Acta Crystallographica Section D

Biological Crystallography

Volume 68, Part 7 (July 2012)

Cover illustration: Surface diagram of Staphylococcus aureus peptide deformylase (PDF) with the active-site pocket depicted with four inhibitors (p. 784). The molecular surface is coloured green (S1'), blue (S2') and magenta (S3'). The P1', P2' and P3' residues of the four inhibitors corresponding to the S1', S2' and S3' sites are indicated by yellow dashes. The Zn²⁺ ion is shown as a sphere

research papers
addenda and errata
book reviews

research papers

Acta Cryst. (2012). D68, 735-742 [ doi:10.1107/S0907444912007044 ]

The structure of a GH10 xylanase from Fusarium oxysporum reveals the presence of an extended loop on top of the catalytic cleft

M. Dimarogona, E. Topakas, P. Christakopoulos and E. D. Chrysina

Synopsis: The structure of a xylanase from F. oxysporum (FoXyn10a) was determined at 1.94 Å resolution. FoXyn10a adopts the ( [beta] / [alpha] )₈-barrel fold of the GH10 family, with an extended loop above the catalytic site with potential implications for enzymatic function.

PDB reference: 3u7b

Online 15 June 2012

Acta Cryst. (2012). D68, 743-750 [ doi:10.1107/S0907444912010281 ]

Structural basis of nuclear import of flap endonuclease 1 (FEN1)

A. C. de Barros, A. A. S. Takeda, C.-W. Chang, B. Kobe and M. R. M. Fontes

Synopsis: The crystal structure of the complex between the nuclear transport factor importin- [alpha] and the peptide corresponding to the nuclear localization sequence from flap 1 endonuclease (FEN1) has been determined. The structure rectifies the binding mode previously proposed and therefore explains the functional results that were previously controversial.

PDB reference: 3uvu

Online 15 June 2012

Acta Cryst. (2012). D68, 751-762 [ doi:10.1107/S0907444912010852 ]

Biochemical and structural characterization of the GTP-preferring succinyl-CoA synthetase from Thermus aquaticus

M. A. Joyce, K. Hayakawa, W. T. Wolodko and M. E. Fraser

Synopsis: Succinyl-CoA synthetase catalyzes the reaction succinyl-CoA + NDP + P_i [rightwards harpoon over leftwards harpoon] succinate + CoA + NTP, where N denotes adenosine or guanosine. The enzyme from T. aquaticus was characterized biochemically and its structure was determined in complex with GDP-Mn²⁺, the preferred nucleotide.

PDB reference: 3ufx

Online 15 June 2012

Acta Cryst. (2012). D68, 763-772 [ doi:10.1107/S0907444912011274 ]

Crystal structure and substrate specificity of the thermophilic serine:pyruvate aminotransferase from Sulfolobus solfataricus

C. Sayer, M. Bommer, M. Isupov, J. Ward and J. Littlechild

Synopsis: X-ray structures of S. solfataricus serine:pyruvate aminotransferase in different intermediate states and in complex with inhibitor have increased our understanding of the enzyme mechanism and have allowed an insight into the substrate specificity of this industrially important enzyme.

PDB references: 3zrp, 3zrq and 3zrr

Online 15 June 2012

Acta Cryst. (2012). D68, 773-783 [ doi:10.1107/S0907444912011407 ]

Structures of Helicobacter pylori uridylate kinase: insight into release of the product UDP

C.-H. Chu, M.-H. Liu, P.-C. Chen, M.-H. Lin, Y.-C. Li, C.-D. Hsiao and Y.-J. Sun

Synopsis: Two crystal structures of UMPK from Helicobacter pylori in complex with GTP and with UDP are reported.

PDB references: 4a7w and 4a7x

Online 15 June 2012

Acta Cryst. (2012). D68, 784-793 [ doi:10.1107/S0907444912011912 ]

Structures of Staphylococcus aureus peptide deformylase in complex with two classes of new inhibitors

S. J. Lee, S.-J. Lee, S. K. Lee, H.-J. Yoon, H. H. Lee, K. K. Kim, B. J. Lee, B. I. Lee and S. W. Suh

Synopsis: Crystal structures of peptide deformylase from S. aureus in complex with novel inhibitors are presented together with their functional analysis. A detailed comparative analysis of these structures as well as the activities of the inhibitors allowed the elucidation of distinctive structural changes which depend upon the class of inhibitor.

PDB references: 3u7k, 3u7l, 3u7m and 3u7n

Online 15 June 2012

Acta Cryst. (2012). D68, 794-799 [ doi:10.1107/S090744491201222X ]

Structure of a post-translationally processed heterodimeric double-headed Kunitz-type serine protease inhibitor from potato

E. M. Meulenbroek, E. A. J. Thomassen, L. Pouvreau, J. P. Abrahams, H. Gruppen and N. S. Pannu

Synopsis: The structure of potato serine protease inhibitor, the most abundant protease inhibitor in potatoes, is reported and sheds light on the inhibition mechanism of this protein.

