Virtual Issues

• Structural Biology May 2009
• Molecular Enzymology November 2008

TopStructural Biology May 2009

Papers Selected by Alex Wlodawer

We are in the midst of celebrating 50 years of protein crystallography, counted from publication of the preliminary and complete structures of myoglobin [1,2]. During the first few years of the application of this technique the appearance of each new structure was a major event and was usually published in journals that are now considered to be in the “high impact” category. Much has changed since then as the number of macromolecular structures deposited in the Protein Data Bank (PDB) now exceeds 50,000. Although some of them were solved using NMR or even electron microscopy, a vast majority still resulted from crystallographic investigations. A new (and rather disturbing) development is that many novel structures, solved in various centers for structural genomics, are only available as PDB entries, since they are not being published in peer-reviewed literature at all. Under these circumstances, one could ask about the role of a general-interest biochemistry journal, such as this one, in publishing the results of investigations that utilize protein crystallography as their major experimental technique. Also, how is it that, according to a recent analysis [3], the technical quality of the structures published in the FEBS Journal appears to be among the highest among all journals? An answer can be found in the papers selected for this Virtual Issue, which give a cross-section of articles that featured crystallographic investigations and were published in 2008 and 2009. Several of these papers are reviews aimed at providing the readers with either the ways of critically interpreting crystal structures, or with detailed comparative analyses of particular families of proteins, based on multiple crystal structures of their members. A vast majority of the structures presented in original articles were solved using molecular replacement with models based on related proteins. Although these structures may not be truly novel, they are often very important, since they can elucidate enzymatic properties through analysis of inhibitor binding, compare related proteins from several species with the aim of creating selective inhibitors, or explain the biophysical properties such as thermostability or cold adaptation. Such results are crucial in both enhancing our understanding of the ways protein fold and work, as well as in practical applications such as drug design. Some structures published here are still solved from scratch through the application of methods such as isomorphous replacement or anomalous scattering, and they represent proteins with less well studied folds. What is not shown in this Virtual Issue are many papers (actually, a fairly large fraction of all papers published in this journal) that contain figures showing protein structures that are used to interpret a variety of biological, biochemical, or biophysical data, although these papers do not report crystallographic studies at all. The fact that the availability of crystal structures is now taken completely for granted and that such structures are routinely used for interpretation of a wide range of phenomena testifies to the success of the last 50 years of macromolecular crystallography.

References

1. Kendrew JC, Bodo G, Dintzis HM, Parrish RG, Wyckoff H, & Phillips DC (1958) A three-dimensional model of the myoglobin molecule obtained by x-ray analysis. Nature 181, 662-666.
2. Kendrew JC, Dickerson RE, Strandberg BE, Hart RG, Davies DR, Phillips DC, & Shore VC (1960) Structure of myoglobin. A three-dimensional fourier synthesis at 2 Å resolution. Nature 185, 422-427.
3. Brown EN & Ramaswamy S (2007) Quality of protein crystal structures. Acta Crystallogr D63, 941-950.

Review Articles

Protein crystallography for non-crystallographers, or how to get the best (but not more) from published macromolecular structures (275, p 1-21)
Alexander Wlodawer, Wladek Minor, Zbigniew Dauter, Mariusz Jaskolski

Ribonuclease H: molecular diversities, substrate binding domains, and catalytic mechanism of the prokaryotic enzymes (275, p 1482-1493)
Takashi Tadokoro, Shigenori Kanaya

Structure, regulation and evolution of Nox-family NADPH oxidases that produce reactive oxygen species (275, p 3249-3277)
Hideki Sumimoto

Piecing together the structure of retroviral integrase, an important target in AIDS therapy (276, p2926 - 2946)
Mariusz Jaskolski, Jerry N. Alexandratos, Grzegorz Bujacz, Alexander Wlodawer

