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Ivanova ME, Lukoyanova N, Malhotra S, Topf M, Trapani JA, Voskoboinik I, Saibil HR. The pore conformation of lymphocyte perforin. SCIENCE ADVANCES 2022; 8:eabk3147. [PMID: 35148176 PMCID: PMC8836823 DOI: 10.1126/sciadv.abk3147] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/08/2021] [Accepted: 12/17/2021] [Indexed: 05/05/2023]
Abstract
Perforin is a pore-forming protein that facilitates rapid killing of pathogen-infected or cancerous cells by the immune system. Perforin is released from cytotoxic lymphocytes, together with proapoptotic granzymes, to bind to a target cell membrane where it oligomerizes and forms pores. The pores allow granzyme entry, which rapidly triggers the apoptotic death of the target cell. Here, we present a 4-Å resolution cryo-electron microscopy structure of the perforin pore, revealing previously unidentified inter- and intramolecular interactions stabilizing the assembly. During pore formation, the helix-turn-helix motif moves away from the bend in the central β sheet to form an intermolecular contact. Cryo-electron tomography shows that prepores form on the membrane surface with minimal conformational changes. Our findings suggest the sequence of conformational changes underlying oligomerization and membrane insertion, and explain how several pathogenic mutations affect function.
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Affiliation(s)
- Marina E. Ivanova
- Institute of Structural and Molecular Biology, Birkbeck, University of London, Malet St, London WC1E 7HX, UK
- Imperial College London, Hammersmith Campus, Du Cane Road, London W12 0NN, UK
| | - Natalya Lukoyanova
- Institute of Structural and Molecular Biology, Birkbeck, University of London, Malet St, London WC1E 7HX, UK
| | - Sony Malhotra
- Institute of Structural and Molecular Biology, Birkbeck, University of London, Malet St, London WC1E 7HX, UK
- Scientific Computing Department, Science and Technology Facilities Council, Rutherford Appleton Laboratory, Fermi Ave, Harwell, Didcot OX11 0QX, UK
| | - Maya Topf
- Institute of Structural and Molecular Biology, Birkbeck, University of London, Malet St, London WC1E 7HX, UK
- Centre for Structural Systems Biology, Leibniz-Institut für Experimentelle Virologie and Universitätsklinikum Hamburg-Eppendorf (UKE), Hamburg, Germany
| | - Joseph A. Trapani
- Peter MacCallum Cancer Centre, 305 Grattan St, Melbourne, VIC 3000, Australia
| | - Ilia Voskoboinik
- Peter MacCallum Cancer Centre, 305 Grattan St, Melbourne, VIC 3000, Australia
| | - Helen R. Saibil
- Institute of Structural and Molecular Biology, Birkbeck, University of London, Malet St, London WC1E 7HX, UK
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Andreeva A, Howorth D, Chothia C, Kulesha E, Murzin AG. SCOP2 prototype: a new approach to protein structure mining. Nucleic Acids Res 2013; 42:D310-4. [PMID: 24293656 PMCID: PMC3964979 DOI: 10.1093/nar/gkt1242] [Citation(s) in RCA: 198] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
Abstract
We present a prototype of a new structural classification of proteins, SCOP2 (http://scop2.mrc-lmb.cam.ac.uk/), that we have developed recently. SCOP2 is a successor to the Structural Classification of Proteins (SCOP, http://scop.mrc-lmb.cam.ac.uk/scop/) database. Similarly to SCOP, the main focus of SCOP2 is to organize structurally characterized proteins according to their structural and evolutionary relationships. SCOP2 was designed to provide a more advanced framework for protein structure annotation and classification. It defines a new approach to the classification of proteins that is essentially different from SCOP, but retains its best features. The SCOP2 classification is described in terms of a directed acyclic graph in which nodes form a complex network of many-to-many relationships and are represented by a region of protein structure and sequence. The new classification project is expected to ensure new advances in the field and open new areas of research.
