[IUCr 2014 Congress]

Acta Crystallographica Section D

Biological Crystallography

Volume 70, Part 3 (March 2014)



[Issue Author Index][Volume Author Index]
[Cover illustration] Cover illustration: 'Symmetrical merging' of the South rose window of the Gothic cathedral of Burgos in Northern Spain combined with the high symmetry axis view of the cylindrical enclosure (vault) formed by the major vault protein (MVP) from rat liver. Cathedral windows are magnificent examples of planar circular symmetry that are iconic representations of the cosmic view of the Middle Ages. Highly symmetrical atomic objects are frequent in biological structures, representing an atomic view of the biological microcosmos. Further details and discussion are given in the essay by C. Abad-Zapatero on p. 907. The images are from the author's personal collection and from T. Tsukihara and H. Tanaka, respectively.

research papers


thumbnail of article figure

[HTML version][PDF version][Supplementary Material]   [AD]  [Buy article online]

Acta Cryst. (2014). D70, 615-626  [ doi:10.1107/S1399004713030794 ]

Structural and functional characterization of an Isd-type haem-degradation enzyme from Listeria monocytogenes

T. Duong, K. Park, T. Kim, S. W. Kang, M. J. Hahn, H.-Y. Hwang and K. K. Kim

Synopsis: The structural and functional characterization of Isd-LmHde, an Isd-type haem-degrading enzyme in Listeria monocytogenes, is presented. The haem-degradation product of Isd-LmHde was verified to be biliverdin and the active residues were identified by structure-based mutagenesis and following function studies.

PDB reference: 4kia

Online 15 February 2014


thumbnail of article figure

[HTML version][PDF version]  [Buy article online]

Acta Cryst. (2014). D70, 627-635  [ doi:10.1107/S1399004713032070 ]

Improving the chances of successful protein structure determination with a random forest classifier

S. Jahandideh, L. Jaroszewski and A. Godzik

Synopsis: Using an extended set of protein features calculated separately for protein surface and interior, a new version of XtalPred based on a random forest classifier achieves a significant improvement in predicting the success of structure determination from the primary amino-acid sequence.

Online 15 February 2014


thumbnail of article figure

[HTML version][PDF version][Supplementary Material]  [Open access]

Acta Cryst. (2014). D70, 636-646  [ doi:10.1107/S1399004713032112 ]

Crystal structure and conformational flexibility of the unligated FK506-binding protein FKBP12.6

H. Chen, S. M. Mustafi, D. M. LeMaster, Z. Li, A. Héroux, H. Li and G. Hernández

Synopsis: Two crystal forms of unligated FKBP12.6 exhibit multiple conformations in the active site and in the 80s loop, the primary site for known protein-recognition interactions. The previously unreported NMR backbone assignment of FKBP12.6 revealed extensive doubling of amide resonances, which reflects a slow conformational transition centered in the 80s loop.

PDB references: 4iq2 and 4iqc

Online 15 February 2014


thumbnail of article figure

[HTML version][PDF version][Supplementary Material]  [Buy article online]

Acta Cryst. (2014). D70, 647-657  [ doi:10.1107/S1399004713032100 ]

Promoting protein crystallization using a plate with simple geometry

R.-Q. Chen, D.-C. Yin, Y.-M. Liu, Q.-Q. Lu, J. He and Y. Liu

Synopsis: A novel and simple protein crystallization method called the cross-diffusion microbatch method is presented. This method can dramatically increase the number of crystallization conditions and is a potentially useful technique in practical protein crystallization screening.

Online 15 February 2014


thumbnail of article figure

[HTML version][PDF version][Supplementary Material]  [Buy article online]

Acta Cryst. (2014). D70, 658-667  [ doi:10.1107/S1399004713032240 ]

Conformational transitions in the [gamma] subunit of the archaeal translation initiation factor 2

O. Nikonov, E. Stolboushkina, V. Arkhipova, O. Kravchenko, S. Nikonov and M. Garber

Synopsis: Four high-resolution crystal structures of aIF2[gamma] from Sulfolobus solfataricus are reported: aIF2[gamma]-GDPCP (a nonhydrolyzable GTP analogue), aIF2[gamma]-GDP-formate (in which a formate ion possibly mimics Pi), aIF2[gamma]-GDP and nucleotide-free aIF2[gamma]. The structures describe the different states of aIF2[gamma] and demonstrate the conformational transitions that take place in the aIF2[gamma] `life cycle'.

