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Acta Crystallographica Section D

Biological Crystallography

Volume 69, Part 8 (August 2013)



[Issue Author Index][Volume Author Index]
[Cover illustration] Cover illustration: Top view of an ATP-independent Lon-like protease with open axial pores in tube representation with a semi-transparent surface (p. 1395). The N-terminal coil, the flexible Lon-insertion domain, the AAA-[alpha]/[beta], the AAA-[alpha], and the protease domains are colored in red, wheat, blue, cyan, and brown, respectively.

feature articles


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Acta Cryst. (2013). D69, 1333-1341  [ doi:10.1107/S090744491301158X ]

Half a century of Ramachandran plots

O. Carugo and K. Djinovic-Carugo

Synopsis: The most relevant aspects of fifty-year history of the Ramachandran plot are summarized, from the original ideas of Gopalasamudram Narayana Ramachandran to subsequent revisions and to applications in structural biology.

Online 13 July 2013


research papers


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Acta Cryst. (2013). D69, 1342-1357  [ doi:10.1107/S0907444913008408 ]

MAIN software for density averaging, model building, structure refinement and validation

D. Turk

Synopsis: MAIN is interactive software designed to interactively perform the complex tasks of macromolecular crystal structure determination and validation. The features of MAIN and its tools for electron-density map calculations, model building, refinement in real and reciprocal space, and validation exploiting noncrystallographic symmetry in single and multiple crystal forms are presented.

Online 13 June 2013


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Acta Cryst. (2013). D69, 1358-1366  [ doi:10.1107/S0907444913004459 ]

The structure of an MDM2-Nutlin-3a complex solved by the use of a validated MDM2 surface-entropy reduction mutant

B. Anil, C. Riedinger, J. A. Endicott and M. E. M. Noble

Synopsis: The design, validation, proof of mechanism and exploitation of a surface-entropy reduction mutant to solve the structure of the benchmark inhibitor Nutlin-3a bound to the cancer drug-discovery target MDM2 are reported.

PDB references: 4hfz and 4hg7

Online 13 July 2013


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Acta Cryst. (2013). D69, 1367-1380  [ doi:10.1107/S090744491300735X ]

Tying down the arm in Bacillus dUTPase: structure and mechanism

J. García-Nafría, J. Timm, C. Harrison, J. P. Turkenburg and K. S. Wilson

Synopsis: Structures of the B. subtilis dUTPases in a novel complex with dU-PPi-Mg2+ and in complex with dUMP provide insights into the mechanism and identify features unique to the B. subtilis enzymes.

PDB references: 4apz, 4aoo, 4aoz, 4b0h and 4ao5

Online 13 July 2013


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Acta Cryst. (2013). D69, 1381-1386  [ doi:10.1107/S0907444913007658 ]

Anatomy of secretin binding to the Dickeya dadantii type II secretion system pilotin

S. Rehman, S. Gu, V. E. Shevchik and R. W. Pickersgill

Synopsis: The crystal structure of the C-terminal peptide of secretin bound to the surface of its cognate pilotin reveals interactions that are essential for the assembly of a functional type II secretion system in D. dadantii and related secretion systems.

PDB reference: 3uym

Online 13 July 2013


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Acta Cryst. (2013). D69, 1387-1394  [ doi:10.1107/S0907444913008160 ]

Protein HP1028 from the human pathogen Helicobacter pylori belongs to the lipocalin family

N. Barison, L. Cendron, V. Loconte, E. A. Proctor, N. V. Dokholyan and G. Zanotti

Synopsis: The crystal structure of HP1028, a protein from the human pathogen H. pylori, demonstrates that it belongs to the lipocalin family.

PDB reference: 4inn

Online 13 July 2013


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Acta Cryst. (2013). D69, 1395-1402  [ doi:10.1107/S0907444913008214 ]

Structures of an ATP-independent Lon-like protease and its complexes with covalent inhibitors

J.-H. Liao, K. Ihara, C.-I. Kuo, K.-F. Huang, S. Wakatsuki, S.-H. Wu and C.-I. Chang

Synopsis: The crystal structure of an ATP-independent LonC protease revealed a proteolytic chamber with two open axial pores. A LonC-specific N-terminal coil tethers the AAA+ and protease domains together. Structures with covalent inhibitors bound to the proteolytic active sites provide mechanistic insights into the recognition of inhibitors and polypeptide substrates within the conserved Lon proteolytic chamber.