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Affiliation(s)
- Antonina Andreeva
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge, CB2 0QH, UK and European Bioinformatics Institute, Hinxton, Cambridge, CB10 1SD, UK
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3
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Tiessen A, Pérez-Rodríguez P, Delaye-Arredondo LJ. Mathematical modeling and comparison of protein size distribution in different plant, animal, fungal and microbial species reveals a negative correlation between protein size and protein number, thus providing insight into the evolution of proteomes. BMC Res Notes 2012; 5:85. [PMID: 22296664 PMCID: PMC3296660 DOI: 10.1186/1756-0500-5-85] [Citation(s) in RCA: 76] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2011] [Accepted: 02/01/2012] [Indexed: 11/29/2022] Open
Abstract
BACKGROUND The sizes of proteins are relevant to their biochemical structure and for their biological function. The statistical distribution of protein lengths across a diverse set of taxa can provide hints about the evolution of proteomes. RESULTS Using the full genomic sequences of over 1,302 prokaryotic and 140 eukaryotic species two datasets containing 1.2 and 6.1 million proteins were generated and analyzed statistically. The lengthwise distribution of proteins can be roughly described with a gamma type or log-normal model, depending on the species. However the shape parameter of the gamma model has not a fixed value of 2, as previously suggested, but varies between 1.5 and 3 in different species. A gamma model with unrestricted shape parameter described best the distributions in ~48% of the species, whereas the log-normal distribution described better the observed protein sizes in 42% of the species. The gamma restricted function and the sum of exponentials distribution had a better fitting in only ~5% of the species. Eukaryotic proteins have an average size of 472 aa, whereas bacterial (320 aa) and archaeal (283 aa) proteins are significantly smaller (33-40% on average). Average protein sizes in different phylogenetic groups were: Alveolata (628 aa), Amoebozoa (533 aa), Fornicata (543 aa), Placozoa (453 aa), Eumetazoa (486 aa), Fungi (487 aa), Stramenopila (486 aa), Viridiplantae (392 aa). Amino acid composition is biased according to protein size. Protein length correlated negatively with %C, %M, %K, %F, %R, %W, %Y and positively with %D, %E, %Q, %S and %T. Prokaryotic proteins had a different protein size bias for %E, %G, %K and %M as compared to eukaryotes. CONCLUSIONS Mathematical modeling of protein length empirical distributions can be used to asses the quality of small ORFs annotation in genomic releases (detection of too many false positive small ORFs). There is a negative correlation between average protein size and total number of proteins among eukaryotes but not in prokaryotes. The %GC content is positively correlated to total protein number and protein size in prokaryotes but not in eukaryotes. Small proteins have a different amino acid bias than larger proteins. Compared to prokaryotic species, the evolution of eukaryotic proteomes was characterized by increased protein number (massive gene duplication) and substantial changes of protein size (domain addition/subtraction).
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Affiliation(s)
- Axel Tiessen
- Departamento de Ingeniería Genética, CINVESTAV Irapuato, Irapuato, CP 36821, Mexico
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4
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Duguet M, Serre MC, Bouthier de La Tour C. A universal type IA topoisomerase fold. J Mol Biol 2006; 359:805-12. [PMID: 16647715 DOI: 10.1016/j.jmb.2006.04.021] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2006] [Revised: 04/05/2006] [Accepted: 04/06/2006] [Indexed: 10/24/2022]
Abstract
A class of enzymes, called DNA topoisomerases, is responsible for controlling the topological state of cellular DNA. Among these, type IA topoisomerases form a vast family that is present in all living organisms, including higher eukaryotes, in which they play important roles in genome stability. The known 3D structures of three of these enzymes indicate that they share a common toroidal architecture. We previously showed that the toroidal structure could be split off from the core enzyme of Thermotoga maritima topoisomerase I by limited proteolysis. This structure is produced by the association of two tandemly repeated elementary folds in a head-to-tail orientation. By using a combination of structural and sequence data analysis, we show that the elementary fold of about 150 amino acid residues, referred to as the topofold, is likely to be present in the whole topoisomerase IA family. Within each enzyme, the successive topofolds share two conserved sequence motifs located at the base of the ring, and referred to as the MI and MII motifs. However, the overall sequences of the folds have largely diverged. By contrast, secondary and tertiary structures appear remarkably conserved. We suggest that this twofold repeat has evolved by gene duplication/fusion from an ancestral topofold.
