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Keywords: structure
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Journal:
Biochemical Journal
Biochem J (2023) 480 (21): 1767–1789.
Published: 15 November 2023
... to give an overview of what is known to date about these interactions including metabolic remodelling, mitochondrial morphology, mitochondrial turnover, cellular processes and muscle cell structure and function. Each of these topics is at a different stage of understanding, with some being well researched...
Articles
Searching for methyllysine-binding aromatic cages
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Journal:
Biochemical Journal
Biochem J (2021) 478 (19): 3613–3619.
Published: 08 October 2021
... is well established, the processes associated with methylation of non-histone proteins, particularly in the cytoplasm of the cell, are not well understood. Here, we describe a search for potential methyllysine readers using a rapid structural motif-mining algorithm Erebus , the PDB database, and knowledge...
Includes: Supplementary data
Articles
Crystal structure of human APPL BAR-PH heterodimer reveals a flexible dimeric BAR curve: implication in mutual regulation of endosomal targeting
Available to Purchase
Journal:
Biochemical Journal
Biochem J (2020) 477 (24): 4769–4783.
Published: 24 December 2020
... either homodimerize or heterodimerize in vivo , we hypothesized that heterodimerization of APPL proteins might account for the mechanism. By solving the crystal structure of APPL1–APPL2 BAR-PH heterodimer, we find that the overall structure is crescent-shaped with a longer curvature radius of 76...
Includes: Supplementary data
Articles
Crystal structure of HECT domain of UBE3C E3 ligase and its ubiquitination activity
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Journal:
Biochemical Journal
Biochem J (2020) 477 (5): 905–923.
Published: 04 March 2020
...Sunil Singh; J. Sivaraman The HECT family of E3 ubiquitin ligase is divided into three subfamilies: the NEDD4, the HERC, and the ‘other’. Previous studies have mostly targeted members of the NEDD4 subfamily for structural and functional analysis. The UBE3C E3 ligase is a member of the ‘other...
Includes: Supplementary data
Articles
Journal:
Biochemical Journal
Biochem J (2019) 476 (7): 1037–1051.
Published: 04 April 2019
... of substrates, and CDC42 or Rac binding to the regulatory domain relieves this auto-inhibition allowing auto-phosphorylation on the KD activation loop. We have determined the crystal structure of the PAK3 catalytic domain and by small angle X-ray scattering, the solution-phase structures of full-length inactive...
Includes: Supplementary data
Articles
Collagen degradation in tuberculosis pathogenesis: the biochemical consequences of hosting an undesired guest
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Journal:
Biochemical Journal
Biochem J (2018) 475 (19): 3123–3140.
Published: 12 October 2018
... regions of the lung, in a process that can become fatal. Here, we review structure and function of the main molecular actors of ECM degradation due to M. tuberculosis infection and the proposed mechanisms of tissue destruction, mainly attacking fibrillar collagen. Importantly, enzymes responsible...
Articles
Trz1, the long form RNase Z from yeast, forms a stable heterohexamer with endonuclease Nuc1 and mutarotase
Available to PurchaseMiao Ma, Ines Li de la Sierra-Gallay, Noureddine Lazar, Olivier Pellegrini, Jean Lepault, Ciarán Condon, Dominique Durand, Herman van Tilbeurgh
Journal:
Biochemical Journal
Biochem J (2017) 474 (21): 3599–3613.
Published: 18 October 2017
... nucleases in mammalian cells (42% sequence identity and 62% similarity to human EndoG). Crystal structures of worm and fly EndoG showed that it closely resembles NucA nuclease from Anabaena and Serratia and that it forms a tight dimer [ 23 , 24 ]. The recent crystal structure of CPS-6...
Includes: Supplementary data
Articles
New insights into the structure, assembly and biological roles of 10–12 nm connective tissue microfibrils from fibrillin-1 studies
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Journal:
Biochemical Journal
Biochem J (2016) 473 (7): 827–838.
Published: 29 March 2016
...Sacha A. Jensen; Penny A. Handford The 10–12 nm diameter microfibrils of the extracellular matrix (ECM) impart both structural and regulatory properties to load-bearing connective tissues. The main protein component is the calcium-dependent glycoprotein fibrillin, which assembles into microfibrils...
Articles
Journal:
Biochemical Journal
Biochem J (2015) 467 (3): 365–386.
Published: 17 April 2015
... and structure of CRL complexes, and outline the current state of the field in terms of available knowledge of small-molecule inhibitors and modulators of CRL activity. A comprehensive overview of the reported crystal structures of CRL subunits, components and full-size complexes, alone or with bound small...
