Acta Crystallographica Section D

Biological Crystallography

Volume 69, Part 3 (March 2013)



[Issue Author Index][Volume Author Index]
[Cover illustration] Cover illustration: The electrostatic surface of A. thaliana porphobilinogen deaminase (p. 471). The solvent-accessible surface of the enzyme is shown coloured according to the electrostatic potential. The surface has been clipped to show the large and highly electropositive (blue) binding site for the cofactor, which is formed predominantly of conserved arginine residues. The dipyrromethane and the cysteine residue to which it is attached (Cys254) are displayed in ball-and-stick representation.

research papers


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Acta Cryst. (2013). D69, 313-323  [ doi:10.1107/S0907444912046161 ]

Dimeric Sfh3 has structural changes in its binding pocket that are associated with a dimer-monomer state transformation induced by substrate binding

Y. Yuan, W. Zhao, X. Wang, Y. Gao, L. Niu and M. Teng

Synopsis: The dimeric structure of Sfh3 (Sec14 family homologue 3 in yeast) is reported for the first time and differs from the Sec14 proteins reported to date, all of which are monomeric.

PDB reference: 4fmm

Online 16 February 2013


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Acta Cryst. (2013). D69, 324-332  [ doi:10.1107/S0907444912046690 ]

Structural insights into the role of Bacillus subtilis YwfH (BacG) in tetrahydrotyrosine synthesis

M. Rajavel, K. Perinbam and B. Gopal

Synopsis: The structure of B. subtilis YwfH was determined at three conformational steps: the apo form, an apo-like conformation and the NADPH complex. The structures revealed synchronized conformational changes that facilitate cofactor binding and catalytic activity of the enzyme.

PDB references: 3u49, 3u4c and 3u4d

Online 16 February 2013


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Acta Cryst. (2013). D69, 333-344  [ doi:10.1107/S0907444912047099 ]

Structure of the N-terminal domain of human thioredoxin-interacting protein

G. Polekhina, D. B. Ascher, S. F. Kok, S. Beckham, M. Wilce and M. Waltham

Synopsis: The crystal structure of the N-terminal domain of human thioredoxin-interacting protein (TXNIP), which belongs to a recently classified [alpha]-arrestin protein family, has been determined. This study provides the first structural information on any of the [alpha]-arrestins. Although TXNIP adopts a [beta]-arrestin fold as predicted, it is structurally more similar to Vps26 proteins than to [beta]-arrestins, while sharing below 15% pairwise sequence identity with either.

PDB references: 4gei and 4gej

Online 16 February 2013


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Acta Cryst. (2013). D69, 345-351  [ doi:10.1107/S0907444912047294 ]

Direct metal recognition by guanine nucleotide-exchange factor in the initial step of the exchange reaction

T. Uejima, K. Ihara, M. Sunada, M. Kawasaki, T. Ueda, R. Kato, A. Nakano and S. Wakatsuki

Synopsis: The plant Rab5 GTPase homologue ARA7 in complex with its guanine nucleotide-exchange factor VPS9a was crystallized in the presence of GDP and Ca2+, representing an initial intermediate of the exchange reaction.

PDB reference: 4g01

Online 16 February 2013


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Acta Cryst. (2013). D69, 352-366  [ doi:10.1107/S0907444912047269 ]

Novel c-di-GMP recognition modes of the mouse innate immune adaptor protein STING

K.-H. Chin, Z.-L. Tu, Y.-C. Su, Y.-J. Yu, H.-C. Chen, Y.-C. Lo, C.-P. Chen, G. N. Barber, M.L.-C. Chuah, Z.-X. Liang and S.-H. Chou

Synopsis: The mouse innate immune adaptor protein mSTING adopts a distinct conformation with two novel c-di-GMP binding modes.

PDB references: 4g3l and 4g4d

Online 16 February 2013


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Acta Cryst. (2013). D69, 367-372  [ doi:10.1107/S0907444912047464 ]

PRR1 coat protein binding to its RNA translational operator

M. Persson, K. Tars and L. Liljas

Synopsis: The structure of virus-like particles of the small RNA phage PRR1 bound to an RNA segment corresponding to a stem-loop that includes the start codon for the replicase gene has been solved and the binding was compared with the related, and better investigated, phage MS2.A.