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Affiliation(s)
- Michel Duguet
- Laboratoire d'Enzymologie des Acides Nucléiques, Institut de Génétique et Microbiologie, Université Paris-Sud, Unité Mixte de Recherche 8621, Centre National de la Recherche Scientifique, 91405 Orsay, France
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5
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Babajide A, Farber R, Hofacker IL, Inman J, Lapedes AS, Stadler PF. Exploring protein sequence space using knowledge-based potentials. J Theor Biol 2001; 212:35-46. [PMID: 11527443 DOI: 10.1006/jtbi.2001.2343] [Citation(s) in RCA: 41] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Knowledge-based potentials can be used to decide whether an amino acid sequence is likely to fold into a prescribed native protein structure. We use this idea to survey the sequence-structure relations in protein space. In particular, we test the following two propositions which were found to be important for efficient evolution: the sequences folding into a particular native fold form extensive neutral networks that percolate through sequence space. The neutral networks of any two native folds approach each other to within a few point mutations. Computer simulations using two very different potential functions, M. Sippl's PROSA pair potential and a neural network based potential, are used to verify these claims.
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Affiliation(s)
- A Babajide
- Institut für Theoretische Chemie und Molekulare Strukturbiologie, Universität Wien, Währingerstrasse 17, A-1090 Vienna, Austria
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Han GW, Lee JY, Song HK, Chang C, Min K, Moon J, Shin DH, Kopka ML, Sawaya MR, Yuan HS, Kim TD, Choe J, Lim D, Moon HJ, Suh SW. Structural basis of non-specific lipid binding in maize lipid-transfer protein complexes revealed by high-resolution X-ray crystallography. J Mol Biol 2001; 308:263-78. [PMID: 11327766 DOI: 10.1006/jmbi.2001.4559] [Citation(s) in RCA: 137] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Non-specific lipid-transfer proteins (nsLTPs) are involved in the movement of phospholipids, glycolipids, fatty acids, and steroids between membranes. Several structures of plant nsLTPs have been determined both by X-ray crystallography and nuclear magnetic resonance. However, the detailed structural basis of the non-specific binding of hydrophobic ligands by nsLTPs is still poorly understood. In order to gain a better understanding of the structural basis of the non-specific binding of hydrophobic ligands by nsLTPs and to investigate the plasticity of the fatty acid binding cavity in nsLTPs, seven high-resolution (between 1.3 A and 1.9 A) crystal structures have been determined. These depict the nsLTP from maize seedlings in complex with an array of fatty acids.A detailed comparison of the structures of maize nsLTP in complex with various ligands reveals a new binding mode in an nsLTP-oleate complex which has not been seen before. Furthermore, in the caprate complex, the ligand binds to the protein cavity in two orientations with equal occupancy. The volume of the hydrophobic cavity in the nsLTP from maize shows some variation depending on the size of the bound ligands. The structural plasticity of the ligand binding cavity and the predominant involvement of non-specific van der Waals interactions with the hydrophobic tail of the ligands provide a structural explanation for the non-specificity of maize nsLTP. The hydrophobic cavity accommodates various ligands from C10 to C18. The C18:1 ricinoleate with its hydroxyl group hydrogen bonding to Ala68 possibly mimics cutin monomer binding which is of biological importance. Some of the myristate binding sites in human serum albumin resemble the maize nsLTP, implying the importance of a helical bundle in accommodating the non-specific binding of fatty acids.
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Affiliation(s)
- G W Han
- Molecular Biology Institute, University of California at Los Angeles, Los Angeles, CA 90095-1570, USA
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7
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Baykov AA, Cooperman BS, Goldman A, Lahti R. Cytoplasmic inorganic pyrophosphatase. PROGRESS IN MOLECULAR AND SUBCELLULAR BIOLOGY 1999; 23:127-50. [PMID: 10448675 DOI: 10.1007/978-3-642-58444-2_7] [Citation(s) in RCA: 74] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- A A Baykov
- A.N. Belozersky Institute of Physico-Chemical Biology, Moscow State University, Russia
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8
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Liu Q, Wang JC. Similarity in the catalysis of DNA breakage and rejoining by type IA and IIA DNA topoisomerases. Proc Natl Acad Sci U S A 1999; 96:881-6. [PMID: 9927662 PMCID: PMC15319 DOI: 10.1073/pnas.96.3.881] [Citation(s) in RCA: 50] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Studies of yeast DNA topoisomerase II with various alanine-substitution mutations provide strong biochemical support of a recent hypothesis that the type IA and IIA DNA topoisomerases act similarly in their cleavage and rejoining of DNA. DNA breakage and rejoining by either a type IA or a type IIA enzyme are shown to involve cooperation between a DNA-binding domain containing the active-site tyrosine and a Rossmann fold containing several highly conserved acidic residues. For a homodimeric type IIA enzyme, cooperation occurs in trans: the active-site tyrosine in the DNA-binding domain of one protomer cooperates with several residues in the Rossmann fold as well as other regions of the other protomer.
