology and Biotechnology, Krebs Institute for Biomolecular Research, University of Sheffield, Sheffield S10 2TN, United Kingdom
| | - Anthony R Clarke
- From the Department of Neurodegenerative Disease, MRC Prion Unit, UCL Institute of Neurology, Queen Square, London WC1N 3BG,
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15
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Mesnage S, Dellarole M, Baxter NJ, Rouget JB, Dimitrov JD, Wang N, Fujimoto Y, Hounslow AM, Lacroix-Desmazes S, Fukase K, Foster SJ, Williamson MP. Molecular basis for bacterial peptidoglycan recognition by LysM domains. Nat Commun 2014; 5:4269. [PMID: 24978025 PMCID: PMC4083421 DOI: 10.1038/ncomms5269] [Citation(s) in RCA: 140] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2014] [Accepted: 06/02/2014] [Indexed: 02/06/2023] Open
Abstract
Carbohydrate recognition is essential for growth, cell adhesion and signalling in all living organisms. A highly conserved carbohydrate binding module, LysM, is found in proteins from viruses, bacteria, fungi, plants and mammals. LysM modules recognize polysaccharides containing N-acetylglucosamine (GlcNAc) residues including peptidoglycan, an essential component of the bacterial cell wall. However, the molecular mechanism underpinning LysM-peptidoglycan interactions remains unclear. Here we describe the molecular basis for peptidoglycan recognition by a multimodular LysM domain from AtlA, an autolysin involved in cell division in the opportunistic bacterial pathogen Enterococcus faecalis. We explore the contribution of individual modules to the binding, identify the peptidoglycan motif recognized, determine the structures of free and bound modules and reveal the residues involved in binding. Our results suggest that peptide stems modulate LysM binding to peptidoglycan. Using these results, we reveal how the LysM module recognizes the GlcNAc-X-GlcNAc motif present in polysaccharides across kingdoms.
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Affiliation(s)
- Stéphane Mesnage
- Krebs Institute, University of Sheffield, Firth Court, Western Bank, Sheffield S10 2TN, UK
- Department of Molecular Biology and Biotechnology, University of Sheffield, Firth Court, Western Bank, Sheffield S10 2TN, UK
| | - Mariano Dellarole
- Centre de Biochimie Structurale, CNRS UMR 5048—UM 1—INSERM UMR 1054, F-34090 Montpellier, France
- These authors contributed equally to this work
- Present address: Institut Pasteur, Unité de Virologie Structurale, 28 Rue du Docteur Roux, F-75015 Paris, France
| | - Nicola J. Baxter
- Krebs Institute, University of Sheffield, Firth Court, Western Bank, Sheffield S10 2TN, UK
- Department of Molecular Biology and Biotechnology, University of Sheffield, Firth Court, Western Bank, Sheffield S10 2TN, UK
- These authors contributed equally to this work
| | - Jean-Baptiste Rouget
- Centre de Biochimie Structurale, CNRS UMR 5048—UM 1—INSERM UMR 1054, F-34090 Montpellier, France
| | - Jordan D. Dimitrov
- INSERM, U872, Centre de Recherche des Cordeliers, Equipe 16, F-75006 Paris, France
- Université Pierre et Marie Curie, UMR-S 872, F-75006 Paris, France
- Université Paris Descartes, UMR-S 872, F-75006 Paris, France
| | - Ning Wang
- Department of Chemistry, Laboratory for Natural Products Chemistry, Osaka University, Osaka 560-0043, Japan
| | - Yukari Fujimoto
- Department of Chemistry, Laboratory for Natural Products Chemistry, Osaka University, Osaka 560-0043, Japan
| | - Andrea M. Hounslow
- Krebs Institute, University of Sheffield, Firth Court, Western Bank, Sheffield S10 2TN, UK
- Department of Molecular Biology and Biotechnology, University of Sheffield, Firth Court, Western Bank, Sheffield S10 2TN, UK
| | - Sébastien Lacroix-Desmazes
- INSERM, U872, Centre de Recherche des Cordeliers, Equipe 16, F-75006 Paris, France
- Université Pierre et Marie Curie, UMR-S 872, F-75006 Paris, France
- Université Paris Descartes, UMR-S 872, F-75006 Paris, France
| | - Koichi Fukase
- Department of Chemistry, Laboratory for Natural Products Chemistry, Osaka University, Osaka 560-0043, Japan
| | - Simon J. Foster
- Krebs Institute, University of Sheffield, Firth Court, Western Bank, Sheffield S10 2TN, UK
- Department of Molecular Biology and Biotechnology, University of Sheffield, Firth Court, Western Bank, Sheffield S10 2TN, UK
| | - Michael P. Williamson
- Krebs Institute, University of Sheffield, Firth Court, Western Bank, Sheffield S10 2TN, UK
- Department of Molecular Biology and Biotechnology, University of Sheffield, Firth Court, Western Bank, Sheffield S10 2TN, UK
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16
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Pudney CR, Guerriero A, Baxter NJ, Johannissen LO, Waltho JP, Hay S, Scrutton NS. Fast protein motions are coupled to enzyme H-transfer reactions. J Am Chem Soc 2013; 135:2512-7. [PMID: 23373704 DOI: 10.1021/ja311277k] [Citation(s) in RCA: 76] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Coupling of fast protein dynamics to enzyme chemistry is controversial and has ignited considerable debate, especially over the past 15 years in relation to enzyme-catalyzed H-transfer. H-transfer can occur by quantum tunneling, and the temperature dependence of kinetic isotope effects (KIEs) has emerged as the "gold standard" descriptor of these reactions. The anomalous temperature dependence of KIEs is often rationalized by invoking fast motions to facilitate H-transfer, yet crucially, direct evidence for coupled motions is lacking. The fast motions hypothesis underpinning the temperature dependence of KIEs is based on inference. Here, we have perturbed vibrational motions in pentaerythritol tetranitrate reductase (PETNR) by isotopic substitution where all non-exchangeable atoms were replaced with the corresponding heavy isotope ((13)C, (15)N, and (2)H). The KIE temperature dependence is perturbed by heavy isotope labeling, demonstrating a direct link between (promoting) vibrations in the protein and the observed KIE. Further we show that temperature-independent KIEs do not necessarily rule out a role for fast dynamics coupled to reaction chemistry. We show causality between fast motions and enzyme chemistry and demonstrate how this impacts on experimental KIEs for enzyme reactions.
