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Crystal structure of the entire respiratory complex I

Rozbeh Baradaran, John M. Berrisford, Gurdeep S. Minhas, Leonid A. Sazanov
2013 Nature  
Batista b , Alvaro Alonso a , Manuela M. Pereira b , Marisela Vélez a , Antonio L.  ... 
doi:10.1038/nature11871 pmid:23417064 pmcid:PMC3672946 fatcat:xjovhrhs2nfwnhf47asfu4palu

Structural Basis for the Mechanism of Respiratory Complex I

John M. Berrisford, Leonid A. Sazanov
2009 Journal of Biological Chemistry  
In contrast, NADH has high affinity for both the oxidized (ϳ10 M) and the reduced enzyme (ϳ100 M) (4, 19) .  ...  In the O2 structure (crystals grown in 0.1 M MnCl 2 ), six to eight cations bound per molecule were resolved.  ... 
doi:10.1074/jbc.m109.032144 pmid:19635800 pmcid:PMC2785608 fatcat:y53k3ejquzf4lnnrslwcitbnri

NADH binding to complex I: Implications for the mechanism

John M. Berrisford, Leonid A. Sazanov
2010 Biochimica et Biophysica Acta - Bioenergetics  
oxygen species (ROS) production and to enzymatic activity assays. Submitochondrial particles (SMP) were treated with class A or B inhibitors. NADH addition initiated the electron transfer. In our system class A inhibitors (rotenone, piericidin A) increase ROS production from complex I, whereas class B inhibitors (stigmatellin, mucidin, CoQ2) have no effect on ROS production. We measured the presence of semiquinone (SQ) at 180 K and state of reduction of the iron sulfur cluster N2 at 12 K in SMP
more » ... inhibited with class A and class B inhibitors. Our data confirm a strong SQ signal reduction in the presence of rotenone while the signal intensity is less reduced in samples treated with stigmatellin [2]. N2 spectra show different reduction state in presence of rotenone and stigmatellin. In presence of stigmatellin the center is mainly oxidized. We hypothesize a twostep reduction performed by N2, possibly following a rearrangement of the site [3]. Rotenone like inhibitors, not allowing the access of the quinone to the active site, would block the enzyme in a conformation that only permits electron delivery from N2 to oxygen. In this conformation hydrophilic quinones like CoQ1 can be reduced by N2 to a semiquinone species in a non physiological site. This semiquinone can rapidly react with molecular oxygen to form anion superoxide. Stigmatellin like inhibitors would block the enzyme in a conformation allowing only the first step of quinone reduction (Q → SQ) in the physiological reduction site, but blocking any further reduction; this conformation does not allow reaction of N2 with oxygen. Complex I plays a central role in cellular energy production, coupling electron transfer between NADH and quinone to proton translocation. We have determined several X-ray structures of the oxidized and reduced hydrophilic domain of complex I from Thermus thermophilus at up to 3.1 Å resolution. The structures reveal the mode of interaction of complex I with NADH, explaining known kinetic data and providing implications for the mechanism of ROS production at the flavin site of complex I. Bound metals were identified in the channel at the interface with the frataxin-like subunit Nqo15, indicating possible iron-binding sites. Conformational changes upon reduction of the complex involve adjustments in the nucleotide binding pocket, as well as small, but significant, shifts of several αhelices at the interface with the membrane domain. These shifts are likely to be driven by the reduction of nearby Fe-S clusters N2 (the electron donor to quinone) and N6a/b. Cluster N2 is coordinated by unique motif involving two consecutive (tandem) cysteines. An unprecedented "on/off switch" (disconnection) of coordinating bonds between the tandem cysteines and this cluster was observed upon reduction. Comparison of the structures suggests a novel mechanism of coupling between electron transfer and proton translocation, combining conformational changes and protonation/ de-protonation of tandem cysteines.
doi:10.1016/j.bbabio.2010.04.053 fatcat:5osmsmwl3bf2zkywlmdzzjxtpa