PDB references: 4m0l, 4m2l, 4m4s and 4m53

Online 15 February 2014


thumbnail of article figure

[HTML version][PDF version][Supplementary Material]  [Buy article online]

Acta Cryst. (2014). D70, 668-675  [ doi:10.1107/S1399004713032252 ]

Structure of a proteolytically resistant analogue of (NLys)5SFTI-1 in complex with trypsin: evidence for the direct participation of the Ser214 carbonyl group in serine protease-mediated proteolysis

S. Krzywda, M. Jaskolski, K. Rolka and M. J. Stawikowski

Synopsis: The structure of a peptide-peptoid analogue inhibitor was determined by X-ray crystallography. It is the first structure to reveal the structural basis of the complete proteolytic resistance towards serine proteases by inhibitors containing a peptoid residue at the P1 position.

PDB reference: 4hgc

Online 15 February 2014


thumbnail of article figure

[HTML version][PDF version][Supplementary Material]  [Buy article online]

Acta Cryst. (2014). D70, 676-684  [ doi:10.1107/S1399004713032264 ]

Crystal structures of substrate-bound chitinase from the psychrophilic bacterium Moritella marina and its structure in solution

P. H. Malecki, C. E. Vorgias, M. V. Petoukhov, D. I. Svergun and W. Rypniewski

Synopsis: A low-activity mutant of a cold-adapted chitinase from M. marina has been crystallized and examined in an unliganded form and in complex with four and five N-acetyl-D-glucosamine units to reveal its substrate-binding mode. The oligomerization and conformational flexibility of this multi-domain protein in solution has also been examined.

PDB references: 4mb3, 4mb4 and 4mb5

Online 15 February 2014


thumbnail of article figure

[HTML version][PDF version][Supplementary Material]  [Buy article online]

Acta Cryst. (2014). D70, 685-693  [ doi:10.1107/S1399004713032392 ]

Exploiting large non-isomorphous differences for phase determination of a G-segment invertase-DNA complex

C. J. Ritacco, T. A. Steitz and J. Wang

Synopsis: An accumulation of severely non-isomorphous native data sets using the swelling-and-shrinking method or during search for the isomorphous replacement solutions can be beneficial for phase improvement and perhaps for structure refinement.

PDB reference: 4m6f

Online 15 February 2014


thumbnail of article figure

[HTML version][PDF version][Supplementary Material]  [Buy article online]

Acta Cryst. (2014). D70, 694-707  [ doi:10.1107/S1399004713032355 ]

Structural insights into the molecular mechanism of Escherichia coli SdiA, a quorum-sensing receptor

T. Kim, T. Duong, C. Wu, J. Choi, N. Lan, S. W. Kang, N. K. Lokanath, D. Shin, H.-Y. Hwang and K. K. Kim

Synopsis: Crystal structures of the full-length E. coli quorum-sensing receptor SdiA reveal that it forms a symmetrical dimer and exhibits broad ligand-binding selectivity. The ligand binding increases the stability of SdiA but does not modulate its DNA-binding ability. The DNA-binding activity of SdiA can be regulated through the formation of an intersubunit disulfide bond.

PDB references: 4lfu and 4lgw

Online 15 February 2014


thumbnail of article figure

[HTML version][PDF version][Supplementary Material]  [Open access]

Acta Cryst. (2014). D70, 708-719  [ doi:10.1107/S1399004713032446 ]

Role of [kappa][rightwards arrow][lambda] light-chain constant-domain switch in the structure and functionality of A17 reactibody

N. Ponomarenko, S. D. Chatziefthimiou, I. Kurkova, Yu. Mokrushina, Y. Mokrushina, A. Stepanova, I. Smirnov, M. Avakyan, T. Bobik, A. Mamedov, V. Mitkevich, A. Belogurov, O. S. Fedorova, M. Dubina, A. Golovin, V. Lamzin, A. Friboulet, A. A. Makarov, M. Wilmanns and A. Gabibov

Synopsis: Catalytic antibody variants with [kappa] and [lambda] light-chain constant domains show differences in their crystal structures which lead to subtle changes in catalytic efficiency and thermodynamic parameters as well as in their affinity for peptide substrates.