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Affiliation(s)
- Christopher R Pudney
- Manchester Institute of Biotechnology, The University of Manchester, 131 Princess Street, Manchester M1 7DN, UK
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17
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Abstract
Around half of all protein structures solved nowadays using solution-state nuclear magnetic resonance (NMR) spectroscopy have been because of automated data analysis. The pervasiveness of computational approaches in general hides, however, a more nuanced view in which the full variety and richness of the field appears. This review is structured around a comparison of methods associated with three NMR observables: classical nuclear Overhauser effect (NOE) constraint gathering in contrast with more recent chemical shift and residual dipole coupling (RDC) based protocols. In each case, the emphasis is placed on the latest research, covering mainly the past 5 years. By describing both general concepts and representative programs, the objective is to map out a field in which--through the very profusion of approaches--it is all too easy to lose one's bearings.
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18
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Ratcliffe EC, Tunnicliffe RB, Ng IW, Adams PG, Qian P, Holden-Dye K, Jones MR, Williamson MP, Hunter CN. Experimental evidence that the membrane-spanning helix of PufX adopts a bent conformation that facilitates dimerisation of the Rhodobacter sphaeroides RC-LH1 complex through N-terminal interactions. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2010; 1807:95-107. [PMID: 20937243 DOI: 10.1016/j.bbabio.2010.10.003] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/12/2010] [Revised: 09/27/2010] [Accepted: 10/04/2010] [Indexed: 10/19/2022]
Abstract
The PufX polypeptide is an integral component of some photosynthetic bacterial reaction center-light harvesting 1 (RC-LH1) core complexes. Many aspects of the structure of PufX are unresolved, including the conformation of its long membrane-spanning helix and whether C-terminal processing occurs. In the present report, NMR data recorded on the Rhodobacter sphaeroides PufX in a detergent micelle confirmed previous conclusions derived from equivalent data obtained in organic solvent, that the α-helix of PufX adopts a bent conformation that would allow the entire helix to reside in the membrane interior or at its surface. In support of this, it was found through the use of site-directed mutagenesis that increasing the size of a conserved glycine on the inside of the bend in the helix was not tolerated. Possible consequences of this bent helical structure were explored using a series of N-terminal deletions. The N-terminal sequence ADKTIFNDHLN on the cytoplasmic face of the membrane was found to be critical for the formation of dimers of the RC-LH1 complex. It was further shown that the C-terminus of PufX is processed at an early stage in the development of the photosynthetic membrane. A model in which two bent PufX polypeptides stabilise a dimeric RC-LH1 complex is presented, and it is proposed that the N-terminus of PufX from one half of the dimer engages in electrostatic interactions with charged residues on the cytoplasmic surface of the LH1α and β polypeptides on the other half of the dimer.
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Affiliation(s)
- Emma C Ratcliffe
- Department of Molecular Biology and Biotechnology, University of Sheffield, Sheffield S10 2TN, UK
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19
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Marston FY, Grainger WH, Smits WK, Hopcroft NH, Green M, Hounslow AM, Grossman AD, Craven CJ, Soultanas P. When simple sequence comparison fails: the cryptic case of the shared domains of the bacterial replication initiation proteins DnaB and DnaD. Nucleic Acids Res 2010; 38:6930-42. [PMID: 20587500 PMCID: PMC2978336 DOI: 10.1093/nar/gkq465] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/05/2022] Open
Abstract
DnaD and DnaB are essential DNA-replication-initiation proteins in low-G+C content Gram-positive bacteria. Here we use sensitive Hidden Markov Model-based techniques to show that the DnaB and DnaD proteins share a common structure that is evident across all their structural domains, termed DDBH1 and DDBH2 (DnaD DnaB Homology 1 and 2). Despite strong sequence divergence, many of the DNA-binding and oligomerization properties of these domains have been conserved. Although eluding simple sequence comparisons, the DDBH2 domains share the only strong sequence motif; an extremely highly conserved YxxxIxxxW sequence that contributes to DNA binding. Sequence alignments of DnaD alone fail to identify another key part of the DNA-binding module, since it includes a poorly conserved sequence, a solvent-exposed and somewhat unstable helix and a mobile segment. We show by NMR, in vitro mutagenesis and in vivo complementation experiments that the DNA-binding module of Bacillus subtilis DnaD comprises the YxxxIxxxW motif, the unstable helix and a portion of the mobile region, the latter two being essential for viability. These structural insights lead us to a re-evaluation of the oligomerization and DNA-binding properties of the DnaD and DnaB proteins.