Includes: Supplementary data
Articles
Journal:
Biochemical Journal
Biochem J (2014) 458 (3): 421–437.
Published: 28 February 2014
... protein C-terminus) E3 ligase families, directly catalysing ubiquitin transfer from an intrinsic catalytic cysteine housed in the C-terminal domain, as well as recruiting thioester-bound E2 enzymes via a RING domain. Recent three-dimensional structures and biochemical findings of the RBRs have revealed...
Articles
gp130 activation is regulated by D2–D3 interdomain connectivity
Available to PurchaseAntje Schütt, Martin Zacharias, Nico Schneider, Silke Horn, Joachim Grötzinger, Stefan Rose-John, Dirk Schmidt-Arras
Journal:
Biochemical Journal
Biochem J (2013) 450 (3): 487–496.
Published: 28 February 2013
... structure-based approach we identified for the first time amino acids critical for gp130 activation. We can show that gp130 D2–D3 interdomain connectivity by hydrophobic residues stabilizes inactive gp130 conformation. Conformational destabilization of the EF loop present in domain D2 and disruption of D2...
Includes: Supplementary data
Articles
Residue mutations and their impact on protein structure and function: detecting beneficial and pathogenic changes
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Journal:
Biochemical Journal
Biochem J (2013) 449 (3): 581–594.
Published: 09 January 2013
...Romain A. Studer; Benoit H. Dessailly; Christine A. Orengo The present review focuses on the evolution of proteins and the impact of amino acid mutations on function from a structural perspective. Proteins evolve under the law of natural selection and undergo alternating periods of conservative...
Articles
Architecture of the catalytic HPN motif is conserved in all E2 conjugating enzymes
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Journal:
Biochemical Journal
Biochem J (2012) 445 (2): 167–174.
Published: 27 June 2012
...Benjamin W. Cook; Gary S. Shaw E2 conjugating enzymes are the central enzymes in the ubiquitination pathway and are responsible for the transfer of ubiquitin and ubiquitin-like proteins on to target substrates. The secondary structural elements of the catalytic domain of these enzymes is highly...
Includes: Supplementary data
Articles
Dissecting structure–function–stability relationships of a thermostable GH5-CBM3 cellulase from Bacillus subtilis 168
Available to PurchaseCamila R. Santos, Joice H. Paiva, Maurício L. Sforça, Jorge L. Neves, Rodrigo Z. Navarro, Júnio Cota, Patrícia K. Akao, Zaira B. Hoffmam, Andréia N. Meza, Juliana H. Smetana, Maria L. Nogueira, Igor Polikarpov, José Xavier-Neto, Fábio M. Squina, Richard J. Ward, Roberto Ruller, Ana C. Zeri, Mário T. Murakami
Journal:
Biochemical Journal
Biochem J (2012) 441 (1): 95–104.
Published: 14 December 2011
... lignocellulosic biomass. However, industrial use of cellulases is somewhat limited by both their low catalytic efficiency and stability. In the present study, we conducted a detailed functional and structural characterization of the thermostable BsCel5A ( Bacillus subtilis cellulase 5A), which consists of a GH5...
Includes: Supplementary data
Articles
Ljiljana Sjekloća, Petr V. Konarev, John Eccleston, Ian A. Taylor, Dmitri I. Svergun, Annalisa Pastore
Journal:
Biochemical Journal
Biochem J (2009) 419 (2): 347–357.
Published: 27 March 2009
.... Understanding the structural properties of FMRP is essential for correlating it with its functions. The structures of isolated domains of FMRP have been reported, but nothing is yet known with regard to the spatial arrangement of the different modules, partly because of difficulties in producing both the full...
Includes: Supplementary data
Articles
MAP1 structural organization in Drosophila : in vivo analysis of FUTSCH reveals heavy- and light-chain subunits generated by proteolytic processing at a conserved cleavage site
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Journal:
Biochemical Journal
Biochem J (2008) 414 (1): 63–71.
Published: 29 July 2008
... interactions of the microtubule-based cytoskeleton in neural development and function. The characteristic structural organization of mammalian MAP1s, which are composed of heavy- and light-chain subunits, requires proteolytic cleavage of a precursor polypeptide encoded by the corresponding map1 gene. MAP1...
Articles
Structure, mechanism and regulation of pyruvate carboxylase
Available to PurchaseSarawut Jitrapakdee, Martin St Maurice, Ivan Rayment, W. Wallace Cleland, John C. Wallace, Paul V. Attwood
Journal:
Biochemical Journal
Biochem J (2008) 413 (3): 369–387.
