Acta Crystallographica Section D Biological Crystallography (ACTA CRYSTALLOGR D)

Publications in this journal

• Article: A novel interdomain interface in crystallins: structural characterization of the bc-crystallin from Geodia cydonium at 0.99A˚ resolution

  Alessandro Vergara, Marco Grassi, Filomena Sica, Elio Pizzo, Giuseppe D’Alessio, Lelio Mazzarella, Antonello Merlino
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  ABSTRACT: The ��-crystallin superfamily includes highly diverse proteins belonging to all of the kingdoms of life. Based on structural topology, these proteins are considered to be evolutionarily related to the long-lived ��-crystallins that constitute the vertebrate eye lens. This study reports the crystallographic structure at 0.99 A ˚ resolution of the two-domain ��-crystallin (geodin) from the sponge Geodia cydonium. This is the most ancient member of the ��-crystallin superfamily in metazoans. The X-ray structure shows that the geodin domains adopt the typical ��-crystallin fold with a paired Greek-key motif, thus confirming the hypothesis that the crystallin-type scaffold used in the evolution of bacteria and moulds was recruited very early in metazoans. As a significant new structural feature, the sponge protein possesses a unique interdomain interface made up by pairing between the second motif of the first domain and the first motif of the second domain. The atomic resolution also allowed a detailed analysis of the calcium-binding site of the protein
  Acta Crystallographica Section D Biological Crystallography 05/2013; D69(6):960-967.
• Article: Visual automated macromolecular model building

  Gerrit G Langer, Saul Hazeldine, Tim Wiegels, Ciaran Carolan, Victor S Lamzin
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  ABSTRACT: Automated model-building software aims at the objective interpretation of crystallographic diffraction data by means of the construction or completion of macromolecular models. Automated methods have rapidly gained in popularity as they are easy to use and generate reproducible and consistent results. However, the process of model building has become increasingly hidden and the user is often left to decide on how to proceed further with little feedback on what has preceded the output of the built model. Here, ArpNavigator, a molecular viewer tightly integrated into the ARP/wARP automated model-building package, is presented that directly controls model building and displays the evolving output in real time in order to make the procedure transparent to the user.
  Acta Crystallographica Section D Biological Crystallography 03/2013; D69:635-641.
• Article: Structural insights into lipid-dependent reversible dimerization of human GLTP

  V. R. Samygina, B. Ochoa-Lizarralde, A. N. Popov, A. Cabo-Bilbao, F. Goni-de-Cerio, J. G. Molotkovsky, D. J. Patel, R. E. Brown, L. Malinina
  Acta Crystallographica Section D Biological Crystallography 03/2013; D69(4):603-616.
• Article: Crystal structure of translation initiation factor IF2 in apo, GTP and GDP forms

  Angelita Simonetti, Stefano Marzi, Attilio Fabbretti, Isabelle Hazemann, Lasse Jenner, Alexandre Urzhumtsev, Claudio O. Gualerzi, Bruno P. Klaholz
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  ABSTRACT: Translation initiation factor 2 (IF2) is involved in the early steps of bacterial protein synthesis. It promotes the stabilisation of the initiator tRNA on the 30S initiation complex (IC) and triggers GTP hydrolysis upon ribosomal subunit joining. While the structure of an archaeal homologue (a/eIF5B) is known, there are significant sequence and functional differences in eubacterial IF2, while the eukaryotic trimeric IF2 is completely unrelated. We have determined the crystal structure of the apo-IF2 protein core from T. thermophilus by MAD phasing and obtained also structures with GTP and GDP. The GTP IF2 complex has been trapped by GTP-soaking provided within the cryo-protectant. The structures reveal conformational changes of the protein upon nucleotide binding, in particular the P-loop region, which extend to the functionally relevant switch II region. The latter carries a catalytically important and conserved histidine residue which is seen in different conformation in the GTP and GDP complexes. Together, this work provides the first crystal structure of a eubacterial IF2 and suggests that activation of GTP-hydrolysis may occur by a conformational repositioning of the histidine residue.
  Acta Crystallographica Section D Biological Crystallography 03/2013;
• Article: Structure, recombinant expression and mutagenesis studies of the catalase with oxidase activity from Scytalidium thermophilum

  Yonca Yuzugullu, Chi H. Trinh, Mark A. Smith, Arwen R. Pearson, Simon E. V. Phillips, Didem Sutay Kocabas, Ufuk Bakir, Zumrut B. Ogel and Michael J. McPherson
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  ABSTRACT: Scytalidium thermophilum produces a catalase with phenol oxidase activity (CATPO) that catalyses the decomposition of hydrogen peroxide into oxygen and water and also oxidizes various phenolic compounds. A codon-optimized catpo gene was cloned and expressed in Escherichia coli. The crystal structures of native and recombinant S. thermophilum CATPO and two variants, H82N and V123F, were determined at resolutions of 2.7, 1.4, 1.5 and 1.9 A , respectively. The structure of CATPO reveals a homotetramer with 698 residues per subunit and with strong structural similarity to Penicillium vitale catalase. The haem component is cis-hydroxychlorin �-spirolactone, which is rotated 180� with respect to smallsubunit catalases. The haem-binding pocket contains two highly conserved water molecules on the distal side. The H82N mutation resulted in conversion of the native d-type haem to a b-type haem. Kinetic studies of the H82N and V123F mutants indicate that both activities are likely to be associated with the haem centre and suggest that the secondary oxidase activity may be a general feature of catalases in the absence of hydrogen peroxide.
  Acta Crystallographica Section D Biological Crystallography 02/2013; 69:3.
• Article: Ultratight crystal packing of a 10 kDa protein

