Biological Crystallography

 

Acta Cryst. (2012). D68, 201-209  [ doi:10.1107/S0907444911054308 ]

Structure of the cytoplasmic domain of Yersinia pestis YscD, an essential component of the type III secretion system

G. T. Lountos, J. E. Tropea and D. S. Waugh

Synopsis: The crystal structure of the cytoplasmic domain of Y. pestis YscD is presented at 2.04 Å resolution.

PDB reference: 4a0e

Online 7 February 2012

 

Acta Cryst. (2012). D68, 210-217  [ doi:10.1107/S0907444911054898 ]

The epithelial adhesin 1 (Epa1p) from the human-pathogenic yeast Candida glabrata: structural and functional study of the carbohydrate-binding domain

F. S. Ielasi, K. Decanniere and R. G. Willaert

Synopsis: The N-terminal domain of the adhesin Epa1p from C. glabrata is a C-type lectin with a -sandwich topology.

PDB reference: 4a3x

Online 7 February 2012

 

Acta Cryst. (2012). D68, 218-231  [ doi:10.1107/S0907444911055090 ]

High-resolution structures of complexes of plant S-adenosyl-L-homocysteine hydrolase (Lupinus luteus)

K. Brzezinski, Z. Dauter and M. Jaskolski

Synopsis: Crystal structures of S-adenosyl-L-homocysteine hydrolase from L. luteus in complex with adenosine, cordycepin and adenine are presented.

PDB references: 3ond, 3one and 3onf

Online 7 February 2012

 

Acta Cryst. (2012). D68, 232-238  [ doi:10.1107/S0907444912000327 ]

Structure of the DNA (6-4) photoproduct dTT(6-4)TT in complex with the 64M-2 antibody Fab fragment implies increased antibody-binding affinity by the flanking nucleotides

H. Yokoyama, R. Mizutani, Y. Satow, K. Sato, Y. Komatsu, E. Ohtsuka and O. Nikaido

Synopsis: The crystal structure of the DNA photoproduct dTT(6-4)TT in complex with an antibody Fab indicates that the central dT(6-4)T segment is fully accommodated in the concave pocket and its flanking 5'-side thymidylate and 3'-side phosphate groups are responsible for the increased antibody-binding affinity of longer photoproducts.

PDB reference: 1keg

Online 7 February 2012

 

Acta Cryst. (2012). D68, 239-248  [ doi:10.1107/S090744491200073X ]

Structural basis of the substrate specificity of Bacillus cereus adenosine phosphorylase

P. Dessanti, Y. Zhang, S. Allegrini, M. G. Tozzi, F. Sgarrella and S. E. Ealick

Synopsis: Adenosine phosphorylase from B. cereus shows a strong preference for adenosine over other 6-oxopurine nucleosides. Mutation of Asp204 to asparagine reduces the efficiency of adenosine cleavage but does not affect inosine cleavage, effectively reversing the substrate specificity. The structures of D204N complexes explain these observations.

PDB references: 3uav, 3uaw, 3uax, 3uay and 3uaz

Online 14 February 2012

 

Acta Cryst. (2012). D68, 249-252  [ doi:10.1107/S0907444911051699 ]

A corrected space group for Sulfolobus sulfataricus 5'-deoxy-5'-methylthioadenosine phosphorylase II

Y. Zhang, P. H. Zwart and S. E. Ealick

Synopsis: The structure of 5'-deoxy-5'-methylthioadenosine phosphorylase II was incorrectly reported in space group P1 with pseudo-R32 symmetry. Post-analysis showed that the correct space group is C2, a maximal non-isomorphic subgroup of space group R32.

Online 7 February 2012

 

Acta Cryst. (2012). D68, 253-260  [ doi:10.1107/S0907444912001138 ]

Catechol-O-methyltransferase in complex with substituted 3'-deoxyribose bisubstrate inhibitors

M. Ellermann, C. Lerner, G. Burgy, A. Ehler, C. Bissantz, R. Jakob-Roetne, R. Paulini, O. Allemann, H. Tissot, D. Grünstein, M. Stihle, F. Diederich and M. G. Rudolph

Synopsis: High-resolution structures of catechol-O-methyltransferase with ribose-modified inhibitors and Mg²⁺ identify the side chain of Glu90 as crucial for hydrogen bonding to the ribose hydroxyl groups. Glu90 subtly aligns with the 2'-hydroxyl, but not the 3'-hydroxyl, group to increase binding affinity, explaining the observed activities of bisubstrate inhibitors with a 3'-desoxyribose moiety.