PDB references: 4fw9, 4fwd, 4fwg and 4fwh

Online 13 July 2013


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Acta Cryst. (2013). D69, 1403-1413  [ doi:10.1107/S0907444913008354 ]

Trapped intermediates in crystals of the FMN-dependent oxidase PhzG provide insight into the final steps of phenazine biosynthesis

N. Xu, E. G. Ahuja, P. Janning, D. V. Mavrodi, L. S. Thomashow and W. Blankenfeldt

Synopsis: The structures of tricyclic intermediates trapped in crystals of PhzG suggest a basis for the chemistry and promiscuity of the final steps of phenazine biosynthesis.

PDB references: 4hms, 4hmt, 4hmu, 4hmw, 4hmx and 4hmv

Online 13 July 2013


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Acta Cryst. (2013). D69, 1414-1422  [ doi:10.1107/S0907444913008743 ]

Structural and catalytic characterization of a thermally stable and acid-stable variant of human carbonic anhydrase II containing an engineered disulfide bond

C. D. Boone, A. Habibzadegan, C. Tu, D. N. Silverman and R. McKenna

Synopsis: The X-ray crystallographic structure of the disulfide-containing HCAII (dsHCAII) has been solved to 1.77 Å resolution and revealed that successful oxidation of the cysteine bond was achieved while also retaining desirable active-site geometry.

PDB reference: 4hba

Online 13 July 2013


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Acta Cryst. (2013). D69, 1423-1432  [ doi:10.1107/S0907444913015448 ]

Structures of human sirtuin 3 complexes with ADP-ribose and with carba-NAD+ and SRT1720: binding details and inhibition mechanism

G. T. T. Nguyen, S. Schaefer, M. Gertz, M. Weyand and C. Steegborn

Synopsis: Crystal structures of human Sirt3 ligand complexes, complemented by biochemical analyses, reveal the binding site and mechanism for the small-molecule inhibitor SRT1720. The compound induces a unique co-factor binding-loop conformation and packs sandwich-like between a hydrophobic active-site patch and the nicotinamide moiety of the NAD+ cosubstrate.

PDB references: 4bn4 and 4bn5

Online 17 July 2013


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Acta Cryst. (2013). D69, 1433-1446  [ doi:10.1107/S0907444913015126 ]

Structure of arylamine N-acetyltransferase from Mycobacterium tuberculosis determined by cross-seeding with the homologous protein from M. marinum: triumph over adversity

A. Abuhammad, E. D. Lowe, M. A. McDonough, P. D. Shaw Stewart, S. A. Kolek, E. Sim and E. F. Garman

Synopsis: The three-dimensional structure of an arylamine N-acetyltransferase enzyme from M. tuberculosis has been determined using cross-seeding with the homologous protein from M. marinum.

PDB reference: 4bgf

Online 17 July 2013


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Acta Cryst. (2013). D69, 1447-1462  [ doi:10.1107/S0907444913009050 ]

On the reproducibility of protein crystal structures: five atomic resolution structures of trypsin

D. Liebschner, M. Dauter, A. Brzuszkiewicz and Z. Dauter

Synopsis: Details of five very high-resolution accurate structures of bovine trypsin are compared in the context of the reproducibility of models obtained from crystals grown under identical conditions.

PDB references: 4i8g, 4i8h, 4i8j, 4i8k and 4i8l

Online 17 July 2013


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Acta Cryst. (2013). D69, 1463-1469  [ doi:10.1107/S0907444913009335 ]

Mitigation of X-ray damage in macromolecular crystallography by submicrometre line focusing

Y. Z. Finfrock, E. A. Stern, R. W. Alkire, J. J. Kas, K. Evans-Lutterodt, A. Stein, N. Duke, K. Lazarski and A. Joachimiak

Synopsis: Reported here are measurements of the penetration depth and spatial distribution of photoelectron damage excited by 18.6 keV X-ray photons in a lysozyme crystal with a vertical submicrometre line-focus beam of 0.7 µm full-width half-maximum.

PDB references: 4htk, 4htn and 4htq

Online 17 July 2013


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Acta Cryst. (2013). D69, 1470-1481  [ doi:10.1107/S0907444913009347 ]

Structures of enzyme-intermediate complexes of yeast Nit2: insights into its catalytic mechanism and different substrate specificity compared with mammalian Nit2

H. Liu, Y. Gao, M. Zhang, X. Qiu, A. J. L. Cooper, L. Niu and M. Teng

Synopsis: Structures of yeast Nit2 in complex with [alpha]-ketoglutarate and with oxaloacetate revealed the molecular-recognition mechanism of the enzyme for the first time, while that of the C169S mutant of yeast Nit2 showed a new ligand located in the catalytic cavity.