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Affiliation(s)
- Farhat Y Marston
- Krebs Institute, Department of Molecular Biology and Biotechnology, University of Sheffield, Firth Court, Western Bank, Sheffield S10 2TN, UK
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20
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Marston JP, Cliff MJ, Reed MAC, Blackburn GM, Hounslow AM, Craven CJ, Waltho JP. Structural tightening and interdomain communication in the catalytic cycle of phosphoglycerate kinase. J Mol Biol 2010; 396:345-60. [PMID: 19944703 DOI: 10.1016/j.jmb.2009.11.052] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2009] [Revised: 11/16/2009] [Accepted: 11/19/2009] [Indexed: 11/25/2022]
Abstract
Changes in amide-NH chemical shift and hydrogen exchange rates as phosphoglycerate kinase progresses through its catalytic cycle have been measured to assess whether they correlate with changes in hydrogen bonding within the protein. Four representative states were compared: the free enzyme, a product complex containing 3-phosphoglyceric acid (3PG), a substrate complex containing ADP and a transition-state analogue (TSA) complex containing a 3PG-AlF(4)(-)-ADP moiety. There are an overall increases in amide protection from hydrogen exchange when the protein binds the substrate and product ligands and an additional increase when the TSA complex is formed. This is consistent with stabilisation of the protein structure by ligand binding. However, there is no correlation between the chemical shift changes and the protection factor changes, indicating that the protection factor changes are not associated with an overall shortening of hydrogen bonds in the protected ground state, but rather can be ascribed to the properties of the high-energy, exchange-competent state. Therefore, an overall structural tightening mechanism is not supported by the data. Instead, we observed that some cooperativity is exhibited in the N-domain, such that within this domain the changes induced upon forming the TSA complex are an intensification of those induced by binding 3PG. Furthermore, chemical shift changes induced by 3PG binding extend through the interdomain region to the C-domain beta-sheet, highlighting a network of hydrogen bonds between the domains that suggests interdomain communication. Interdomain communication is also indicated by amide protection in one domain being significantly altered by binding of substrate to the other, even where no associated change in the structure of the substrate-free domain is indicated by chemical shifts. Hence, the communication between domains is also manifested in the accessibility of higher-energy, exchange-competent states. Overall, the data that are consistent with structural tightening relate to defined regions and are close to the 3PG binding site and in the hinge regions of 3-phosphoglycerate kinase.
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Affiliation(s)
- James P Marston
- Department of Molecular Biology and Biotechnology, Firth Court, The University of Sheffield, Western Bank, Sheffield, UK
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21
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Hosszu LLP, Trevitt CR, Jones S, Batchelor M, Scott DJ, Jackson GS, Collinge J, Waltho JP, Clarke AR. Conformational properties of beta-PrP. J Biol Chem 2009; 284:21981-21990. [PMID: 19369250 PMCID: PMC2755922 DOI: 10.1074/jbc.m809173200] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2008] [Revised: 03/19/2009] [Indexed: 11/06/2022] Open
Abstract
Prion propagation involves a conformational transition of the cellular form of prion protein (PrPC) to a disease-specific isomer (PrPSc), shifting from a predominantly alpha-helical conformation to one dominated by beta-sheet structure. This conformational transition is of critical importance in understanding the molecular basis for prion disease. Here, we elucidate the conformational properties of a disulfide-reduced fragment of human PrP spanning residues 91-231 under acidic conditions, using a combination of heteronuclear NMR, analytical ultracentrifugation, and circular dichroism. We find that this form of the protein, which similarly to PrPSc, is a potent inhibitor of the 26 S proteasome, assembles into soluble oligomers that have significant beta-sheet content. The monomeric precursor to these oligomers exhibits many of the characteristics of a molten globule intermediate with some helical character in regions that form helices I and III in the PrPC conformation, whereas helix II exhibits little evidence for adopting a helical conformation, suggesting that this region is a likely source of interaction within the initial phases of the transformation to a beta-rich conformation. This precursor state is almost as compact as the folded PrPC structure and, as it assembles, only residues 126-227 are immobilized within the oligomeric structure, leaving the remainder in a mobile, random-coil state.