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Affiliation(s)
- Q Liu
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA 02138, USA
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9
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Hubbard TJ, Ailey B, Brenner SE, Murzin AG, Chothia C. SCOP: a Structural Classification of Proteins database. Nucleic Acids Res 1999; 27:254-6. [PMID: 9847194 PMCID: PMC148149 DOI: 10.1093/nar/27.1.254] [Citation(s) in RCA: 179] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
The Structural Classification of Proteins (SCOP) database provides a detailed and comprehensive description of the relationships of all known proteins structures. The classification is on hierarchical levels: the first two levels, family and superfamily, describe near and far evolutionary relationships; the third, fold, describes geometrical relationships. The distinction between evolutionary relationships and those that arise from the physics and chemistry of proteins is a feature that is unique to this database, so far. The database can be used as a source of data to calibrate sequence search algorithms and for the generation of population statistics on protein structures. The database and its associated files are freely accessible from a number of WWW sites mirrored from URL http://scop. mrc-lmb.cam.ac.uk/scop/
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Affiliation(s)
- T J Hubbard
- Sanger Centre, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire CB10 1SA, UK
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10
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Abstract
Over the last several years topoisomerases have finally begun to yield to high-resolution structural studies. These models have greatly aided our understanding of the mechanisms of topoisomerase catalysis and drug interactions. This review will cover advances in the structural biology of topoisomerases and discuss their implications for topoisomerase function.
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Affiliation(s)
- J M Berger
- Division of Biochemistry and Molecular Biology, Department of Molecular and Cellular Biology, 229 Stanley Hall, University of California, Berkeley, Berkeley, CA 94720, USA
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11
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Berger JM, Fass D, Wang JC, Harrison SC. Structural similarities between topoisomerases that cleave one or both DNA strands. Proc Natl Acad Sci U S A 1998; 95:7876-81. [PMID: 9653108 PMCID: PMC20897 DOI: 10.1073/pnas.95.14.7876] [Citation(s) in RCA: 76] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/24/1998] [Indexed: 02/08/2023] Open
Abstract
Type IA and type II DNA topoisomerases are distinguished by their ability to cleave one or two strands, respectively, of a DNA duplex. Both types have been proposed to use an "enzyme-bridging" mechanism, in which a break is formed in a DNA strand and a gap is opened between the broken pieces to allow passage of a second DNA strand or duplex segment. Although the type IA and type II topoisomerase structures appear overall quite different from one another, unexpected similarities between several structural elements suggest that members of the two subfamilies may use comparable mechanisms to bind and cleave DNA.
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Affiliation(s)
- J M Berger
- Whitehead Institute, 9 Cambridge Center, Cambridge, MA 02142, USA
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12
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Babajide A, Hofacker IL, Sippl MJ, Stadler PF. Neutral networks in protein space: a computational study based on knowledge-based potentials of mean force. FOLDING & DESIGN 1997; 2:261-9. [PMID: 9261065 DOI: 10.1016/s1359-0278(97)00037-0] [Citation(s) in RCA: 84] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
BACKGROUND Many protein sequences, often unrelated, adopt similar folds. Sequences folding into the same shape thus form subsets of sequence space. The shape and the connectivity of these sets have implications for protein evolution and de novo design. RESULTS We investigate the topology of these sets for some proteins with known three-dimensional structure using inverse folding techniques. First, we find that sequences adopting a given fold do not cluster in sequence space and that there is no detectable sequence homology among them. Nevertheless, these sequences are connected in the sense that there exists a path such that every sequence can be reached from every other sequence while the fold remains unchanged. We find similar results for restricted amino acid alphabets in some cases (e. g. ADLG). In other cases, it seems impossible to find sequences with native-like behavior (e.g. QLR). These findings seem to be independent of the particular structure considered. CONCLUSIONS Amino acid sequences folding into a common shape are distributed homogeneously in sequence space. Hence, the connectivity of the set of these sequences implies the existence of very long neutral paths on all examined protein structures. Regarding protein design, these results imply that sequences with more or less arbitrary chemical properties can be attached to a given structural framework. But we also observe that designability varies significantly among native structures. These features of protein sequence space are similar to what has been found for nucleic acids.