PDB reference: 3zl4

Online 15 February 2014


thumbnail of article figure

[HTML version][PDF version][Supplementary Material]  [Buy article online]

Acta Cryst. (2014). D70, 720-732  [ doi:10.1107/S1399004713032434 ]

Structures of the Ca2+-regulated photoprotein obelin Y138F mutant before and after bioluminescence support the catalytic function of a water molecule in the reaction

P. V. Natashin, W. Ding, E. V. Eremeeva, S. V. Markova, J. Lee, E. S. Vysotski and Z.-J. Liu

Synopsis: Crystal structures of the Y138F obelin mutant before and after bioluminescence have been determined at 1.72 and 1.30 Å resolution, respectively. Their spatial structures support the catalytic function of a water molecule found in an internal cavity in the light-emission reaction of Ca2+-regulated photoproteins.

PDB references: 4mrx and 4mry

Online 15 February 2014


thumbnail of article figure

[HTML version][PDF version][Supplementary Material]  [Open access]

Acta Cryst. (2014). D70, 733-743  [ doi:10.1107/S1399004713032549 ]

Ensemble refinement shows conformational flexibility in crystal structures of human complement factor D

F. Forneris, B. T. Burnley and P. Gros

Synopsis: Ensemble-refinement analysis of native and mutant factor D (FD) crystal structures indicates a dynamical transition in FD from a self-inhibited inactive conformation to a substrate-bound active conformation that is reminiscent of the allostery in thrombin. Comparison with previously observed dynamics in thrombin using NMR data supports the crystallographic ensembles.

PDB references: 4cbn and 4cbo

Online 15 February 2014


thumbnail of article figure

[HTML version][PDF version]  [Open access]

Acta Cryst. (2014). D70, 744-751  [ doi:10.1107/S139900471303294X ]

Structural evidence for the partially oxidized dipyrromethene and dipyrromethanone forms of the cofactor of porphobilinogen deaminase: structures of the Bacillus megaterium enzyme at near-atomic resolution

N. Azim, E. Deery, M. J. Warren, B. A. A. Wolfenden, P. Erskine, J. B. Cooper, A. Coker, S. P. Wood and M. Akhtar

Synopsis: The enzyme porphobilinogen deaminase (PBGD; hydroxymethylbilane synthase; EC 2.5.1.61) catalyses a key early step in the biosynthesis of tetrapyrroles in which four molecules of the monopyrrole porphobilinogen are condensed to form a linear tetrapyrrole. Two near-atomic resolution structures of PBGD from B. megaterium are reported that demonstrate the time-dependent accumulation of partially oxidized forms of the cofactor, including one that possesses a tetrahedral C atom in the terminal pyrrole ring.

PDB references: 4mlv and 4mlq

Online 15 February 2014


thumbnail of article figure

[HTML version][PDF version]   [AD]  [Open access]

Acta Cryst. (2014). D70, 752-759  [ doi:10.1107/S1399004713032987 ]

The structure of an authentic spore photoproduct lesion in DNA suggests a basis for recognition

I. Singh, Y. Lian, L. Li and M. M. Georgiadis

Synopsis: The structure of a spore photoproduct lesion in duplex DNA is described.

PDB references: 4m94 and 4m95

Online 15 February 2014


thumbnail of article figure

[HTML version][PDF version]  [Buy article online]

Acta Cryst. (2014). D70, 760-771  [ doi:10.1107/S1399004713033014 ]

Structure of the extended-spectrum class C [beta]-lactamase ADC-1 from Acinetobacter baumannii

M. Bhattacharya, M. Toth, N. T. Antunes, C. A. Smith and S. B. Vakulenko

Synopsis: The crystal structure of the class C extended-spectrum cepahalosporinase ADC-1 has been solved to 1.2 Å resolution.

PDB reference: 4net

Online 22 February 2014


thumbnail of article figure

[HTML version][PDF version][Supplementary Material]  [Buy article online]

Acta Cryst. (2014). D70, 772-779  [ doi:10.1107/S1399004713033051 ]

New insights into the catalytic active-site structure of multicopper oxidases

H. Komori, R. Sugiyama, K. Kataoka, K. Miyazaki, Y. Higuchi and T. Sakurai

Synopsis: In the present study, crystal structures of multicopper oxidases were determined and density for an O atom was found inside the trinuclear copper centre.

PDB references: 4ner, 4e9q, 4e9r, 4e9s, 4e9t, 4e9v, 4e9w, 4e9x and 4e9y

Online 22 February 2014


thumbnail of article figure

[HTML version][PDF version][Supplementary Material]  [Buy article online]

Acta Cryst. (2014). D70, 780-788  [ doi:10.1107/S139900471303318X ]

Structural insights into the novel ARM-repeat protein CTNNBL1 and its association with the hPrp19-CDC5L complex

J.-W. Ahn, S. Kim, E.-J. Kim, Y.-J. Kim and K.-J. Kim

Synopsis: The crystal structure of the dimer form of CTNNBL1 was determined, and the CDC5L binding site was also identified. Based on the structural and the biochemical experiments of CTNNBL1, an improved molecular architecture of the Prp19-CDC5L complex was presented.