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Affiliation(s)
- Laszlo L. P. Hosszu
- From the MRC Prion Unit, Department of Neurodegenerative Disease, Institute of Neurology, Queen Square, London WC1N 3BG
- the Krebs Institute for Biomolecular Research, Department of Molecular Biology and Biotechnology, University of Sheffield, Sheffield S10 2TN, and
| | - Clare R. Trevitt
- From the MRC Prion Unit, Department of Neurodegenerative Disease, Institute of Neurology, Queen Square, London WC1N 3BG
| | - Samantha Jones
- From the MRC Prion Unit, Department of Neurodegenerative Disease, Institute of Neurology, Queen Square, London WC1N 3BG
| | - Mark Batchelor
- From the MRC Prion Unit, Department of Neurodegenerative Disease, Institute of Neurology, Queen Square, London WC1N 3BG
| | - David J. Scott
- the National Centre for Macromolecular Hydrodynamics, School of Biosciences, University of Nottingham, Sutton Bonington Campus, Leicestershire LE12 5RD, United Kingdom
| | - Graham S. Jackson
- From the MRC Prion Unit, Department of Neurodegenerative Disease, Institute of Neurology, Queen Square, London WC1N 3BG
| | - John Collinge
- From the MRC Prion Unit, Department of Neurodegenerative Disease, Institute of Neurology, Queen Square, London WC1N 3BG
| | - Jonathan P. Waltho
- the Krebs Institute for Biomolecular Research, Department of Molecular Biology and Biotechnology, University of Sheffield, Sheffield S10 2TN, and
| | - Anthony R. Clarke
- From the MRC Prion Unit, Department of Neurodegenerative Disease, Institute of Neurology, Queen Square, London WC1N 3BG
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22
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Catalysis by Glomerella cingulata Cutinase Requires Conformational Cycling between the Active and Inactive States of Its Catalytic Triad. J Mol Biol 2009; 385:226-35. [DOI: 10.1016/j.jmb.2008.10.050] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2008] [Revised: 10/09/2008] [Accepted: 10/15/2008] [Indexed: 11/24/2022]
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23
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Morgan GJ, Giannini S, Hounslow AM, Craven CJ, Zerovnik E, Turk V, Waltho JP, Staniforth RA. Exclusion of the native alpha-helix from the amyloid fibrils of a mixed alpha/beta protein. J Mol Biol 2008; 375:487-98. [PMID: 18021806 DOI: 10.1016/j.jmb.2007.10.033] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2007] [Revised: 10/08/2007] [Accepted: 10/13/2007] [Indexed: 11/17/2022]
Abstract
Members of the cystatin superfamily are involved in an inherited form of cerebral amyloid angiopathy and readily form amyloid fibrils in vitro. We have determined the structured core of human stefin B (cystatin B) amyloid fibrils using quenched hydrogen exchange and NMR. The core contains residues from four of the five strands of the native beta-sheet, delimited by unprotected loop regions analogous to those of the native monomeric structure. However, non-native features are also apparent, the most striking of which is the exclusion of the native alpha-helix. Before forming amyloid in vitro, cystatins dimerise via 3D domain swapping, and assemble into tetramers with trans to cis isomerism of a conserved proline. In the fibril, the hinge loop that forms an extended beta-structure in the dimer remains protected, consistent with the domain-swapping interface being maintained. However, the fibril data are not compatible with a simple 3D domain-swapping model for amyloid formation, and the displacement of the helix points to alternative packing arrangements of native-like beta-structure, in which proline isomerism is important in preventing steric clashing.
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Affiliation(s)
- Gareth J Morgan
- Department of Molecular Biology and Biotechnology, University of Sheffield, Western Bank, Sheffield, S10 2TN, UK
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24
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Yang Y, Mak ANS, Shaw PC, Sze KH. (1)H, (13)C and (15)N backbone and side chain resonance assignments of a 28 kDa active mutant of maize ribosome-inactivating protein (MOD). BIOMOLECULAR NMR ASSIGNMENTS 2007; 1:187-189. [PMID: 19636861 DOI: 10.1007/s12104-007-9051-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/16/2007] [Accepted: 09/21/2007] [Indexed: 05/28/2023]
Abstract
We report the full resonance assignments of MOD, which is an active mutant of maize ribosome-inactivating protein (mRIP). mRIP is a unique RIP which is synthesized as an inactive precursor and processed by removal of an internal inactivation region to yield an active form.
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Affiliation(s)
- Yinhua Yang
- Chemistry Department and Open Laboratory of Chemical Biology of the Institute of Molecular Technology for Drug Discovery and Synthesis, The University of Hong Kong, P.R. China
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25
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Nagy T, Tunnicliffe RB, Higgins LD, Walters C, Gilbert HJ, Williamson MP. Characterization of a double dockerin from the cellulosome of the anaerobic fungus Piromyces equi. J Mol Biol 2007; 373:612-22. [PMID: 17869267 DOI: 10.1016/j.jmb.2007.08.007] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2007] [Accepted: 08/01/2007] [Indexed: 10/22/2022]
Abstract
The assembly into supramolecular complexes of proteins having complementary activities is central to cellular function. One such complex of considerable biological and industrial significance is the plant cell wall-degrading apparatus of anaerobic microorganisms, termed the cellulosome. A central feature of bacterial cellulosomes is a large non-catalytic protein, the scaffoldin, which contains multiple cohesin domains. An array of digestive enzymes is incorporated into the cellulosome through the interaction of the dockerin domains, present in the catalytic subunits, with the cohesin domains that are present in the scaffoldin. By contrast, in anaerobic fungi, such as Piromyces equi, the dockerins of cellulosomal enzymes are often present in tandem copies; however, the identity of the cognate cohesin domains in these organisms is unclear, hindering further biotechnological development of the fungal cellulosome. Here, we characterise the solution structure and function of a double-dockerin construct from the P. equi endoglucanase Cel45A. We show that the two domains are connected by a flexible linker that is short enough to keep the binding sites of the two domains on adjacent surfaces, and allows the double-dockerin construct to bind more tightly to cellulosomes than a single domain and with greater coverage. The double dockerin binds to the GH3 beta-glucosidase component of the fungal cellulosome, which is thereby identified as a potential scaffoldin.