PDB references: 4h5u, 4hg3, 4hg5 and 4hgd

Online 18 July 2013


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Acta Cryst. (2013). D69, 1482-1492  [ doi:10.1107/S0907444913009372 ]

Structure determination of the functional domain interaction of a chimeric nonribosomal peptide synthetase from a challenging crystal with noncrystallographic translational symmetry

J. A. Sundlov and A. M. Gulick

Synopsis: The structure of the functional interaction of NRPS adenylation and carrier protein domains, trapped with a mechanism-based inhibitor, is described. Crystals exhibit translational non-crystallographic symmetry, which challenged structure determination and refinement.

PDB reference: 4iz6

Online 18 July 2013


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Acta Cryst. (2013). D69, 1493-1503  [ doi:10.1107/S0907444913010020 ]

The sequence and structure of snake gourd (Trichosanthes anguina) seed lectin, a three-chain nontoxic homologue of type II RIPs

A. Sharma, G. Pohlentz, K. B. Bobbili, A. A. Jeyaprakash, T. Chandran, M. Mormann, M. J. Swamy and M. Vijayan

Synopsis: A novel three-chain nontoxic homologue of type II ribosome-inactivating proteins has been sequenced by mass spectrometry and its crystal structure has been determined. The evolutionary history of type II RIPs and the molecular basis for the loss of toxicity in some of them have been explored.

PDB reference: 4hr6

Online 18 July 2013


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Acta Cryst. (2013). D69, 1504-1513  [ doi:10.1107/S090744491301010X ]

Hfq binds ribonucleotides in three different RNA-binding sites

V. Murina, N. Lekontseva and A. Nikulin

Synopsis: The ribonucleotide-binding properties of Hfq were probed using crystallography.

PDB references: 3qui, 4j5y, 4j6w, 4j6x and 4j6y

Online 18 July 2013


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Acta Cryst. (2013). D69, 1514-1521  [ doi:10.1107/S0907444913010196 ]

Structural asymmetry of procaspase-7 bound to a specific inhibitor

H. J. Kang, Y. Lee, K.-H. Bae, S. J. Kim and S. J. Chung

Synopsis: The first structural analysis of a procaspase-7 variant bound to a specific inhibitor, Ac-DEVD-CHO, revealed a structural asymmetry that the two L2 loops in homodimeric procaspase-7 served as inherent L2 and L2' loops forming a complete active site in one monomer, which may be responsible to a basal activity level, but not in the other. This provides insight into the basal activity of procaspase-7 and the folding mechanism during caspase-7 activation.

PDB references: 4hq0 and 4hqr

Online 18 July 2013


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Acta Cryst. (2013). D69, 1522-1529  [ doi:10.1107/S0907444913010457 ]

Structural basis for the dephosphorylating activity of PTPRQ towards phosphatidylinositide substrates

K. R. Yu, Y. J. Kim, S.-K. Jung, B. Ku, H. Park, S. Y. Cho, H. Jung, S. J. Chung, K. H. Bae, S. C. Lee, B. Y. Kim, R. L. Erikson, S. E. Ryu and S. J. Kim

Synopsis: The crystal structure of human PTPRQ and the following kinetic data provide the explanation for its dephosphosphorylating activity towards phosphatidyl inositides.

PDB reference: 4ikc

Online 19 July 2013


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Acta Cryst. (2013). D69, 1530-1539  [ doi:10.1107/S0907444913010664 ]

Invariom refinement of a new monoclinic solvate of thiostrepton at 0.64 Å resolution

K. Pröpper, J. J. Holstein, C. B. Hübschle, C. S. Bond and B. Dittrich

Synopsis: Structure refinement with nonspherical scattering factors from the invariom database is performed on thiostrepton, a heavily modified hexadecapeptide with antibiotic activity.

PDB reference: 4hp2

Online 19 July 2013


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Acta Cryst. (2013). D69, 1540-1552  [ doi:10.1107/S0907444913010640 ]

Combining crystallography and EPR: crystal and solution structures of the multidomain cochaperone DnaJ

T. R. M. Barends, R. W. W. Brosi, A. Steinmetz, A. Scherer, E. Hartmann, J. Eschenbach, T. Lorenz, R. Seidel, R. L. Shoeman, S. Zimmermann, R. Bittl, I. Schlichting and J. Reinstein

Synopsis: The crystal structure of the N-terminal part of T. thermophilus DnaJ unexpectedly showed an ordered GF domain and guided the design of a construct enabling the first structure determination of a complete DnaJ cochaperone molecule. By combining the crystal structures with spin-labelling EPR and cross-linking in solution, a dynamic view of this flexible molecule was developed.