PDB reference: 4ang

Online 16 February 2013


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Acta Cryst. (2013). D69, 373-380  [ doi:10.1107/S0907444912047828 ]

The structure of the ARE-binding domains of Hu antigen R (HuR) undergoes conformational changes during RNA binding

H. Wang, F. Zeng, Q. Liu, H. Liu, Z. Liu, L. Niu, M. Teng and X. Li

Synopsis: The crystal structures of the N-terminal tandem RRM domains of HuR are reported in RNA-free and RNA-bound forms.

PDB references: 4egl and 4ed5

Online 16 February 2013


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Acta Cryst. (2013). D69, 381-387  [ doi:10.1107/S0907444912048019 ]

REACH: Robotic Equipment for Automated Crystal Harvesting using a six-axis robot arm and a micro-gripper

M. Y. Heidari Khajepour, X. Vernede, D. Cobessi, H. Lebrette, P. Rogues, M. Terrien, C. Berzin and J.-L. Ferrer

Synopsis: A six-axis robot arm equipped with a micro-gripper is used to harvest protein crystals from their crystallization drops. Once harvested, the sample is inserted into the X-ray beam by the robot for direct data collection.

Online 16 February 2013


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Acta Cryst. (2013). D69, 388-397  [ doi:10.1107/S0907444912048664 ]

Structure of a human IgA1 Fab fragment at 1.55 Å resolution: potential effect of the constant domains on antigen-affinity modulation

A. Correa, F. Trajtenberg, G. Obal, O. Pritsch, G. Dighiero, P. Oppezzo and A. Buschiazzo

Synopsis: The three-dimensional structure of a human IgA Fab is reported for the first time in three different crystal forms. Compared with a FabG with identical variable domains, the FabA displays a more rigid architecture which can explain the long-distance effects of the constant regions on antigen-binding affinity.

PDB references: 3m8o, 3qnx, 3qny, 3qo1 and 3qnz

Online 16 February 2013


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Acta Cryst. (2013). D69, 398-408  [ doi:10.1107/S0907444912049001 ]

Structure, recombinant expression and mutagenesis studies of the catalase with oxidase activity from Scytalidium thermophilum

Y. Yuzugullu, C. H. Trinh, M. A. Smith, A. R. Pearson, S. E. V. Phillips, D. Sutay Kocabas, U. Bakir, Z. B. Ogel and M. J. McPherson

Synopsis: The catalytic and oxidative activities of the catalase from Scytalidium thermophilum are likely to be associated with the same haem active centre. The secondary oxidase activity may be a general feature of monofunctional catalases in the absence of hydrogen peroxide. This bifunctionality may provide some advantages for industry if the oxidase activity can be enhanced through engineering or directed evolution.

PDB references: 4aue, 4aum, 4aul and 4aun

Online 16 February 2013


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Acta Cryst. (2013). D69, 409-419  [ doi:10.1107/S0907444912049311 ]

Effect of Rap1 binding on DNA distortion and potassium permanganate hypersensitivity

Y.-V. Le Bihan, B. Matot, O. Pietrement, M.-J. Giraud-Panis, S. Gasparini, E. Le Cam, E. Gilson, B. Sclavi, S. Miron and M.-H. Le Du

Synopsis: The binding of Rap1 to DNA induces potassium permanganate hypersensitivity that is driven by a specific Arg residue in Rap1 but is not associated with major DNA distortion.

PDB reference: 4gfb

Online 16 February 2013


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Acta Cryst. (2013). D69, 420-431  [ doi:10.1107/S0907444912048998 ]

Structural basis for the inhibition of Mycobacterium tuberculosis L,D-transpeptidase by meropenem, a drug effective against extensively drug-resistant strains

H. S. Kim, J. Kim, H. N. Im, J. Y. Yoon, D. R. An, H. J. Yoon, J. Y. Kim, H. K. Min, S.-J. Kim, J. Y. Lee, B. W. Han and S. W. Suh

Synopsis: The crystal structure of M. tuberculosis L,D-transpeptidase (LdtMt2; Rv2518c) has been determined in both ligand-free and meropenem-bound forms. The detailed view of the interactions between meropenem and LdtMt2 will be useful in structure-guided discovery of new antituberculosis drugs.