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Affiliation(s)
- Tibor Nagy
- Institute for Cell and Molecular Biosciences, The University of Newcastle upon Tyne, The Medical School, Framlington Place, Newcastle upon Tyne NE2 4HH, UK
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26
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Tunnicliffe RB, Ratcliffe EC, Hunter CN, Williamson MP. The solution structure of the PufX polypeptide from Rhodobacter sphaeroides. FEBS Lett 2006; 580:6967-71. [PMID: 17161397 DOI: 10.1016/j.febslet.2006.11.065] [Citation(s) in RCA: 34] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2006] [Revised: 11/16/2006] [Accepted: 11/24/2006] [Indexed: 11/29/2022]
Abstract
PufX organizes the photosynthetic reaction centre-light harvesting complex 1 (RC-LH1) core complex of Rhodobacter sphaeroides and facilitates quinol/quinone exchange between the RC and cytochrome bc(1) complexes. The structure of PufX in organic solvent reveals two hydrophobic helices flanked by unstructured termini and connected by a helical bend. The proposed location of basic residues and tryptophans at the membrane interface orients the C-terminal helix along the membrane normal, with the GXXXG motifs in positions unsuitable as direct drivers of dimerisation of the RC-LH1 complex. The N-terminal helix is predicted to extend approximately 40 Anggstrom along the membrane interface.
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Affiliation(s)
- Richard B Tunnicliffe
- Department of Molecular Biology and Biotechnology, University of Sheffield, Firth Court, Western Bank, Sheffield S10 2TN, UK
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27
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Cliff MJ, Alizadeh T, Jelinska C, Craven CJ, Staniforth RA, Waltho JP. A Thiol Labelling Competition Experiment as a Probe for Sidechain Packing in the Kinetic Folding Intermediate of N-PGK. J Mol Biol 2006; 364:810-23. [PMID: 17030040 DOI: 10.1016/j.jmb.2006.09.014] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2006] [Revised: 09/01/2006] [Accepted: 09/03/2006] [Indexed: 10/24/2022]
Abstract
Protein folding is directed by the sequence of sidechains along the polypeptide backbone, but despite this the developement of sidechain interactions during folding is not well understood. Here, the thiol-active reagent, dithio-nitrobenzoic acid (DTNB), is used to probe the exposure of the cysteine sidechain thiols in the kinetic folding intermediates of the N-terminal domain of phosphoglycerate kinase (N-PGK) and a number of conservative (I-, L-, or V-to-C) single cysteine variants. Rapid dilution of chemically denatured protein into folding conditions in the presence of DTNB allowed the degree of sidechain protection in any rapidly formed intermediate to be determined through the analysis of the kinetics of labelling. The protection factors derived for the intermediate(s) were generally small (<25), indicating only partial burial of the sidechains. The distribution of protection parallels the previously reported backbone amide protection for the folding intermediate of N-PGK. These observations are consistent with the hypothesis that such intermediates resemble molten globule states; i.e. with native-like backbone hydrogen bonding and overall tertiary structure, but with the sidechains that make up the hydrophobic protein core dynamic and intermittently solvent exposed. The success of the competition technique in characterizing this kinetic intermediate invites application to other model systems.
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Affiliation(s)
- Matthew J Cliff
- Department of Molecular Biology and Biotechnology, University of Sheffield, Firth Court, Western Bank, Sheffield, S10 2TN, UK.
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28
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Batey S, Clarke J. Apparent cooperativity in the folding of multidomain proteins depends on the relative rates of folding of the constituent domains. Proc Natl Acad Sci U S A 2006; 103:18113-8. [PMID: 17108086 PMCID: PMC1636339 DOI: 10.1073/pnas.0604580103] [Citation(s) in RCA: 49] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Approximately 75% of eukaryotic proteins contain more than one so-called independently folding domain. However, there have been relatively few systematic studies to investigate the effect of interdomain interactions on protein stability and fewer still on folding kinetics. We present the folding of pairs of three-helix bundle spectrin domains as a paradigm to indicate how complex such an analysis can be. Equilibrium studies show an increase in denaturant concentration required to unfold the domains with only a single unfolding transition; however, in some cases, this is not accompanied by the increase in m value, which would be expected if the protein is a truly cooperative, all-or-none system. We analyze the complex kinetics of spectrin domain pairs, both wild-type and carefully selected mutants. By comparing these pairs, we are able to demonstrate that equilibrium data alone are insufficient to describe the folding of multidomain proteins and to quantify the effects that one domain can have on its neighbor.