The architecture of bacterial respiratory complex I

Leonid A. Sazanov, Rouslan G. Efremov, Rozbeh Baradaran, John M. Berrisford
2010 Biochimica et Biophysica Acta - Bioenergetics  
Earlier, T. Ohnishi and her collaborators detected two distinct protein-associated semiquinone species (SQNf and SQNs). Only SQNf signal intensity is strongly dependent on the proton motive force, thus we proposed a novel mechanistic hypothesis of a "proton pump gated by SQNf and redox-driven conformational change of its binding protein (Ohnishi & Salerno, FEBS Lett., 2005, 579: 4555-4561). This model is now modified to include both QNf and QNs molecules. To investigate the indirect proton-pump
more » ... mechanism, we focused on the largest transmembrane NuoL subunit which has a high sequence similarity to the multi-subunit (Na + /H + ) antiporter, like NuoM and N. (NuoN, however, does not contain active acidic residues, and localizes most likely the SQNs-binding site.) We constructed 13 NuoL mutants of highly conserved acidic residues. Similar amount of fully assembled protein were obtained in most of these mutants. Their dNADH-oxidase activities were mostly at the control level or modestly reduced. The proton pumping efficiency, however, was decreased in these NuoL mutants by 30-50% without affecting IC 50 values for asimicin (a potent inhibitor for E. coli complex I). This suggests that the (H + /e − ) stoichiometry has changed from (4H + /2e − ) to either (3H + /2e − ) or (2H + /2e − ). Furthermore, 5-(N-ethyl-N-isopropyl)-amiloride (EIPA), a specific inhibitor for (Na + /H + ) antiporters, caused a 38 ± 5% decrease in the initial (H + ) pump activity in the wild-type membranes. However, no change was observed in D178N, D303A and D400A mutants (in which the (H + ) pumping efficiency had already been decreased by the NuoL mutation). The electron transfer activities were unaffected by EIPA in all of the mutants. Our data indicate that the NuoL subunit is involved in the indirect proton pump, although the NuoM subunit may also be involved. Thus, we propose that electron-proton coupling in complex I consists of "QNf-gated (H + ) pump" and "QNs-induced conformationally-driven (H + ) pump", each of which transports (2H + ) coupled with 2 electron transfer. Both pumps must be operated by the redox energy. In the indirect pump, the conformational linkage to the (Na + /H + ) antiporter homologs is provided by quinone binding site occupancy. After the uptake of scalar (H + ) from the N-side, the binding of quinone to the SQNs site, and the release of quinol from there, conformationally triggers ion pump reorientation, enabling vectorial (H + ) movement. We propose that QNf carries (2H + ) (direct pump) and QNs induces the transport of (2H + ) (indirect pump).
doi:10.1016/j.bbabio.2010.04.048 fatcat:oqf4ai4vfvf45cixn3e42jpr54

Crystal Structure ofPyrococcus furiosusPhosphoglucose Isomerase

John M. Berrisford, Jasper Akerboom, Andrew P. Turnbull, Daniel de Geus, Svetlana E. Sedelnikova, Ian Staton, Cameron W. McLeod, Corne H. Verhees, John van der Oost, David W. Rice, Patrick J. Baker
2003 Journal of Biological Chemistry  
FIG. 4 . 4 Sequence alignment of PGIs from Pfu (PfuPGI), Tli (TliPGI), and the putative PGIs from S. meliloti (SmPGI1 and -2), M. mazei (MmPGI), and M. acetivorans (MaPGI).  ...  Soaks with metal ions were performed by adding 1 l of 10 mM MnSO 4 or ZnSO 4 in 1.6 M sodium citrate dihydrate, pH 6.5, to the 2-l drop containing the crystal for 4 h.  ... 
doi:10.1074/jbc.m305170200 pmid:12796486 fatcat:qrs7c6k63bhj7b4crcthkni6na

The Bacterial Stressosome: A Modular System that Has Been Adapted to Control Secondary Messenger Signaling

Maureen B. Quin, John M. Berrisford, Joseph A. Newman, Arnaud Baslé, Richard J. Lewis, Jon Marles-Wright
2012 Structure  
Ragsdale for the kind gift of M. thermoacetica genomic DNA and Dr. T. Schirmer for the kind gift of an expression plasmid containing E. coli ydeH.  ...  The M. thermoacetica RsbS equivalent is encoded by moth_1474 and is referred to herein as MtS (M. thermoacetica RsbS-like protein).  ...  -1 , k d 2.75 ± 0.03 3 10 À2 s -1 , K D 1 3 10 À6 M and chi 2 3.27.  ... 
doi:10.1016/j.str.2012.01.003 pmid:22325782 fatcat:dmpxic55fnhutjku32kdzstroy

Purification, crystallization and preliminary crystallographic analysis of phosphoglucose isomerase from the hyperthermophilic archaeonPyrococcus furiosus

