Acta Crystallographica Section D: Biological Crystallography Volume 67, Part 12 (December 2011) Copyright (c) International Union of Crystallography 2011 ----------------------------------------------------------------- [Issue Author Index][Volume Author Index] * research papers * short communications * addenda and errata ----------------------------------------------------------------- research papers ----------------------------------------------------------------- Acta Cryst. (2011). D67, 997-1008 [ doi:10.1107/S090744491104039X ] The structure and inhibition of a GGDEF diguanylate cyclase complexed with (c-di-GMP)[2] at the active site C.-Y. Yang, K.-H. Chin, M.L.-C. Chuah, Z.-X. Liang, A.H.-J. Wang and S.-H. Chou Synopsis: The crystal structure of the XCC4471^GGDEF-c-di-GMP complex reveals detailed interactions between a c-di-GMP dimer with a significant number of highly conserved residues around the active site. This structure may serve as a good model for designing lead compounds for blocking DGC activities in a cell and for treating biofilm-related chronic diseases. PDB reference: 3qyy Online 18 November 2011 ----------------------------------------------------------------- Acta Cryst. (2011). D67, 1009-1016 [ doi:10.1107/S0907444911041102 ] Role of the MotB linker in the assembly and activation of the bacterial flagellar motor J. O'Neill, M. Xie, M. Hijnen and A. Roujeinikova Synopsis: The crystallographic analysis of a series of N-terminally truncated H. pylori MotB variants is presented. This analysis reveals how the structure responds to linker separation and suggests the mechanism of MotB activation, which entails linker unfolding and rotational displacement of MotB transmembrane helices. PDB references: 3s0y, 3s02, 3s03, 3s06, 3s0h and 3s0w Online 5 November 2011 ----------------------------------------------------------------- Acta Cryst. (2011). D67, 1017-1022 [ doi:10.1107/S0907444911042971 ] Structural and functional characterization of Mycobacterium tuberculosis triosephosphate isomerase S. E. Connor, G. C. Capodagli, M. K. Deaton and S. D. Pegan Synopsis: The structure of M. tuberculosis triosephosphate isomerase (MtTPI) was elucidated in the apo form as well as bound to the reaction-intermediate analog phosphoglycolohydroxamate (PGH). The enzymatic parameters for the conversion of dihydroxyacetone phosphate to D-glyceraldehyde-3-phosphate by MtTPI were also obtained as well as the binding constant for the reaction-intermediate analog PGH. PDB references: 3ta6 and 3tao Online 5 November 2011 ----------------------------------------------------------------- Acta Cryst. (2011). D67, 1023-1027 [ doi:10.1107/S0907444911043435 ] Structural analysis of interdomain mobility in ribosomal L1 proteins S. Tishchenko, E. Nikonova, O. Kostareva, A. Gabdulkhakov, W. Piendl, N. Nevskaya, M. Garber and S. Nikonov Synopsis: It is shown that interdomain mobility in bacterial ribosomal L1 proteins emerges from their amino-acid sequences and consequently the closed conformation should be characteristic of the structures of all bacterial L1 proteins in the isolated state. PDB reference: 3tg8 Online 5 November 2011 ----------------------------------------------------------------- Acta Cryst. (2011). D67, 1028-1034 [ doi:10.1107/S090744491104385X ] Structure of E69Q mutant of human muscle fructose-1,6-bisphosphatase M. Zarzycki, R. Kolodziejczyk, E. Maciaszczyk-Dziubinska, R. Wysocki, M. Jaskolski and A. Dzugaj Synopsis: Human muscle fructose-1,6-bisphosphatase has been characterized in complex with its allosteric inhibitor AMP and in addition with the enzymatic reaction product [alpha]-fructose 6-phosphate bound in the active site. PDB references: 3ifa and 3ifc Online 18 November 2011 ----------------------------------------------------------------- Acta Cryst. (2011). D67, 1035-1044 [ doi:10.1107/S090744491104491X ] Structural insights into a zinc-dependent pathway leading to Leu55Pro transthyretin amyloid fibrils A. F. Castro-Rodrigues, L. Gales, M. J. Saraiva and A. M. Damas Synopsis: The