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Affiliation(s)
- Sarah Batey
- Department of Chemistry, University of Cambridge, Medical Research Council Centre for Protein Engineering, Lensfield Road, Cambridge CB2 1EW, United Kingdom
| | - Jane Clarke
- Department of Chemistry, University of Cambridge, Medical Research Council Centre for Protein Engineering, Lensfield Road, Cambridge CB2 1EW, United Kingdom
- To whom correspondence should be addressed. E-mail:
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29
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Baxter NJ, Olguin LF, Goličnik M, Feng G, Hounslow AM, Bermel W, Blackburn GM, Hollfelder F, Waltho JP, Williams NH. A Trojan horse transition state analogue generated by MgF3- formation in an enzyme active site. Proc Natl Acad Sci U S A 2006; 103:14732-7. [PMID: 16990434 PMCID: PMC1595420 DOI: 10.1073/pnas.0604448103] [Citation(s) in RCA: 60] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Identifying how enzymes stabilize high-energy species along the reaction pathway is central to explaining their enormous rate acceleration. beta-Phosphoglucomutase catalyses the isomerization of beta-glucose-1-phosphate to beta-glucose-6-phosphate and appeared to be unique in its ability to stabilize a high-energy pentacoordinate phosphorane intermediate sufficiently to be directly observable in the enzyme active site. Using (19)F-NMR and kinetic analysis, we report that the complex that forms is not the postulated high-energy reaction intermediate, but a deceptively similar transition state analogue in which MgF(3)(-) mimics the transferring PO(3)(-) moiety. Here we present a detailed characterization of the metal ion-fluoride complex bound to the enzyme active site in solution, which reveals the molecular mechanism for fluoride inhibition of beta-phosphoglucomutase. This NMR methodology has a general application in identifying specific interactions between fluoride complexes and proteins and resolving structural assignments that are indistinguishable by x-ray crystallography.
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Affiliation(s)
- Nicola J. Baxter
- Department of Molecular Biology and Biotechnology, University of Sheffield, Sheffield S10 2TN, United Kingdom
| | - Luis F. Olguin
- Department of Biochemistry, University of Cambridge, Cambridge CB2 1GA, United Kingdom
| | - Marko Goličnik
- Department of Biochemistry, University of Cambridge, Cambridge CB2 1GA, United Kingdom
| | - Guoqiang Feng
- Centre for Chemical Biology, Department of Chemistry, University of Sheffield, Sheffield S3 7HF, United Kingdom; and
| | - Andrea M. Hounslow
- Department of Molecular Biology and Biotechnology, University of Sheffield, Sheffield S10 2TN, United Kingdom
| | - Wolfgang Bermel
- Bruker BioSpin GmbH, Silberstreifen 4, 76287 Rheinstetten, Germany
| | - G. Michael Blackburn
- Centre for Chemical Biology, Department of Chemistry, University of Sheffield, Sheffield S3 7HF, United Kingdom; and
| | - Florian Hollfelder
- Department of Biochemistry, University of Cambridge, Cambridge CB2 1GA, United Kingdom
- To whom correspondence may be addressed. E-mail:
, , or
| | - Jonathan P. Waltho
- Department of Molecular Biology and Biotechnology, University of Sheffield, Sheffield S10 2TN, United Kingdom
- To whom correspondence may be addressed. E-mail:
, , or
| | - Nicholas H. Williams
- Centre for Chemical Biology, Department of Chemistry, University of Sheffield, Sheffield S3 7HF, United Kingdom; and
- To whom correspondence may be addressed. E-mail:
, , or
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30
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Reed MAC, Jelinska C, Syson K, Cliff MJ, Splevins A, Alizadeh T, Hounslow AM, Staniforth RA, Clarke AR, Craven CJ, Waltho JP. The Denatured State under Native Conditions: A Non-native-like Collapsed State of N-PGK. J Mol Biol 2006; 357:365-72. [PMID: 16430920 DOI: 10.1016/j.jmb.2005.12.080] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2005] [Revised: 12/22/2005] [Accepted: 12/26/2005] [Indexed: 12/01/2022]
Abstract
The guanidinium-denatured state of the N-domain of phosphoglycerate kinase (PGK) has been characterized using solution NMR. Rather than behaving as a homogenous ensemble of random coils, chemical shift changes for the majority of backbone amide resonances indicate that the denatured ensemble undergoes two definable equilibrium transitions upon titration with guanidinium, in addition to the major refolding event. (13)C and (15)N chemical shift changes indicate that both intermediary states have distinct helical character. At denaturant concentrations immediately above the mid-point of unfolding, size-exclusion chromatography shows N-PGK to have a compact, denatured form, suggesting that it forms a helical molten globule. Within this globule, the helices extend into some regions that become beta strands in the native state. This predisposition of the denatured state to extensive non-native-like conformation, illustrates that, rather than directing folding, conformational pre-organization in the denatured state can compete with the normal folding direction. The corresponding reduction in control of the direction of folding as proteins become larger, could thus constitute a restriction on the size of protein domains.