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Affiliation(s)
- A Babajide
- Institut für Theoretische Chemie University of Vienna Währingerstrasse 17, A-1090, Vienna, Austria
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Hubbard TJ, Murzin AG, Brenner SE, Chothia C. SCOP: a structural classification of proteins database. Nucleic Acids Res 1997; 25:236-9. [PMID: 9016544 PMCID: PMC146380 DOI: 10.1093/nar/25.1.236] [Citation(s) in RCA: 164] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023] Open
Abstract
The Structural Classification of Proteins (SCOP) database provides a detailed and comprehensive description of the relationships of all known proteins structures. The classification is on hierarchical levels: the first two levels, family and superfamily, describe near and far evolutionary relationships; the third, fold, describes geometrical relationships. The distinction between evolutionary relationships and those that arise from the physics and chemistry of proteins is a feature that is unique to this database, so far. SCOP also provides for each structure links to atomic co-ordinates, images of the structures, interactive viewers, sequence data, data on any conformational changes related to function and literature references. The database is freely accessible on the World Wide Web (WWW) with an entry point at URL http://scop.mrc-lmb.cam.ac.uk/scop/
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Affiliation(s)
- T J Hubbard
- MRC Laboratory of Molecular Biology, Cambridge CB2 2QH, UK
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15
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Chothia C, Hubbard T, Brenner S, Barns H, Murzin A. Protein folds in the all-beta and all-alpha classes. ANNUAL REVIEW OF BIOPHYSICS AND BIOMOLECULAR STRUCTURE 1997; 26:597-627. [PMID: 9241431 DOI: 10.1146/annurev.biophys.26.1.597] [Citation(s) in RCA: 92] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
Analysis of the structures in the Protein Databank, released in June 1996, shows that the number of different protein folds, i.e. the number of different arrangements of major secondary structures and/or chain topologies, is 327. Of these folds, approximately 25% belong to the all-alpha class, 20% belong to the all-beta class, 30% belong to the alpha/beta class, and 25% belong to the alpha + beta class. We describe the types of folds now known for the all-beta and all-alpha classes, emphasizing those that have been discovered recently. Detailed theories for the physical determinants of the structures of most of these folds now exist, and these are reviewed.
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Affiliation(s)
- C Chothia
- MRC Laboratory of Molecular Biology, Cambridge, United Kingdom
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16
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Hamelryck TW, Dao-Thi MH, Poortmans F, Chrispeels MJ, Wyns L, Loris R. The crystallographic structure of phytohemagglutinin-L. J Biol Chem 1996; 271:20479-85. [PMID: 8702788 DOI: 10.1074/jbc.271.34.20479] [Citation(s) in RCA: 91] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023] Open
Abstract
The structure of phytohemagglutinin-L (PHA-L), a leucoagglutinating seed lectin from Phaseolus vulgaris, has been solved with molecular replacement using the coordinates of lentil lectin as model, and refined at a resolution of 2.8 A. The final R-factor of the structure is 20.0%. The quaternary structure of the PHA-L tetramer differs from the structures of the concanavalin A and peanut lectin tetramers, but resembles the structure of the soybean agglutinin tetramer. PHA-L consists of two canonical legume lectin dimers that pack together through the formation of a close contact between two beta-strands. Of the two covalently bound oligosaccharides per monomer, only one GlcNAc residue per monomer is visible in the electron density. In this article we describe the structure of PHA-L, and we discuss the putative position of the high affinity adenine-binding site present in a number of legume lectins. A comparison with transthyretin, a protein that shows a remarkable resemblance to PHA-L, gives further ground to our proposal.
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Affiliation(s)
- T W Hamelryck
- Dienst Ultrastructuur, Vlaams Interuniversitair Instituut voor Biotechnologie, Vrije Universiteit Brussel, Paardenstraat 65, B-1640 Sint-Genesius-Rode, Belgium
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17
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Abstract
Examination of a protein's structural 'neighbors' can reveal distant evolutionary relationships that are otherwise undetectable, and perhaps suggest unsuspected functional properties. In the past, such analyses have often required specialized software and computer skills, but new structural comparison methods, developed in the past two years, increasingly offer this opportunity to structural and molecular biologists in general. These methods are based on similarity-search algorithms that are fast enough to have effectively removed the computer-time limitation for structure-structure search and alignment, and have made it possible for several groups to conduct systematic comparisons of all publicly available structures, and offer this information via the World Wide Web. Furthermore, and perhaps surprisingly given the difficulty of the structure-comparison problem, these groups seem to have converged on quite similar approaches with respect to both fast search algorithms and the identification of statistically significant similarities.