Published: 15 July 2008
.... The enzyme was discovered in 1959 and over the last decade there has been much progress in understanding its structure and function. PC from most organisms is a tetrameric protein that is allosterically regulated by acetyl-CoA and aspartate. High-resolution crystal structures of the holoenzyme with various...
Articles
Differential effects of N-glycans on surface expression suggest structural differences between the acid-sensing ion channel (ASIC) 1a and ASIC1b
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Journal:
Biochemical Journal
Biochem J (2008) 412 (3): 469–475.
Published: 28 May 2008
..., cytoplasmic termini and a large ectodomain between the transmembrane domains; this topology has been confirmed by the crystal structure of chicken ASIC1. ASIC1a and ASIC1b are two variants encoded by the asic1 gene. The variable part of the protein includes the cytoplasmic N-terminus, the first transmembrane...
Articles
Structural basis for non-competitive product inhibition in human thymidine phosphorylase: implications for drug design
Available to PurchaseKamel EL Omari, Annelies Bronckaers, Sandra Liekens, Maria-Jésus Pérez-Pérez, Jan Balzarini, David K. Stammers
Journal:
Biochemical Journal
Biochem J (2006) 399 (2): 199–204.
Published: 27 September 2006
... is implicated in angiogenesis and apoptosis and therefore is a prime target for drug design, including antitumour therapies. An HTP structure in a closed conformation complexed with an inhibitor has previously been solved. Earlier kinetic studies revealed an ordered release of thymine followed by ribose...
Articles
Slow thrombin in solution
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Journal:
Biochemical Journal
Biochem J (2005) 390 (2): e1.
Published: 23 August 2005
... accessible to the general biochemist and we have thus witnessed an exponential increase in the number of protein structures deposited every year. It is now commonplace for several structures to be published of the same protein under different crystallization conditions, sometimes resulting in conflicting...
Articles
Towards a better understanding of the substrate specificity of the UDP- N -acetylglucosamine C4 epimerase WbpP
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Journal:
Biochemical Journal
Biochem J (2005) 389 (1): 173–180.
Published: 21 June 2005
...Melinda DEMENDI; Noboru ISHIYAMA; Joseph S. LAM; Albert M. BERGHUIS; Carole CREUZENET WbpP is the only genuine UDP-GlcNAc (UDP- N -acetylglucosamine) C4 epimerase for which both biochemical and structural data are available. This represents a golden opportunity to elucidate the molecular basis...
Articles
The high concentration of Arg 213 →Gly extracellular superoxide dismutase (EC-SOD) in plasma is caused by a reduction of both heparin and collagen affinities
Available to PurchaseSteen V. PETERSEN, Dorte Aa. OLSEN, John M. KENNEY, Tim D. OURY, Zuzana VALNICKOVA, Ida B. THØGERSEN, James D. CRAPO, Jan J. ENGHILD
Journal:
Biochemical Journal
Biochem J (2005) 385 (2): 427–432.
Published: 07 January 2005
.... In the present study we confirm, using R213G EC-SOD purified from a homozygous individual, that the heparin affinity is reduced. Significantly, the collagen affinity of the R213G EC-SOD variant was similarly affected and both the heparin and collagen affinities were reduced by 12-fold. Structural analysis...
Articles
Purification and biochemical characterization of the D6 chemokine receptor
Available to PurchasePaul E. BLACKBURN, Clare V. SIMPSON, Robert J. B. NIBBS, Maureen O'HARA, Rhona BOOTH, Jemma POULOS, Neil W. ISAACS, Gerard J. GRAHAM
Journal:
Biochemical Journal
Biochem J (2004) 379 (2): 263–272.
Published: 15 April 2004
... such studies is the lack of accurate three-dimensional structural models of these molecules. The CC-chemokine receptor D6 is expressed at exceptionally high levels in heterologous transfectants. Here we report the purification and biochemical characterization of milligram quantities of D6 protein from...
Articles
Localization of dynein light chains 1 and 2 and their pro-apoptotic ligands
Available to PurchaseCatherine L. DAY, Hamsa PUTHALAKATH, Gretchen SKEA, Andreas STRASSER, Igor BARSUKOV, Lu-Yun LIAN, David C. S. HUANG, Mark G. HINDS
Journal:
Biochemical Journal
Biochem J (2004) 377 (3): 597–605.
Published: 01 February 2004
...Catherine L. DAY; Hamsa PUTHALAKATH; Gretchen SKEA; Andreas STRASSER; Igor BARSUKOV; Lu-Yun LIAN; David C. S. HUANG; Mark G. HINDS The dynein and myosin V motor complexes are multi-protein structures that function to transport molecules and organelles within the cell. DLC (dynein light-chain...