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Affiliation(s)
- Michelle A C Reed
- Department of Molecular Biology and Biotechnology, University of Sheffield, Sheffield S10 2TN, UK
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31
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Baxter NJ, Roetzer A, Liebig HD, Sedelnikova SE, Hounslow AM, Skern T, Waltho JP. Structure and dynamics of coxsackievirus B4 2A proteinase, an enyzme involved in the etiology of heart disease. J Virol 2006; 80:1451-62. [PMID: 16415022 PMCID: PMC1346940 DOI: 10.1128/jvi.80.3.1451-1462.2006] [Citation(s) in RCA: 35] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The 2A proteinases (2A(pro)) from the picornavirus family are multifunctional cysteine proteinases that perform essential roles during viral replication, involving viral polyprotein self-processing and shutting down host cell protein synthesis through cleavage of the eukaryotic initiation factor 4G (eIF4G) proteins. Coxsackievirus B4 (CVB4) 2A(pro) also cleaves heart muscle dystrophin, leading to cytoskeletal dysfunction and the symptoms of human acquired dilated cardiomyopathy. We have determined the solution structure of CVB4 2A(pro) (extending in an N-terminal direction to include the C-terminal eight residues of CVB4 VP1, which completes the VP1-2A(pro) substrate region). In terms of overall fold, it is similar to the crystal structure of the mature human rhinovirus serotype 2 (HRV2) 2A(pro), but the relatively low level (40%) of sequence identity leads to a substantially different surface. We show that differences in the cI-to-eI2 loop between HRV2 and CVB4 2A(pro) translate to differences in the mechanism of eIF4GI recognition. Additionally, the nuclear magnetic resonance relaxation properties of CVB4 2A(pro), particularly of residues G1 to S7, F64 to S67, and P107 to G111, reveal that the substrate region is exchanging in and out of a conformation in which it occupies the active site with association and dissociation rates in the range of 100 to 1,000 s(-1). This exchange influences the conformation of the active site and points to a mechanism for how self-processing can occur efficiently while product inhibition is avoided.
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Affiliation(s)
- Nicola J Baxter
- Krebs Institute for Biomolecular Research, Department of Molecular Biology and Biotechnology, University of Sheffield, Firth Court, Western Bank, Sheffield, S10 2TN, United Kingdom
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32
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Zecchinon L, Oriol A, Netzel U, Svennberg J, Gerardin-Otthiers N, Feller G. Stability domains, substrate-induced conformational changes, and hinge-bending motions in a psychrophilic phosphoglycerate kinase. A microcalorimetric study. J Biol Chem 2005; 280:41307-14. [PMID: 16227206 DOI: 10.1074/jbc.m506464200] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The cold-active phosphoglycerate kinase from the Antarctic bacterium Pseudomonas sp. TACII18 exhibits two distinct stability domains in the free, open conformation. It is shown that these stability domains do not match the structural N- and C-domains as the heat-stable domain corresponds to about 80 residues of the C-domain, including the nucleotide binding site, whereas the remaining of the protein contributes to the main heat-labile domain. This was demonstrated by spectroscopic and microcalorimetric analyses of the native enzyme, of its mutants, and of the isolated recombinant structural domains. It is proposed that the heat-stable domain provides a compact structure improving the binding affinity of the nucleotide, therefore increasing the catalytic efficiency at low temperatures. Upon substrate binding, the enzyme adopts a uniformly more stable closed conformation. Substrate-induced stability changes suggest that the free energy of ligand binding is converted into an increased conformational stability used to drive the hinge-bending motions and domain closure.
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Affiliation(s)
- Laurent Zecchinon
- Laboratory of Biochemistry, University of Liège, Institute of Chemistry B6a, B-4000 Liège-Sart Tilman, Belgium
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33
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Syson K, Thirlway J, Hounslow AM, Soultanas P, Waltho JP. Solution structure of the helicase-interaction domain of the primase DnaG: a model for helicase activation. Structure 2005; 13:609-16. [PMID: 15837199 PMCID: PMC3033578 DOI: 10.1016/j.str.2005.01.022] [Citation(s) in RCA: 42] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2004] [Revised: 01/20/2005] [Accepted: 01/26/2005] [Indexed: 11/30/2022]
Abstract
The helicase-primase interaction is a critical event in DNA replication and is mediated by a putative helicase-interaction domain within the primase. The solution structure of the helicase-interaction domain of DnaG reveals that it is made up of two independent subdomains: an N-terminal six-helix module and a C-terminal two-helix module that contains the residues of the primase previously identified as important in the interaction with the helicase. We show that the two-helix module alone is sufficient for strong binding between the primase and the helicase but fails to activate the helicase; both subdomains are required for helicase activation. The six-helix module of the primase has only one close structural homolog, the N-terminal domain of the corresponding helicase. This surprising structural relationship, coupled with the differences in surface properties of the two molecules, suggests how the helicase-interaction domain may perturb the structure of the helicase and lead to activation.
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Affiliation(s)
- Karl Syson
- Department of Molecular Biology and Biotechnology, Krebs Institute, Western Bank, University of Sheffield, Sheffield S10 2TN, United Kingdom
| | - Jenny Thirlway
- Centre for Biomolecular Sciences, University of Nottingham, University Park, Nottingham NG7 2RD, United Kingdom
| | - Andrea M. Hounslow
- Department of Molecular Biology and Biotechnology, Krebs Institute, Western Bank, University of Sheffield, Sheffield S10 2TN, United Kingdom
| | - Panos Soultanas
- Centre for Biomolecular Sciences, University of Nottingham, University Park, Nottingham NG7 2RD, United Kingdom
- Correspondence: (P.S.); (J.P.W.)
| | - Jonathan P. Waltho
- Department of Molecular Biology and Biotechnology, Krebs Institute, Western Bank, University of Sheffield, Sheffield S10 2TN, United Kingdom
- Correspondence: (P.S.); (J.P.W.)