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Affiliation(s)
- J F Gibrat
- Unité de Bio-Informatique, Institut National de la Recherche Agronomique, Jouy-en-Josas, France
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18
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Abstract
The structural classification of proteins reveals that it is already more likely to find that a new protein structure has similarity to another structure than to find that it has a new fold. Reviewed here are those new superfamilies that include proteins of general interest: Sonic hedgehog, macrophage migration inhibitory factor, nuclear transport factor-2, double stranded RNA binding domain, GroES, the proteasome, new ATP-hydrolyzing ligases and flavoproteins.
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Affiliation(s)
- A G Murzin
- Centre for Protein Engineering, Medical Research Council Centre, Cambridge, UK.
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19
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Abstract
The crystal structure of a large fragment of yeast type II DNA topoisomerase reveals a heart-shaped dimeric protein with a large central hole. It provides a molecular model of the enzyme as an ATP-modulated clamp with two sets of jaws at opposite ends, connected by multiple joints. An enzyme with bound DNA can admit a second DNA duplex through one set of jaws, transport it through the cleaved first duplex, and expel it through the other set of jaws.
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Affiliation(s)
- J M Berger
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, Massachusetts 02138, USA
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20
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Buchanan SG, Gay NJ. Structural and functional diversity in the leucine-rich repeat family of proteins. PROGRESS IN BIOPHYSICS AND MOLECULAR BIOLOGY 1996; 65:1-44. [PMID: 9029940 DOI: 10.1016/s0079-6107(96)00003-x] [Citation(s) in RCA: 236] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Affiliation(s)
- S G Buchanan
- Department of Biochemistry, University of Cambridge, U.K
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21
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Abstract
Leucine-rich repeats are short sequence motifs present in over sixty proteins, all of which appear to be involved in protein-protein interactions. The crystal structure of ribonuclease inhibitor demonstrated that the repeats correspond to beta-alpha structural units. The recently determined crystal structure of the ribonuclease A-ribonuclease inhibitor complex suggests the basis for the protein-binding function of leucine-rich repeats.
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Affiliation(s)
- B Kobe
- St Vincent's Institute of Medical Research, Fitzroy, Australia
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22
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Shin DH, Lee JY, Hwang KY, Kim KK, Suh SW. High-resolution crystal structure of the non-specific lipid-transfer protein from maize seedlings. Structure 1995; 3:189-99. [PMID: 7735835 DOI: 10.1016/s0969-2126(01)00149-6] [Citation(s) in RCA: 178] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
BACKGROUND The movement of lipids between membranes is aided by lipid-transfer proteins (LTPs). Some LTPs exhibit broad specificity, transferring many classes of lipids, and are termed non-specific LTPs (ns-LTPs). Despite their apparently similar mode of action, no sequence homology exists between mammalian and plant ns-LTPs and no three-dimensional structure has been reported for any plant ns-LTP. RESULTS We have determined the crystal structure of ns-LTP from maize seedlings by multiple isomorphous replacement and refined the structure to 1.9 A resolution. The protein comprises a single compact domain with four alpha-helices and a long C-terminal region. The eight conserved cysteines form four disulfide bridges (assigned as Cys4-Cys52, Cys14-Cys29, Cys30-Cys75, and Cys50-Cys89) resolving the ambiguity that remained from the chemical determination of pairings in the homologous protein from castor bean. Two of the bonds, Cys4-Cys52 and Cys50-Cys89, differ from what would have been predicted from sequence alignment with soybean hydrophobic protein. The complex between maize ns-LTP and hexadecanoate (palmitate) has also been crystallized and its structure refined to 1.8 A resolution. CONCLUSIONS The fold of maize ns-LTP places it in a new category of all-alpha-type structure, first described for soybean hydrophobic protein. In the absence of a bound ligand, the protein has a tunnel-like hydrophobic cavity, which is large enough to accommodate a long fatty acyl chain. In the structure of the complex with palmitate, most of the acyl chain is buried inside this hydrophobic cavity.
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Affiliation(s)
- D H Shin
- Department of Chemistry, College of Natural Sciences, Seoul National University, Korea
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