PDB references: 3u81, 3s68, 3nwb, 3nwe and 3r6t

Online 14 February 2012

 

Acta Cryst. (2012). D68, 261-267  [ doi:10.1107/S0907444912001163 ]

A grid-enabled web service for low-resolution crystal structure refinement

D. J. O'Donovan, I. Stokes-Rees, Y. Nam, S. C. Blacklow, G. F. Schröder, A. T. Brunger and P. Sliz

Synopsis: The deformable elastic network (DEN) method for reciprocal-space crystallographic refinement improves crystal structures, especially at resolutions lower than 3.5 Å. The DEN web service presented here intends to provide structural biologists with access to resources for running computationally intensive DEN refinements.

Online 14 February 2012

 

Acta Cryst. (2012). D68, 268-276  [ doi:10.1107/S0907444912001801 ]

Sequence-dependent effects of cryoprotectants on the active sites of the human ABO(H) blood group A and B glycosyltransferases

A. R. Johal, B. Schuman, J. A. Alfaro, S. Borisova, N. O. L. Seto and S. V. Evans

Synopsis: The use of the common cryoprotectants glycerol and MPD in the structure determination of the human ABO(H) blood group glycosyltransferases GTA, GTB and their chimera causes changes in the structure that could mistakenly be attributed to single point mutations.

PDB references: 3sxg, 3sxe, 3sx5, 3sx3, 3sx8, 3sx7, 3sxb, 3sxa, 3sxd and 3sxc

Online 14 February 2012

 

Acta Cryst. (2012). D68, 277-291  [ doi:10.1107/S090744491200145X ]

Structure and function of CYP108D1 from Novosphingobium aromaticivorans DSM12444: an aromatic hydrocarbon-binding P450 enzyme

S. G. Bell, W. Yang, J. A. Yorke, W. Zhou, H. Wang, J. Harmer, R. Copley, A. Zhang, R. Zhou, M. Bartlam, Z. Rao and L.-L. Wong

Synopsis: The crystal structure and substrate-binding and activity studies of CYP108D1, an aromatic hydrocarbon-binding cytochrome P450 monooxygenase from N. aromaticivorans DSM12444, are presented.

PDB reference: 3tkt

Online 14 February 2012

 

Acta Cryst. (2012). D68, 292-299  [ doi:10.1107/S0907444912001680 ]

Structure and function of the Clostridium thermocellum cellobiohydrolase A X1-module repeat: enhancement through stabilization of the CbhA complex

R. Brunecky, M. Alahuhta, Y. J. Bomble, Q. Xu, J. O. Baker, S.-Y. Ding, M. E. Himmel and V. V. Lunin

Synopsis: The crystal structures of two X1 modules from the multimodular CbhA protein have been solved and it has been proposed that a possible biological function of these domains is to enhance the stability of the complex at higher temperatures.

PDB references: 3pdg, 3pe9 and 3pdd

Online 14 February 2012

 

Acta Cryst. (2012). D68, 300-309  [ doi:10.1107/S0907444912001862 ]

High-pressure-induced water penetration into 3-isopropylmalate dehydrogenase

T. Nagae, T. Kawamura, L. M. G. Chavas, K. Niwa, M. Hasegawa, C. Kato and N. Watanabe

Synopsis: Structures of 3-isopropylmalate dehydrogenase were determined at pressures ranging from 0.1 to 650 MPa. Comparison of these structures gives a detailed picture of the swelling of a cavity at the dimer interface and the generation of a new cleft on the molecular surface, which are accompanied by water penetration.

PDB references: 3vkz, 3vl2, 3vl3, 3vl4, 3vl6 and 3vl7

Online 14 February 2012

 

Acta Cryst. (2012). D68, 310-320  [ doi:10.1107/S0907444912001990 ]

Structure of the catalytic domain of the Clostridium thermocellum cellulase CelT

M. M. Kesavulu, J.-Y. Tsai, H.-L. Lee, P.-H. Liang and C.-D. Hsiao

Synopsis: By determining the structure of the catalytic domain of the C. thermocellum cellulase CelT, the mechanism of function of the enzyme in the absence of an accessory module and the structural elements that might be responsible for its stability have been proposed.

PDB reference: 2yik

Online 14 February 2012

 

Acta Cryst. (2012). D68, 321-323  [ doi:10.1107/S0907444911055296 ]

Crystallography on a chip

A. Zarrine-Afsar, T. R. M. Barends, C. Müller, M. R. Fuchs, L. Lomb, I. Schlichting and R. J. D. Miller

Synopsis: This article describes a new platform for self-assembly of large array of protein crystals on a surface for the purpose of high-throughput room-temperature X-ray diffraction studies.

Online 14 February 2012