Original Articles

Type I receptor binding of bone morphogenetic protein 6 is dependent on N-glycosylation of the ligand (275, p 172-183)
Stefan Saremba, Joachim Nickel, Axel Seher, Alexander Kotzsch, Walter Sebald, Thomas D. Mueller

Structural insights into the substrate specificity and activity of ervatamins, the papain-like cysteine proteases from a tropical plant, Ervatamia coronaria (275, p 421-434)
Raka Ghosh, Sibani Chakraborty, Chandana Chakrabarti, Jiban Kanti Dattagupta, Sampa Biswas

Crystal structure of a cold-adapted class Cβ-lactamase (275, p 1687-1697)
Catherine Michaux, Jan Massant, Frédéric Kerff, Jean-Marie Frère, Jean-Denis Docquier, Isabel Vandenberghe, Bart Samyn, Annick Pierrard, Georges Feller, Paulette Charlier, Jozef Van Beeumen, Johan Wouters

The crystal structure of human WD40 repeat-containing peptidylprolyl isomerase (PPWD1) (275, p 2283-2295)
Tara L. Davis, John R. Walker, Hui Ouyang, Farrell MacKenzie, Christine Butler-Cole, Elena M. Newman, Elan Z. Eisenmesser, Sirano Dhe-Paganon

Crystal structure of highly thermostable glycerol kinase from a hyperthermophilic archaeon in a dimeric form (275, p 2632-2643)
Yuichi Koga, Ryota Katsumi, Dong-Ju You, Hiroyoshi Matsumura, Kazufumi Takano, Shigenori Kanaya

Characterization of Aquifex aeolicus 4-diphosphocytidyl-2C-methyl-d-erythritol kinase – ligand recognition in a template for antimicrobial drug discovery (275, p 2779-2794)
Tanja Sgraja, Magnus S. Alphey, Stephanos Ghilagaber, Rudi Marquez, Murray N. Robertson, Jennifer L. Hemmings, Susan Lauw, Felix Rohdich, Adelbert Bacher, Wolfgang Eisenreich, Victoria Illarionova, William N. Hunter

Hexameric ring structure of the N-terminal domain of Mycobacterium tuberculosis DnaB helicase (275, p 3064-3071)
Tapan Biswas, Oleg V. Tsodikov

Effect of ionic strength and oxidation on the P-loop conformation of the protein tyrosine phosphatase-like phytase, PhyAsr (275, p 3783-3792)
Robert J. Gruninger, L. Brent Selinger, Steven C. Mosimann

Structural and functional insights into Erwinia carotovora l-asparaginase (275, p 4306-4316)
Anastassios C. Papageorgiou, Galina A. Posypanova, Charlotta S. Andersson, Nikolay N. Sokolov, Julya Krasotkina

The role of group bulkiness in the catalytic activity of psychrophile cold-active protein tyrosine phosphatase (275, p 4317-4328)
Hiroki Tsuruta, Bunzo Mikami, Chiaki Yamamoto, Hiroshi Yamagata

Importance of tyrosine residues of Bacillus stearothermophilus serine hydroxymethyltransferase in cofactor binding and l-allo-Thr cleavage : Crystal structure and biochemical studies (275, p 4606-4619)
B. S. Bhavani, V. Rajaram, Shveta Bisht, Purnima Kaul, V. Prakash, M. R. N. Murthy, N. Appaji Rao, H. S. Savithri

Structural and mutational analyses of protein–protein interactions between transthyretin and retinol-binding protein (275, p 5841-5854)
Giuseppe Zanotti, Claudia Folli, Laura Cendron, Beatrice Alfieri, Sonia K. Nishida, Francesca Gliubich, Nicola Pasquato, Alessandro Negro, Rodolfo Berni

The sulfur atoms of the substrate CoA and the catalytic cysteine are required for a productive mode of substrate binding in bacterial biosynthetic thiolase, a thioester-dependent enzyme (275, p 6136-6148)
Gitte Meriläinen, Werner Schmitz, Rik K. Wierenga, Petri Kursula