Jasper Akerboom, Andrew P. Turnbull, David Hargreaves, Martin Fisher, Daniel de Geus, Svetlana E. Sedelnikova, John M. Berrisford, Patrick J. Baker, Corne H. Verhees, John van der Oost, David W. Rice
2003 Acta Crystallographica Section D: Biological Crystallography  
bacterial or eukaryotic phosphoglucose isomerase, has been cloned and overexpressed in Escherichia coli, puri®ed and subsequently crystallized by the hanging-drop method of vapour diffusion using 1.6 M  ...  Consideration of the values of V M suggests that the asymmetric unit contains a monomer with a V M value of 2.1 A Ê 3 Da À1 , which is within the range observed by Matthews for protein crystals (Matthews  ...  Crystals of the methionine and seleno-methionine protein grew optimally in 1.6 M sodium citrate dihydrate pH 6.5 (condition No. 28) after 2±3 weeks.  ... 
doi:10.1107/s090744490301610x pmid:14501126 fatcat:tbg2ukrqtvhdfjz4sguiofsnda

Crystallization and preliminary X-ray analysis of recombinantGlomerella cingulatacutinase

Mun Peak Nyon, David W. Rice, John M. Berrisford, Huazhang Huang, Arthur J. G. Moir, C. Jeremy Craven, Sheila Nathan, Nor Muhammad Mahadi, Farah Diba Abu Bakar
2008 Acta Crystallographica. Section F : Structural Biology and Crystallization Communications  
Considerations of possible values of V M suggested that the asymmetric unit contained two or three subunits, with a V M of 2.82 or 1.86 Å 3 Da À1 , respectively.  ...  0.15 Â 0.15 Â 0.1 mm and were grown in 16-30%(w/v) PEG 4000 in 0.1 M sodium acetate pH 4.6 Figure 3 et al.  ... 
doi:10.1107/s1744309108012086 pmid:18540061 pmcid:PMC2496845 fatcat:pcwxtncwzfhmho6gwrwoby2lzm

Combining satellite observations and reanalysis energy transports to estimate global net surface energy fluxes 1985-2012

Chunlei Liu, Richard P. Allan, Paul Berrisford, Michael Mayer, Patrick Hyder, Norman Loeb, Doug Smith, Pier-Luigi Vidale, John M. Edwards
2015 Journal of Geophysical Research - Atmospheres  
The changes at the surface 397 (Fig. 6i,l) are 2.2W/m 2 and 3.3W/m 2 and the corresponding mean divergence changes of horizontal 398 energy transport (Fig. 6j,m) are 2.7W/m 2 and 3.8W/m 2 , respectively  ...  Sardeshmukh and Hoskins, 1984] with an attenuation of 0.1 at wave number 106 [Berrisford et al., 298 2011].  ... 
doi:10.1002/2015jd023264 fatcat:ozihylz3tbfjlgtfhiezxumzk4

PDBe: towards reusable data delivery infrastructure at protein data bank in Europe

Saqib Mir, Younes Alhroub, Stephen Anyango, David R Armstrong, John M Berrisford, Alice R Clark, Matthew J Conroy, Jose M Dana, Mandar Deshpande, Deepti Gupta, Aleksandras Gutmanas, Pauline Haslam (+10 others)
2017 Nucleic Acids Research  
The Protein Data Bank in Europe (PDBe, pdbe.org) is actively engaged in the deposition, annotation, remediation, enrichment and dissemination of macromolecular structure data. This paper describes new developments and improvements at PDBe addressing three challenging areas: data enrichment, data dissemination and functional reusability. New features of the PDBe Web site are discussed, including a context dependent menu providing links to raw experimental data and improved presentation of
more » ... res solved by hybrid methods. The paper also summarizes the features of the LiteMol suite, which is a set of services enabling fast and interactive 3D visualization of structures, with associated experimental maps, annotations and quality assessment information. We introduce a library of Web components which can be easily reused to port data and functionality available at PDBe to other services. We also introduce updates to the SIFTS resource which maps PDB data to other bioinformatics resources, and the PDBe REST API.
doi:10.1093/nar/gkx1070 pmid:29126160 pmcid:PMC5753225 fatcat:j6ocp5cauvau3d7jd4gw3htwiq