PDB reference: 3tc2

Online 15 June 2012

Acta Cryst. (2012). D68, 800-809 [ doi:10.1107/S0907444912012589 ]

Protonation-state determination in proteins using high-resolution X-ray crystallography: effects of resolution and completeness

S. J. Fisher, M. P. Blakeley, M. Cianci, S. McSweeney and J. R. Helliwell

Synopsis: A bond-distance analysis to determine the protonation states of ionizable amino acids has been made for trypsin at 1.2 Å resolution, subtilisin at 1.26 Å resolution and lysozyme at 0.65 Å resolution. This was effective for Asp and Glu but not for His.

PDB references: 3unr and 3unx

Online 15 June 2012

Acta Cryst. (2012). D68, 810-818 [ doi:10.1107/S0907444912012553 ]

Outrunning free radicals in room-temperature macromolecular crystallography

R. L. Owen, D. Axford, J. E. Nettleship, R. J. Owens, J. I. Robinson, A. W. Morgan, A. S. Doré, G. Lebon, C. G. Tate, E. E. Fry, J. Ren, D. I. Stuart and G. Evans

Synopsis: A systematic increase in lifetime is observed in room-temperature protein and virus crystals through the use of reduced exposure times and a fast detector.

Online 15 June 2012

Acta Cryst. (2012). D68, 819-828 [ doi:10.1107/S0907444912013133 ]

A single mutation reforms the binding activity of an adhesion-deficient family 3 carbohydrate-binding module

O. Yaniv, S. Petkun, L. J. W. Shimon, E. A. Bayer, R. Lamed and F. Frolow

Synopsis: Crystal structures of the family 3b carbohydrate-binding module (CBM3b) of the cellulosomal multimodular hydrolytic enzyme cellobiohydrolase 9A (Cbh9A) from C. thermocellum and of its mutant Cbh9A CBM3b^N126W have been determined at 2.20 and 1.04 Å resolution, respectively. This mutation reforms the cellulose-binding properties of the adhesion-deficient CBM.

PDB references: 2ylk and 3zqx

Online 15 June 2012

Acta Cryst. (2012). D68, 829-838 [ doi:10.1107/S0907444912013224 ]

High-resolution structures of Neotermes koshunensis -glucosidase mutants provide insights into the catalytic mechanism and the synthesis of glucoconjugates

W.-Y. Jeng, N.-C. Wang, C.-T. Lin, W.-J. Chang, C.-I. Liu and A.H.-J. Wang

Synopsis: The single mutation E193D of the catalytic acid/base of Neotermes koshunensis [beta] -glucosidase makes it favour the transglycosylation reaction. The NkBgl E193D mutant may be suitable for development as a useful tool for the enzymatic synthesis of numerous therapeutic oligosaccharides.

PDB references: 3vif, 3vig, 3vih, 3vii, 3vij, 3vik, 3vil, 3vim, 3vin, 3vio and 3vip

Online 19 June 2012

Acta Cryst. (2012). D68, 839-845 [ doi:10.1107/S090744491201373X ]

ATP forms a stable complex with the essential histidine kinase WalK (YycG) domain

R. Celikel, V. H. Veldore, I. Mathews, K. M. Devine and K. I. Varughese

Synopsis: The histidine WalK (YycG) plays a crucial role in coordinating murein synthesis with cell division and the crystal structure of its ATP binding domain has been determined. Interestingly the bound ATP was not hydrolyzed during crystallization and remains intact in the crystal lattice.

PDB reference: 3sl2

Online 15 June 2012

Acta Cryst. (2012). D68, 846-853 [ doi:10.1107/S0907444912014126 ]

The structure of a Xanthomonas general stress protein involved in citrus canker reveals its flavin-binding property

E. Hilario, Y. Li, D. Niks and L. Fan

Synopsis: The crystal structure of a putative general stress protein from the citrus canker bacterium X. citri pv. citri was determined to 2.5 Å resolution.

PDB references: 3u34 and 3u35

Online 19 June 2012

Acta Cryst. (2012). D68, 854-860 [ doi:10.1107/S0907444912014886 ]

Low- and room-temperature X-ray structures of protein kinase A ternary complexes shed new light on its activity

A. Y. Kovalevsky, H. Johnson, B. L. Hanson, M. J. Waltman, S. Z. Fisher, S. Taylor and P. Langan

Synopsis: ATP bound in the active site of protein kinase A is readily hydrolysed to ADP and free phosphate by X-ray irradiation at room temperature. The phosphate ion observed in the active site causes a dramatic conformational change of the bound peptide inhibitor.

PDB references: 4dh1, 4dh3, 4dh5, 4dh7 and 4dh8

Online 15 June 2012

Acta Cryst. (2012). D68, 861-870 [ doi:10.1107/S0907444912015636 ]

Improved crystallographic models through iterated local density-guided model deformation and reciprocal-space refinement

T. C. Terwilliger, R. J. Read, P. D. Adams, A. T. Brunger, P. V. Afonine, R. W. Grosse-Kunstleve and L.-W. Hung

Synopsis: A density-based procedure is described for improving a homology model that is locally accurate but differs globally. The model is deformed to match the map and refined, yielding an improved starting point for density modification and further model-building.

Online 19 June 2012