PDB references: 4gsq, 4gsr and 4gsu

Online 16 February 2013


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Acta Cryst. (2013). D69, 432-441  [ doi:10.1107/S0907444912049268 ]

Structure of LdtMt2, an L,D-transpeptidase from Mycobacterium tuberculosis

D. Böth, E. M. Steiner, D. Stadler, Y. Lindqvist, R. Schnell and G. Schneider

Synopsis: The crystal structures of two fragments of the L,D-transpeptidase from M. tuberculosis have been determined at 1.45 and 1.86 Å resolution. The extramembrane part of this enzyme consists of three domains: two domains related to the immunoglobulin fold and a catalytic domain belonging to the ErfK/YbiS/YhnG family at the C-terminus.

PDB references: 4hu2 and 4huc

Online 16 February 2013


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Acta Cryst. (2013). D69, 442-450  [ doi:10.1107/S0907444912049219 ]

Structure of a novel [alpha]-amylase AmyB from Thermotoga neapolitana that produces maltose from the nonreducing end of polysaccharides

S.-Y. Jun, J.-S. Kim, K.-H. Choi, J. Cha and N.-C. Ha

Synopsis: In this study, the crystal structure of AmyB from T. neapolitana has been determined at 2.4 Å resolution, revealing that the monomeric AmyB comprises domains A, B and C like other [alpha]-amylases, but with structural variations.

PDB reference: 4gkl

Online 16 February 2013


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Acta Cryst. (2013). D69, 451-463  [ doi:10.1107/S0907444912049608 ]

GH1-family 6-P-[beta]-glucosidases from human microbiome lactic acid bacteria

K. Michalska, K. Tan, H. Li, C. Hatzos-Skintges, J. Bearden, G. Babnigg and A. Joachimiak

Synopsis: The crystal structures of two 6-P-[beta]-glucosidases from the GH1 family were determined in the apo form and in the presence of a 6'-P-salicin substrate, of the reaction product 6-P-[beta]-glucose and of glucose corresponding to the aglycon molecule. The presence of natural ligands enabled the definition of the structural elements responsible for the recognition and hydrolysis of 6'-P-[beta]-glucosides.

PDB references: 3qom, 4gze, 3pn8, 4f66 and 4f79

Online 16 February 2013


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Acta Cryst. (2013). D69, 464-470  [ doi:10.1107/S0907444912050135 ]

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 and F. X. Gomis-Rüth

Synopsis: The crystal structure of the C-terminal domain of a putative U32 peptidase from G. thermoleovorans is reported; it is one of the most tightly packed protein structures reported to date.

PDB references: 4he6 and 4he5

Online 16 February 2013


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Acta Cryst. (2013). D69, 471-485  [ doi:10.1107/S0907444912052134 ]

Insights into the mechanism of pyrrole polymerization catalysed by porphobilinogen deaminase: high-resolution X-ray studies of the Arabidopsis thaliana enzyme

A. Roberts, R. Gill, R. J. Hussey, H. Mikolajek, P. T. Erskine, J. B. Cooper, S. P. Wood, E. J. T. Chrystal and P. M. Shoolingin-Jordan

Synopsis: The first X-ray analysis of porphobilinogen deaminase from a plant reveals an extensive highly conserved loop region covering the active site that was completely disordered in previous structures. Structural comparisons suggest that the concerted movements of two enzyme domains may be linked to elongation of the substrate and that during the elongation cycle the bound dipyrromethane cofactor or polypyrrole intermediate moves to vacate one of the cofactor subsites such that an incoming pyrrole moiety can bind.

PDB reference: 4htg

Online 16 February 2013


short communications


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Acta Cryst. (2013). D69, 486-489  [ doi:10.1107/S0907444912051062 ]

Protein-peptide complex crystallization: a case study on the ERK2 mitogen-activated protein kinase

G. Gógl, I. Töro and A. Reményi

Synopsis: A rational surface-engineering approach led to the crystal structure determination of ERK2-docking peptide complexes.

PDB references: 4h3p and 4h3q

Online 16 February 2013


obituaries


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Acta Cryst. (2013). D69, 490-492  [ doi:10.1107/S0907444913004186 ]

Guy Dodson FRS (1937-2012)

E. N. Baker

Synopsis: Obituary for Guy Dodson.

Online 16 February 2013


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