PDBe: Protein Data Bank in Europe

Aleksandras Gutmanas, Younes Alhroub, Gary M. Battle, John M. Berrisford, Estelle Bochet, Matthew J. Conroy, Jose M. Dana, Manuel A. Fernandez Montecelo, Glen van Ginkel, Swanand P. Gore, Pauline Haslam, Rowan Hatherley (+15 others)
2013 Nucleic Acids Research  
The Protein Data Bank in Europe (pdbe.org) is a founding member of the Worldwide PDB consortium (wwPDB; wwpdb.org) and as such is actively engaged in the deposition, annotation, remediation and dissemination of macromolecular structure data through the single global archive for such data, the PDB. Similarly, PDBe is a member of the EMDataBank organisation (emdatabank.org), which manages the EMDB archive for electron microscopy data. PDBe also develops tools that help the biomedical science
more » ... nity to make effective use of the data in the PDB and EMDB for their research. Here we describe new or improved services, including updated SIFTS mappings to other bioinformatics resources, a new browser for the PDB archive based on Gene Ontology (GO) annotation, updates to the analysis of Nuclear Magnetic Resonance-derived structures, redesigned search and browse interfaces, and new or updated visualisation and validation tools for EMDB entries.
doi:10.1093/nar/gkt1180 pmid:24288376 pmcid:PMC3965016 fatcat:rv2cpebl5ffzbdppo654oahfly

PDBe: improved accessibility of macromolecular structure data from PDB and EMDB

Sameer Velankar, Glen van Ginkel, Younes Alhroub, Gary M. Battle, John M. Berrisford, Matthew J. Conroy, Jose M. Dana, Swanand P. Gore, Aleksandras Gutmanas, Pauline Haslam, Pieter M. S. Hendrickx, Ingvar Lagerstedt (+21 others)
2015 Nucleic Acids Research  
', 'MAD' etc. diffrn detector.detector The type of detector used in the diffraction experiment computing.structure refinement Software used for refinement of the structure symmetry.space group name H-M  ... 
doi:10.1093/nar/gkv1047 pmid:26476444 pmcid:PMC4702783 fatcat:sqjtb2p3drbjncdycqrfr3m2lm

OneDep: Unified wwPDB System for Deposition, Biocuration, and Validation of Macromolecular Structures in the PDB Archive

Jasmine Y. Young, John D. Westbrook, Zukang Feng, Raul Sala, Ezra Peisach, Thomas J. Oldfield, Sanchayita Sen, Aleksandras Gutmanas, David R. Armstrong, John M. Berrisford, Li Chen, Minyu Chen (+37 others)
2017 Structure  
OneDep, a unified system for deposition, biocuration, and validation of experimentally determined structures of biological macromolecules to the PDB archive, has been developed as a global collaboration by the worldwide PDB (wwPDB) partners. This new system was designed to ensure that the wwPDB could meet the evolving archiving requirements of the scientific community over the coming decades. OneDep unifies deposition, biocuration, and validation pipelines across all wwPDB, EMDB, and BMRB
more » ... tion sites with improved focus on data quality and completeness in these archives, while supporting growth in the number of depositions and increases in their average size and complexity. In this paper, we describe the design, functional operation, and supporting infrastructure of the OneDep system, and provide initial performance assessments.
doi:10.1016/j.str.2017.01.004 pmid:28190782 pmcid:PMC5360273 fatcat:okamctypwvdrxfomgjio4rsvma

Announcing mandatory submission of PDBx/mmCIF format files for crystallographic depositions to the Protein Data Bank (PDB)

Paul D. Adams, Pavel V. Afonine, Kumaran Baskaran, Helen M. Berman, John Berrisford, Gerard Bricogne, David G. Brown, Stephen K. Burley, Minyu Chen, Zukang Feng, Claus Flensburg, Aleksandras Gutmanas (+23 others)
2019 Acta Crystallographica Section D: Structural Biology  
doi:10.1107/s2059798319004522 pmid:30988261 pmcid:PMC6465986 fatcat:lfqllnbmuzapnc4cv2r4za3ncy

Worldwide Protein Data Bank biocuration supporting open access to high-quality 3D structural biology data

Jasmine Y Young, John D Westbrook, Zukang Feng, Ezra Peisach, Irina Persikova, Raul Sala, Sanchayita Sen, John M Berrisford, G Jawahar Swaminathan, Thomas J Oldfield, Aleksandras Gutmanas, Reiko Igarashi (+39 others)
2018 Database: The Journal of Biological Databases and Curation  
Table 1 . 1 Example of how the PDBx/mmCIF dictionary is used in describing the expression of a protein from M. musculus in E. coli Dictionary item Definition Value _entity_src_gen.entity_id Unique  ...  identifier for each entity 1 _entity_src_gen.pdbx_gene_src_scientific_name Scientific name for source organism M. musculus _entity_src_gen.gene_src_common_name Common name for source organism Mouse  ... 
doi:10.1093/database/bay002 pmid:29688351 pmcid:PMC5804564 fatcat:pymncvy65zghjgdhleavnz7oce
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