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34
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Osváth S, Köhler G, Závodszky P, Fidy J. Asymmetric effect of domain interactions on the kinetics of folding in yeast phosphoglycerate kinase. Protein Sci 2005; 14:1609-16. [PMID: 15883189 PMCID: PMC2253372 DOI: 10.1110/ps.051359905] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Abstract
The aim of this work is to shed more light on the effect of domain-domain interactions on the kinetics and the pathway of protein folding. A model protein system consisting of several single-tryptophan variants of the two-domain yeast phosphoglycerate kinase (PGK) and its individual domains was studied. Refolding was initiated from the guanidine-unfolded state by stopped-flow or manual mixing and monitored by tryptophan fluorescence from 1 msec to 1000 sec. Denaturant titrations of both individual domains showed apparent two-state unfolding transitions. Refolding kinetics of the individual domains from different denaturant concentrations, however, revealed the presence of intermediate structures during titration for both domains. Refolding of the same domains within the complete protein showed that domain-domain interactions direct the folding of both domains, but in an asymmetric way. Folding of the N domain was already altered within 1 msec, while detectable changes in the folding of the C domain occurred only 60-100 msec after initiating refolding. All mutants showed a hyperfluorescent kinetic intermediate. Both the disappearance of this intermediate and the completion of the folding were significantly faster in the individual N domain than in the complete protein. On the contrary, folding of the individual C domain was slower than in the complete protein. The presence of the C domain directs the refolding of the N domain along a completely different pathway than that of the individual N domain, while folding of the individual C domain follows the same path as within the complete protein.
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Affiliation(s)
- Szabolcs Osváth
- Department of Biophysics and Radiation Biology, Hungarian Academy of Sciences-Semmelweis University, Budapest.
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35
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Tunnicliffe RB, Bolam DN, Pell G, Gilbert HJ, Williamson MP. Structure of a mannan-specific family 35 carbohydrate-binding module: evidence for significant conformational changes upon ligand binding. J Mol Biol 2005; 347:287-96. [PMID: 15740741 DOI: 10.1016/j.jmb.2005.01.038] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2004] [Revised: 01/12/2005] [Accepted: 01/17/2005] [Indexed: 10/25/2022]
Abstract
Enzymes that digest plant cell wall polysaccharides generally contain non-catalytic, carbohydrate-binding modules (CBMs) that function by attaching the enzyme to the substrate, potentiating catalytic activity. Here, we present the first structure of a family 35 CBM, derived from the Cellvibrio japonicus beta-1,4-mannanase Man5C. The NMR structure has been determined for both the free protein and the protein bound to mannopentaose. The data show that the protein displays a typical beta-jelly-roll fold. Ligand binding is not located on the concave surface of the protein, as occurs in many CBMs that display the jelly-roll fold, but is formed by the loops that link the two beta-sheets of the protein, similar to family 6 CBMs. In contrast to the majority of CBMs, which are generally rigid proteins, CBM35 undergoes significant conformational change upon ligand binding. The curvature of the binding site and the narrow binding cleft are likely to be the main determinants of binding specificity. The predicted solvent exposure of O6 at several subsites provides an explanation for the observed accommodation of decorated mannans. Two of the key aromatic residues in Man5C-CBM35 that interact with mannopentaose are conserved in mannanase-derived CBM35s, which will guide specificity predictions based on the primary sequence of proteins in this CBM family.
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Affiliation(s)
- Richard B Tunnicliffe
- Department of Molecular Biology and Biotechnology, University of Sheffield, Western Bank, Sheffield S10 2TN, UK
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36
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Zhong Q, Watson MJ, Lazar CS, Hounslow AM, Waltho JP, Gill GN. Determinants of the endosomal localization of sorting nexin 1. Mol Biol Cell 2005; 16:2049-57. [PMID: 15673616 PMCID: PMC1073682 DOI: 10.1091/mbc.e04-06-0504] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
Abstract
The sorting nexin (SNX) family of proteins is characterized by sequence-related phox homology (PX) domains. A minority of PX domains bind with high affinity to phosphatidylinositol 3-phosphate [PI(3)P], whereas the majority of PX domains exhibit low affinity that is insufficient to target them to vesicles. SNX1 is located on endosomes, but its low affinity PX domain fails to localize in vivo. The NMR structure of the PX domain of SNX1 reveals an overall fold that is similar to high-affinity PX domains. However, the phosphatidylinositol (PI) binding pocket of the SNX1 PX domain is incomplete; regions of the pocket that are well defined in high-affinity PX domains are highly mobile in SNX1. Some of this mobility is lost upon binding PI(3)P. The C-terminal domain of SNX1 is a long helical dimer that localizes to vesicles but not to the early endosome antigen-1-containing vesicles where endogenous SNX1 resides. Thus, the obligate dimerization of SNX1 that is driven by the C-terminal domain creates a high-affinity PI binding species that properly targets the holo protein to endosomes.
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Affiliation(s)
- Qi Zhong
- Department of Medicine and Cellular, University of California, San Diego, La Jolla, 92093-0650, USA
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