Destabilization of psychrotrophic RNase HI in a localized fashion as revealed by mutational and X-ray crystallographic analyses (276, p 603-613)
Muhammad S. Rohman, Takashi Tadokoro, Clement Angkawidjaja, Yumi Abe, Hiroyoshi Matsumura, Yuichi Koga, Kazufumi Takano, Shigenori Kanaya

Crystal structure of the parasite inhibitor chagasin in complex with papain allows identification of structural requirements for broad reactivity and specificity determinants for target proteases (276, p 793-806)
Izabela Redzynia, Anna Ljunggren, Anna Bujacz, Magnus Abrahamson, Mariusz Jaskolski, Grzegorz Bujacz

X-ray crystallographic and enzymatic analyses of shikimate dehydrogenase from Staphylococcus epidermidis : Implications for substrate binding and conformational change (276, p 1125-1139)
Cong Han, Tiancen Hu, Dalei Wu, Su Qu, Jiahai Zhou, Jianping Ding, Xu Shen, Di Qu, Hualiang Jiang

Tamavidins – novel avidin-like biotin-binding proteins from the Tamogitake mushroom (276, p 1383-1397)
Yoshimitsu Takakura, Masako Tsunashima, Junko Suzuki, Satoru Usami, Yoshimitsu Kakuta, Nozomu Okino, Makoto Ito, Takeshi Yamamoto

Cytokinin-induced structural adaptability of a Lupinus luteus PR-10 protein (276, p 1596-1609)
Humberto Fernandes, Anna Bujacz, Grzegorz Bujacz, Filip Jelen, Michal Jasinski, Piotr Kachlicki, Jacek Otlewski, Michal M. Sikorski, Mariusz Jaskolski

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TopMolecular Enzymology November 2008

Papers Selected by Nigel Scrutton

Modern enzymology research is interdisciplinary and endeavours to elucidate the relationship between structure, dynamics and chemistry and relate this to metabolic activity within the cell. The aim is to elucidate, at various levels, mechanistic details of biomolecular processes, ranging from complex multi-component pathways and complexes to single proteins (enzymes), either through ensemble measurements, or at the level of isolated (single) molecules. It is an established but rapidly evolving field, uniting structural and computational approaches with analysis of reaction dynamics, engineering, spectroscopy, chemical analysis and theory. Historically, FEBS Journal has encouraged the submission of high quality papers in the field of enzymology and is particularly keen to publish work that reflects the strong interdisciplinary basis of the field. This selection of recent papers reflects this aim and underscores the high quality work published by FEBS Journal in the field of enzymology.

Structure-guided alteration of coenzyme specificity of formate dehydrogenase by saturation mutagenesis to enable efficient utilization of NADP+.
Aggliki Andreadeli, Dimitris Platis, Vladimir Tishkov, Vladimir Popov, Nikolaos Labrou

Importance of tyrosine residues of Bacillus stearothermophilus serine hydroxymethyltransferase in cofactor binding and L-allo-Thr cleavage: crystal structure and biochemical studies.
B. S. Bhavani, V. Rajaram, Shveta Bisht, Purnima Kaul, V. Prakash, M. R. N. Murthy, N. Appaji Rao, H. S. Savithri

Hexameric Ring Structure of the N-terminal Domain of Mycobacterium tuberculosis DnaB Helicase
Tapan Biswas, Oleg Tsodikov

Inter-Flavin Electron Transfer in Cytochrome P450 Reductase: Effects of Solvent and pH Identify Hidden Complexity in Mechanism.
Sibylle Brenner, Sam Hay, Andrew Munro, Nigel Scrutton

An intermediate step in the evolution of ATPases: a hybrid FO-VO rotor in a bacterial Na+ F1FO ATP synthase
Michael Fritz, Adriana Klyszejko, Nina Morgner, Janet Vonck, Bernd Brutschy, Daniel Muller, Thomas Meier, Volker Muller