Articles
beta-Sheet is the bioactive conformation of the anti-angiogenic anginex peptide
Available to PurchaseRuud P. M. DINGS, Monica M. ARROYO, Nathan A. LOCKWOOD, Loes I. van EIJK, Judy R. HASEMAN, Arjan W. GRIFFIOEN, Kevin H. MAYO
Journal:
Biochemical Journal
Biochem J (2003) 373 (1): 281–288.
Published: 01 July 2003
... a nascent β-sheet conformation in solution, the actual bioactive structure formed upon binding to its receptor on the surface of endothelial cells could be quite different. By using a series of double-cysteine disulphide-bridged analogues, we provide evidence in the present study that the β-sheet is in fact...
Articles
Tyrosinases from crustaceans form hexamers
Available to Purchase
Journal:
Biochemical Journal
Biochem J (2003) 371 (2): 515–523.
Published: 15 April 2003
...Elmar JAENICKE; Heinz DECKER Tyrosinases, which are widely distributed among animals, plants and fungi, are involved in many biologically essential functions, including pigmentation, sclerotization, primary immune response and host defence. In the present study, we present a structural...
Articles
Cation-dependent structural features of β-casein-(1–25)
Available to Purchase
Journal:
Biochemical Journal
Biochem J (2001) 356 (1): 277–286.
Published: 08 May 2001
... that were dependent upon the nature of the cation present. Medium-range nuclear Overhauser effect (nOe) enhancements, characteristic of small structured regions in the peptide, were observed and also found to be cation dependent. The secondary structure of the peptide was characterized by sequential...
Articles
Guanylate cyclase in Dictyostelium discoideum with the topology of mammalian adenylate cyclase
Available to Purchase
Journal:
Biochemical Journal
Biochem J (2001) 354 (3): 697–706.
Published: 08 March 2001
[email protected] ). The nucleotide sequence data reported appear in DDBJ, EMBL and GenBank TM Nucleotide Sequence Databases under the accession number AJ238883. 19 6 2000 6 12 2000 12 1 2001 The Biochemical Society, London © 2001 2001 cGMP cloning chemotaxis mutant structure...
Articles
Anginex, a designed peptide that inhibits angiogenesis
Available to PurchaseArjan W. GRIFFIOEN, Daisy W. J. VAN DER SCHAFT, Annemarie F. BARENDSZ-JANSON, Andrew COX, Harry A. J. STRUIJKER BOUDIER, Harry F. P. HILLEN, Kevin H. MAYO
Journal:
Biochemical Journal
Biochem J (2001) 354 (2): 233–242.
Published: 22 February 2001
... is demonstrated in the sprout-formation assay and in vivo in the chick embryo chorio-allantoic membrane angiogenesis assay. Comparison of active and inactive βpep sequences allows structure–function relationships to be deduced. Five hydrophobic residues and two lysines appear to be crucial to activity...
Articles
Combined strong anion-exchange HPLC and PAGE approach for the purification of heparan sulphate oligosaccharides
Available to Purchase
Journal:
Biochemical Journal
Biochem J (2001) 354 (1): 141–147.
Published: 08 February 2001
...-derived oligosaccharides, suggest that specific structural features within the polysaccharide are responsible for ligand recognition and regulation. In the present study, we show that strong anion-exchange HPLC alone, a commonly used technique for purification of heparan sulphate-derived oligosaccharides...
Articles
The second domain of intercellular adhesion molecule-1 (ICAM-1) maintains the structural integrity of the leucocyte function-associated antigen-1 (LFA-1) ligand-binding site in the first domain
Available to Purchase
Journal:
Biochemical Journal
Biochem J (2000) 351 (1): 79–86.
Published: 26 September 2000
...-1 expressed in T-cells. Function-blocking monoclonal antibodies that map to domain 2 of ICAM-1, implicating this domain in ligand binding, were found to act indirectly. In summary our data suggest that the second domain of ICAM-1 has a role in maintaining the structure of the LFA-1 ligand-binding...
Articles
Bacterial lipolytic enzymes: classification and properties
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Journal:
Biochemical Journal
Biochem J (1999) 343 (1): 177–183.
Published: 24 September 1999
... being further divided into six subfamilies. Moreover, the classification enables us to predict (1) important structural features such as residues forming the catalytic site or the presence of disulphide bonds, (2) types of secretion mechanism and requirement for lipase-specific foldases, and (3...