PDB references: 4mfu and 4mfv

Online 22 February 2014


thumbnail of article figure

[HTML version][PDF version][Supplementary Material]  [Buy article online]

Acta Cryst. (2014). D70, 789-801  [ doi:10.1107/S1399004713033488 ]

Structural and functional analyses of a glutaminyl cyclase from Ixodes scapularis reveal metal-independent catalysis and inhibitor binding

K.-F. Huang, H.-L. Hsu, S. Karim and A.H.-J. Wang

Synopsis: A metal-independent glutaminyl cyclase from the black-legged tick I. scapularis is reported. The metal-independent inhibition of glutaminyl cyclases by imidazole-derived inhibitors is described for the first time.

PDB references: 4mhn, 4mhp, 4mhy and 4mhz

Online 22 February 2014


thumbnail of article figure

[HTML version][PDF version][Supplementary Material]  [Buy article online]

Acta Cryst. (2014). D70, 802-810  [ doi:10.1107/S1399004713033221 ]

Structural and thermodynamic basis of the inhibition of Leishmania major farnesyl diphosphate synthase by nitrogen-containing bisphosphonates

S. Aripirala, D. Gonzalez-Pacanowska, E. Oldfield, M. Kaiser, L. M. Amzel and S. B. Gabelli

Synopsis: Structural insights into L. major farnesyl diphosphate synthase, a key enzyme in the mevalonate pathway, are described.

PDB references: 4jzb, 4jzx and 4k10

Online 22 February 2014


thumbnail of article figure

[HTML version][PDF version][Supplementary Material]  [Open access]

Acta Cryst. (2014). D70, 811-820  [ doi:10.1107/S1399004713033609 ]

Structural characteristics of alkaline phosphatase from the moderately halophilic bacterium Halomonas sp. 593

S. Arai, Y. Yonezawa, M. Ishibashi, F. Matsumoto, M. Adachi, T. Tamada, H. Tokunaga, M. Blaber, M. Tokunaga and R. Kuroki

Synopsis: In order to clarify the structural basis of the halophilic characteristics of an alkaline phosphatase derived from the moderate halophile Halomonas sp. 593 (HaAP), the tertiary structure of HaAP was determined to 2.1 Å resolution by X-ray crystallography. The structural properties of surface negative charge and core hydrophobicity were shown to be intermediate between those characteristic of halophiles and non-halophiles, and may explain the unique functional adaptation to a wide range of salt concentrations.

PDB reference: 3wbh

Online 22 February 2014


thumbnail of article figure

[HTML version][PDF version][Supplementary Material]  [Buy article online]

Acta Cryst. (2014). D70, 821-832  [ doi:10.1107/S1399004713033555 ]

The structure of Rv2372c identifies an RsmE-like methyltransferase from Mycobacterium tuberculosis

A. Kumar, S. Kumar and B. Taneja

Synopsis: The structure of Rv2372c from M. tuberculosis reveals it to be an RsmE orthologue that belongs to a distinct class in the SPOUT superfamily and can complement RsmE-deleted E. coli cells.

PDB reference: 4l69

Online 22 February 2014


thumbnail of article figure

[HTML version][PDF version][Supplementary Material]  [Buy article online]

Acta Cryst. (2014). D70, 833-840  [ doi:10.1107/S1399004713033658 ]

Conformational flexibility in the catalytic triad revealed by the high-resolution crystal structure of Streptomyces erythraeus trypsin in an unliganded state

E. Blankenship, K. Vukoti, M. Miyagi and D. T. Lodowski

Synopsis: This work reports the first sub-angstrom resolution structure of S. erythraeus trypsin. The detailed model of a prototypical serine protease at a catalytically relevant pH with an unoccupied active site is presented and is compared with other high-resolution serine protease structures.

PDB reference: 4m7g

Online 22 February 2014


thumbnail of article figure

[HTML version][PDF version]  [Buy article online]

Acta Cryst. (2014). D70, 841-850  [ doi:10.1107/S139900471303366X ]

Structures of SAICAR synthetase (PurC) from Streptococcus pneumoniae with ADP, Mg2+, AIR and Asp

N. M. Wolf, C. Abad-Zapatero, M. E. Johnson and L.W.-M. Fung

Synopsis: The structure of SAICAR synthetase from S. pneumoniae had been solved in complex with ADP, Asp, Mg2+ and AIR. The newly defined binding site for Asp provides information about the mechanism.