Covalent flavinylation of vanillyl-alcohol oxidase is an autocatalytic process
Jianfeng Jin, Hortense Mazon, Robert H.H. van den Heuvel, Dick B. Janssen, Albert J. Heck, Marco Fraaije

A cysteine residue near the propionate side-chain of heme is the radical site in ascorbate peroxidase
Sakhito Kitajima, Miyo Kurioka, Tadashi Yoshimoto, Mayumi Shindo, Kenji Kanaori, Kunihiko Tajima, Kenji Oda

Characterization of mutations in crucial residues around the Qo binding site of the cytochrome bc1 complex from Paracoccus denitrificans
Thomas Kleinschroth, Oliver Anderka, Michaela Ritter, Andreas Stockera, Thomas A. Link, Bernd Ludwig, Petra Hellwig

Directed evolution of a histone acetyltransferase - enhancing thermostability, whilst maintaining catalytic activity and substrate specificity
Hans Leemhuis, Karl P. Nightingale, F Hollfelder

Poly(silicate)-metabolizing silicatein in siliceous spicules and silicasomes of demosponges comprises dual enzymatic activities (silica-polymerase and silica-esterase)
Werner Muller, Ute Schlobmacher, Xiaohung Wang, Alexandra Boreiko, David Brandt, Stephan Wolf, Wolfgang Tremal, Heinz Schroder

Heavy metal ions inhibit molybdoenzyme activity by binding to the dithiolene moiety of molybdopterin in Escherichia coli
Meina Neumann, Silke Leimkühler

Influence of modulated structural dynamics on the kinetics of a-chymotrypsin catalysis. Insights through chemical glycosylation, molecular dynamics, and domain motion analysis
Ricardo J. Sola, Kai Griebenow

Structural and thermodynamic insights into the binding mode of five novel inhibitors of lumazine synthase from mycobacterium tuberculosis
Ekaterina Morganova, Boris Illarionov, Thota Sambaiah, Ilka Haase, Adelbert Bacher, Mark Cushman, Markus Fischer, rudolf Ladenstein

Reactivity of the Heme-Dioxygen complex of the Inducible Nitric Oxide Synthase in the presence of alternative substrates
David Lefevre-Groboillot, Jean-Luc Boucher, Daniel Mansuy, Dennis Stuehr

Interaction of the E2 and E3 components of the pyruvate dehydrogenase multienzyme complex of Bacillus stearothermophilus. Use of a truncated protein domain in NMR spectroscopy
Robert Solomon

Structure of the substrate complex of thymidine kinase from Ureaplasma urealyticum and investigations of possible drug targets for the enzyme
Hans Eklund, Urszula Kosinska , Cecilia Carnrot, Staffan Eriksson, Liya Wang

ATP-dependent ligases in trypanothione biosynthesis: Kinetics of catalysis and inhibition by phosphinic acid pseudopeptides
Sandra L. Oza, Shoujun Chen, Susan Wyllie, James K. Coward, Alan Fairlamb

Replacement of two invariant serine residues in chorismate synthase provides evidence that a proton relay system is essential for intermediate formation and catalytic activity
Gernot Rauch, Heidemarie Ehammer, Stephen Bornemann, Peter Macheroux

Kinetic characterization of methionine [gamma]-lyases from the enteric protozoan parasite Entamoeba histolytica against physiological substrates and trifluoromethionine, a promising lead compound against amoebiasis
Dan Sato, Wataru Yamagata, Shigeharu Harada, Tomoyoshi Nozaki

The role of group bulkiness in the catalytic activity of psychrophile cold-active protein tyrosine phosphatase
Hiroki Tsuruta , Bunzo Mikami, Chiaki Yamamoto, Hiroshi Yamagata

Spectroscopic Characterization of Oxyferrous Complex of Prostacyclin Synthase in Solution and in Trapped Sol-Gel Matrix
Hui-Chun Yeh, Pei-Yung Hsu, Ah-Lim Tsai, Lee-Ho Wang