crystal structure of the TTR L55P-Zn^2+ complex reveals two different tetrahedral Zn^2+-binding sites that lead to a bidimensional array of monomers with a cross- [beta] structure. Biophysical characterization of TTR L55P fibril formation under conditions similar to those in which crystals were obtained confirms the role of Zn^2+ as an amyloid enhancer. PDB reference: 3ssg Online 5 November 2011 ----------------------------------------------------------------- Acta Cryst. (2011). D67, 1045-1053 [ doi:10.1107/S0907444911045033 ] Structural basis for the DNA-binding activity of the bacterial [beta]-propeller protein YncE W. Kagawa, T. Sagawa, H. Niki and H. Kurumizaka Synopsis: Crystal structures of the E. coli YncE protein and its complex with DNA are presented. The structures provide a novel DNA binding mechanism for [beta]-propeller-nucleic acid interactions. PDB references: 3vgz and 3vh0 Online 5 November 2011 ----------------------------------------------------------------- Acta Cryst. (2011). D67, 1054-1064 [ doi:10.1107/S0907444911045264 ] Structure of indole-3-glycerol phosphate synthase from Thermus thermophilus HB8: implications for thermal stability B. Bagautdinov and K. Yutani Synopsis: The crystal structure of indole-3-glycerol phosphate synthase (IGPS) from the thermophilic bacterium T. thermophilus was determined at 1.8 AA resolution. The study highlights the presence of additional salt bridges and stabilization-centre clusters as major contributing factors to the thermal stability of the thermophilic IGPS and thus provides new insights for protein engineering to design thermostable proteins. PDB reference: 1vc4 Online 18 November 2011 ----------------------------------------------------------------- [Open access] Acta Cryst. (2011). D67, 1065-1072 [ doi:10.1107/S0907444911046300 ] The structure of Serratia marcescens Lip, a membrane-bound component of the type VI secretion system V. A. Rao, S. M. Shepherd, G. English, S. J. Coulthurst and W. N. Hunter Synopsis: The high-resolution crystal structure of S. marcescens Lip reveals a new member of the transthyretin family of proteins. Lip, a core component of the type VI secretion apparatus, is localized to the outer membrane and is positioned to interact with other proteins forming this complex system. PDB reference: 4a1r Online 18 November 2011 ----------------------------------------------------------------- short communications ----------------------------------------------------------------- Acta Cryst. (2011). D67, 1073-1075 [ doi:10.1107/S0907444911046105 ] Deprotonated imidodiphosphate in AMPPNP-containing protein structures M. Dauter and Z. Dauter Synopsis: In certain AMPPNP-containing protein structures, the nitrogen bridging the two terminal phosphate groups can be deprotonated. Online 18 November 2011 ----------------------------------------------------------------- addenda and errata ----------------------------------------------------------------- [Open access] Acta Cryst. (2011). D67, 1076 [ doi:10.1107/S0907444911045860 ] Crystallographic analysis of human hemoglobin elucidates the structural basis of the potent and dual antisickling activity of pyridyl derivatives of vanillin. Corrigendum O. Abdulmalik, M. S. Ghatge, F. N. Musayev, A. Parikh, Q. Chen, J. Yang, I. Nnamani, R. Danso-Danquah, D. N. Eseonu, T. Asakura, D. J. Abraham, J. Venitz and M. K. Safo Synopsis: A correction to the paper by Abdulmalik et al. [(2011), Acta Cryst. D67, 920-928]. Online 5 November 2011 ----------------------------------------------------------------- [Open access] Acta Cryst. (2011). D67, 1077 [ doi:10.1107/S0907444911048633 ] The unique structure of carbonic anhydrase [alpha]CA1 from Chlamydomonas reinhardtii. Corrigendum K. Suzuki, S.-Y. Yang, S. Shimizu, E. C. Morishita, J. Jiang, F. Zhang, M. M. Hoque, Y. Sato, M. Tsunoda, T. Sekiguchi and A. Takenaka Synopsis: A correction to the paper by Suzuki et al. [(2011). Acta Cryst. D67, 894-901]. Online 18 November 2011 -----------------------------------------------------------------