PDB references: 4fe2 and 4nye

Online 22 February 2014


thumbnail of article figure

[HTML version][PDF version][Supplementary Material]  [Buy article online]

Acta Cryst. (2014). D70, 851-862  [ doi:10.1107/S1399004713033750 ]

The structure of cytomegalovirus immune modulator UL141 highlights structural Ig-fold versatility for receptor binding

I. Nemcovicová and D. M. Zajonc

Synopsis: The crystal structure of Human cytomegalovirus immune modulator UL141 was solved at 3.25 Å resolution. Here, a detailed analysis of its intimate dimerization interface and the biophysical properties of its receptor (TRAIL-R2 and CD155) binding interactions are presented.

PDB reference: 4jm0

Online 22 February 2014


thumbnail of article figure

[HTML version][PDF version][Supplementary Material]  [Open access]

Acta Cryst. (2014). D70, 863-876  [ doi:10.1107/S1399004713033634 ]

Multi-PAS domain-mediated protein oligomerization of PpsR from Rhodobacter sphaeroides

U. Heintz, A. Meinhart and A. Winkler

Synopsis: Crystal structures of two truncated variants of the transcription factor PpsR from R. sphaeroides are presented that enabled the phasing of a triple PAS domain construct. Together, these structures reveal the importance of [alpha]-helical PAS extensions for multi-PAS domain-mediated protein oligomerization and function.

PDB references: 4l9e, 4l9f and 4l9g

Online 27 February 2014


thumbnail of article figure

[HTML version][PDF version][Supplementary Material]  [Open access]

Acta Cryst. (2014). D70, 877-888  [ doi:10.1107/S1399004713032276 ]

Structural analysis of [beta]-glucosidase mutants derived from a hyperthermophilic tetrameric structure

M. Nakabayashi, M. Kataoka, Y. Mishima, Y. Maeno and K. Ishikawa

Synopsis: Substitutive mutations that convert a tetrameric [beta]-glucosidase into a dimeric state lead to improvement of its crystal quality.

PDB reference: 3wdp

Online 27 February 2014


thumbnail of article figure

[HTML version][PDF version][Supplementary Material]  [Buy article online]

Acta Cryst. (2014). D70, 889-903  [ doi:10.1107/S1399004713033452 ]

Identification of a novel polyfluorinated compound as a lead to inhibit the human enzymes aldose reductase and AKR1B10: structure determination of both ternary complexes and implications for drug design

A. Cousido-Siah, F. X. Ruiz, A. Mitschler, S. Porté, Á. R. de Lera, M. J. Martín, S. Manzanaro, J. A. de la Fuente, F. Terwesten, M. Betz, G. Klebe, J. Farrés, X. Parés and A. Podjarny

Synopsis: The polyfluorinated compound 2,2',3,3',5,5',6,6'-octafluoro-4,4'-biphenyldiol (JF0064) is a potent inhibitor (IC50 [less-than or equal to] 1 µM) of both aldose reductase and AKR1B10. X-ray structures of ternary complexes of both enzymes with JF0064 allow it to be inferred that this lead compound binds to the enzyme active site through an acidic phenol group and allow the extraction of important hints for structure-based drug design.

PDB references: 4igs and 4icc

Online 27 February 2014


short communications


thumbnail of article figure

[HTML version][PDF version]  [Buy article online]

Acta Cryst. (2014). D70, 904-906  [ doi:10.1107/S1399004713031787 ]

How precise are reported protein coordinate data?

A. S. Konagurthu, L. Allison, D. Abramson, P. J. Stuckey and A. M. Lesk

Synopsis: Information theory is used to estimate the precision of reported protein coordinates in the PDB.

Online 27 February 2014


essays


thumbnail of article figure

[HTML version][PDF version]  [Buy article online]

Acta Cryst. (2014). D70, 907-911  [ doi:10.1107/S1399004713032859 ]

Notes of a protein crystallographer: the beauty of rose windows and the different meanings of symmetry

C. Abad-Zapatero

Synopsis: The magnificent rose windows of the Gothic cathedrals provide artistic illustrations of many of the planar point groups of symmetry. It is suggested that the presence of certain symmetry elements and their selection by the artists could have been motivated to convey specific meaning to the resulting compositions.

Online 27 February 2014


Copyright © International Union of Crystallography
IUCr Webmaster