PDB references: 4j7z and 4j80

Online 19 July 2013


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Acta Cryst. (2013). D69, 1553-1566  [ doi:10.1107/S0907444913010792 ]

Structures of purine nucleosidase from Trypanosoma brucei bound to isozyme-specific trypanocidals and a novel metalorganic inhibitor

F. Giannese, M. Berg, P. Van der Veken, V. Castagna, P. Tornaghi, K. Augustyns and M. Degano

Synopsis: The enzymatic and structural characterization of the drug target purine-specific nucleosidase from the pathogen T. brucei provides a rationale for the tight-binding inhibition by iminoribitol-based compounds. The binding of a metalorganic inhibitor to nucleoside hydrolases is reported for the first time, together with the structural basis of metal-mediated noncompetitive inhibition.

PDB references: 4i70, 4i71, 4i72, 4i73, 4i74 and 4i75

Online 20 July 2013


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Acta Cryst. (2013). D69, 1567-1579  [ doi:10.1107/S0907444913011013 ]

Structural and mechanistic studies of the orf12 gene product from the clavulanic acid biosynthesis pathway

K. Valegård, A. Iqbal, N. J. Kershaw, D. Ivison, C. Généreux, A. Dubus, C. Blikstad, M. Demetriades, R. J. Hopkinson, A. J. Lloyd, D. I. Roper, C. J. Schofield, I. Andersson and M. A. McDonough

Synopsis: Structural studies of the protein encoded by orf12 of the clavulanic acid biosynthesis gene cluster from S. clavuligerus reveal a two-domain structure.

PDB references: 2xep, 2xf3, 2xft, 2xfs, 2xgn and 2xh9

Online 20 July 2013


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Acta Cryst. (2013). D69, 1580-1586  [ doi:10.1107/S0907444913010949 ]

Catalysis product captured in lumazine synthase from the fungal pathogen Candida glabrata

M. Shankar, S. M. Wilbanks, Y. Nakatani, B. C. Monk and J. D. A. Tyndall

Synopsis: The crystal structure of lumazine synthase from C. glabrata complexed with its catalytic product 6,7-dimethyl-8-(D-ribityl)lumazine is reported.

PDB reference: 4kq6

Online 20 July 2013


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Acta Cryst. (2013). D69, 1587-1597  [ doi:10.1107/S0907444913011220 ]

Structural basis of intersubunit recognition in elongin BC-cullin 5-SOCS box ubiquitin-protein ligase complexes

Y. K. Kim, M.-J. Kwak, B. Ku, H.-Y. Suh, K. Joo, J. Lee, J. U. Jung and B.-H. Oh

Synopsis: The crystal structure of the SOCS2-elongin BC-Cul5(1-386) complex explains the specificity of Cul2 and Cul5 for elongin BC and their preferential association with Cul2 or Cul5 box-containing proteins.

PDB reference: 4jgh

Online 20 July 2013


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Acta Cryst. (2013). D69, 1598-1608  [ doi:10.1107/S0907444913011360 ]

The structure of full-length human CTNNBL1 reveals a distinct member of the armadillo-repeat protein family

X. Huang, G. Wang, Y. Wu and Z. Du

Synopsis: The crystal structure of full-length human CTNNBL1 reveals many unique structural features that establish it as a distinct member of the armadillo-repeat protein family.

PDB references: 4hm9 and 4hnm

Online 20 July 2013


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Acta Cryst. (2013). D69, 1609-1616  [ doi:10.1107/S0907444913011323 ]

Structure of the cobalamin-binding protein of a putative O-demethylase from Desulfitobacterium hafniense DCB-2

H. Sjuts, M. S. Dunstan, K. Fisher and D. Leys

Synopsis: The first crystal structure of the vitamin B12-binding protein from a three-component O-demethylase enzyme system is reported. During O-demethylation methyl groups are transferred from phenyl methyl ethers to tetrahydrofolate via methyl-B12 intermediates.

PDB reference: 4jgi

Online 20 July 2013


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Acta Cryst. (2013). D69, 1617-1632  [ doi:10.1107/S0907444913012274 ]

Clustering procedures for the optimal selection of data sets from multiple crystals in macromolecular crystallography

J. Foadi, P. Aller, Y. Alguel, A. Cameron, D. Axford, R. L. Owen, W. Armour, D. G. Waterman, S. Iwata and G. Evans

Synopsis: A systematic approach to the scaling and merging of data from multiple crystals in macromolecular crystallography is introduced and explained.

Online 20 July 2013


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