  S. Trillo-Muyo, A. Jasilionis, M. J. Domagalski, M. Chruszcz, W. Minor, N. Kuisiene, J. L. Arolas, M. Solà, F. X. Gomis-Rüth
  Acta Crystallographica Section D Biological Crystallography 02/2013; 69:464-470.
• Article: Structure of FabH and factors affecting the distribution of branched fatty acids in Micrococcus luteus.

  Jose H Pereira, Ee Been Goh, Jay D Keasling, Harry R Beller, Paul D Adams
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  ABSTRACT: Micrococcus luteus is a Gram-positive bacterium that produces iso- and anteiso-branched alkenes by the head-to-head condensation of fatty-acid thioesters [coenzyme A (CoA) or acyl carrier protein (ACP)]; this activity is of interest for the production of advanced biofuels. In an effort to better understand the control of the formation of branched fatty acids in M. luteus, the structure of FabH (MlFabH) was determined. FabH, or β-ketoacyl-ACP synthase III, catalyzes the initial step of fatty-acid biosynthesis: the condensation of malonyl-ACP with an acyl-CoA. Analysis of the MlFabH structure provides insights into its substrate selectivity with regard to length and branching of the acyl-CoA. The most structurally divergent region of FabH is the L9 loop region located at the dimer interface, which is involved in the formation of the acyl-binding channel and thus limits the substrate-channel size. The residue Phe336, which is positioned near the catalytic triad, appears to play a major role in branched-substrate selectivity. In addition to structural studies of MlFabH, transcriptional studies of M. luteus were also performed, focusing on the increase in the ratio of anteiso:iso-branched alkenes that was observed during the transition from early to late stationary phase. Gene-expression microarray analysis identified two genes involved in leucine and isoleucine metabolism that may explain this transition.
  Acta Crystallographica Section D Biological Crystallography 10/2012; 68(Pt 10):1320-8.
• Article: Inhibition of D-xylose isomerase by polyols: atomic details by joint X-ray/neutron crystallography

  Andrey Kovalevsky, B Leif Hanson, Sax A Mason, V Trevor Forsyth, Zoe Fisher, Marat Mustyakimov, Matthew P Blakeley, David A Keen, Paul Langan
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  ABSTRACT: d-Xylose isomerase (XI) converts the aldo-sugars xylose and glucose to their keto analogs xylulose and fructose, but is strongly inhibited by the polyols xylitol and sorbitol, especially at acidic pH. In order to understand the atomic details of polyol binding to the XI active site, a 2.0 Å resolution room-temperature joint X-ray/neutron structure of XI in complex with Ni 2+ cofactors and sorbitol inhibitor at pH 5.9 and a room-temperature X-ray structure of XI containing Mg 2+ ions and xylitol at the physiological pH of 7.7 were obtained. The protonation of oxygen O5 of the inhibitor, which was found to be deprotonated and negatively charged in previous structures of XI complexed with linear glucose and xylulose, was directly observed. The Ni 2+ ions occupying the catalytic metal site (M2) were found at two locations, while Mg 2+ in M2 is very mobile and has a high B factor. Under acidic conditions sorbitol gains a water-mediated interaction that connects its O1 hydroxyl to Asp257. This contact is not found in structures at basic pH. The new interaction that is formed may improve the binding of the inhibitor, providing an explanation for the increased affinity of the polyols for XI at low pH. PDB References: D-xylose isomerase, complex with Mn 2+ and xylitol, 4duo; complex with Ni 2+ and sorbitol, 4dvo.
  Acta Crystallographica Section D Biological Crystallography 09/2012; 68(9):1201-1206.
• Article: The epithelial adhesin 1 (Epa1p) from the human-pathogenic yeast Candida glabrata: structural and functional study of the carbohydrate-binding domain.

  Ielasi FS, Decanniere K, Willaert R
  Acta Crystallographica Section D Biological Crystallography 03/2012; 68:210.
• Article: Crystal structures of ternary complexes of aspartate semialdehyde dehydrogenase (Rv3708c) from Mycobacterium tuberculosis H37Rv

  Rajan Vyas, Rupinder Tewari, Manfred Weiss, Subramanian Karthikeyan
  Acta Crystallographica Section D Biological Crystallography 02/2012;