Acta Crystallographica Section D

Biological Crystallography

Volume 68, Part 11 (November 2012)



[Issue Author Index][Volume Author Index]
[Cover illustration] Cover illustration: Ribbon diagram of the hexameric assembly of the substrate-bound form of geranyl pyrophosphate methyltransferase (p. 1558).

editorial


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Acta Cryst. (2012). D68, 1439-1440  [ doi:10.1107/S0907444912043107 ]

Nobel Prize for Chemistry 2012: GPCRs seen through a crystal ball

E. N. Baker and Z. Dauter

Synopsis: Editorial.

Online 19 October 2012


research papers


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Acta Cryst. (2012). D68, 1441-1449  [ doi:10.1107/S0907444912029459 ]

Structures of haemoglobin from woolly mammoth in liganded and unliganded states

H. Noguchi, K. L. Campbell, C. Ho, S. Unzai, S.-Y. Park and J. R. H. Tame

Synopsis: The haemoglobin (Hb) of the extinct woolly mammoth has been recreated using recombinant genes expressed in Escherichia coli. The crystal structures of mammoth Hb have been determined in the deoxy, carbonmonoxy and aquo-met forms.

PDB references: 3vre, 3vrf and 3vrg

Online 18 October 2012


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Acta Cryst. (2012). D68, 1450-1459  [ doi:10.1107/S090744491203449X ]

A new crystal form of MshB from Mycobacterium tuberculosis with glycerol and acetate in the active site suggests the catalytic mechanism

S. G. Broadley, J. C. Gumbart, B. W. Weber, M. J. Marakalala, D. J. Steenkamp and B. T. Sewell

Synopsis: A new mechanism for hydrolysis of the amide bond in GlcNAc-Ins by MshB, which is supported by structural evidence, is proposed. In particular, the involvement of Tyr142, which was predicted on the basis of kinetic and mutagenic studies, is confirmed.

PDB reference: 4ewl

Online 13 October 2012


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Acta Cryst. (2012). D68, 1460-1467  [ doi:10.1107/S090744491203466X ]

Structural insights into the broadened substrate profile of the extended-spectrum [beta]-lactamase OXY-1-1 from Klebsiella oxytoca

Y.-H. Liang, R. Gao and X.-D. Su

Synopsis: The crystal structure of the extended-spectrum [beta]-lactamase OXY-1-1 has been determined at 1.93 Å resolution. Structural features around the catalytic cavity help to broaden the substrate profile of the enzyme.

PDB reference: 3byd

Online 18 October 2012


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Acta Cryst. (2012). D68, 1468-1478  [ doi:10.1107/S0907444912034646 ]

Endo-[beta]-D-1,4-mannanase from Chrysonilia sitophila displays a novel loop arrangement for substrate selectivity

A. M. D. Gonçalves, C. S. Silva, T. I. Madeira, R. Coelho, D. de Sanctis, M. V. San Romão and I. Bento

Synopsis: The crystal structure of endo-[beta]-D-1,4-mannanase from Chrysonilia sitophila has been solved at 1.40 Å. The enzyme has mixed activity as both an endo-mannanase and endo-glucanase and the crystal structure revealed a unique arrangement of three surface loops surrounding the active site, altering the topography of the binding cleft.

PDB reference: 4awe

Online 18 October 2012


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Acta Cryst. (2012). D68, 1479-1487  [ doi:10.1107/S0907444912037171 ]

A monomeric TIM-barrel structure from Pyrococcus furiosus is optimized for extreme temperatures

H. Repo, J. S. Oeemig, J. Djupsjöbacka, H. Iwaï and P. Heikinheimo

Synopsis: The TrpF structure from the hyperthermophilic archaeon P. furiosus is described at 1.75 Å resolution. Structural comparison with other thermophilic TrpF proteins suggests a mechanism for thermal stability.

PDB reference: 4aaj

Online 13 October 2012


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Acta Cryst. (2012). D68, 1488-1500  [ doi:10.1107/S0907444912037110 ]

Structures of the ribosome-inactivating protein from barley seeds reveal a unique activation mechanism

B.-G. Lee, M. K. Kim, B. Kim, S. W. Suh and H. K. Song

Synopsis: Crystal structures of ribosome-inactivating protein (RIP) from barley seeds have been determined in free, AMP-bound and adenine-bound states. These data revealed a unique activation mechanism for a type I RIP from a monocotyledonous crop.

PDB references: 4fb9, 4fba, 4fbb, 4fbc and 4fbh

Online 13 October 2012


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Acta Cryst. (2012). D68, 1501-1512  [ doi:10.1107/S0907444912037328 ]

Structural studies on the folded domain of the human prion protein bound to the Fab fragment of the antibody POM1

P. K. Baral, B. Wieland, M. Swayampakula, M. Polymenidou, M. H. Rahman, N. N. V. Kav, A. Aguzzi and M. N. G. James

Synopsis: This paper describes the crystal structure of the globular part of the human prion protein bound to the CDR of the Fab fragment of the POM1. The epitope of the huPrPc for POM1 constitutes the N-terminus of helix [alpha]1, a portion of the polypeptide chain linking sheet [beta]1 and helix [alpha]1 and several residues on helix [alpha]3; the measured Kd is 4.5 × 10-7 M.

PDB reference: 4dgi

Online 18 October 2012


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Acta Cryst. (2012). D68, 1513-1521  [ doi:10.1107/S0907444912037638 ]

Modeling the SHG activities of diverse protein crystals

L. M. Haupert, E. L. DeWalt and G. J. Simpson

Synopsis: The origins of the diversity in the SHG signal from protein crystals are investigated and potential protein-crystal coverage by SHG microscopy is assessed.

Online 18 October 2012


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Acta Cryst. (2012). D68, 1522-1534  [ doi:10.1107/S0907444912037961 ]

Error-estimation-guided rebuilding of de novo models increases the success rate of ab initio phasing

R. Shrestha, D. Simoncini and K. Y. J. Zhang

Synopsis: Focused rebuilding of coarse-grained models guided by the probabilistic estimation of residue errors has increased the success rate of ab initio phasing by de novo models using molecular replacement.

Online 18 October 2012


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Acta Cryst. (2012). D68, 1535-1540  [ doi:10.1107/S0907444912038103 ]

The structure of L-amino-acid ligase from Bacillus licheniformis

M. Suzuki, Y. Takahashi, A. Noguchi, T. Arai, M. Yagasaki, K. Kino and J. Saito

Synopsis: This report presents the crystal structure of L-amino-acid ligase from B. licheniformis. This structure provides an initial step towards the efficient industrial production of various useful dipeptide agents.

PDB reference: 3vot

Online 13 October 2012


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Acta Cryst. (2012). D68, 1541-1548  [ doi:10.1107/S090744491203836X ]

Severe diffraction anisotropy, rotational pseudosymmetry and twinning complicate the refinement of a pentameric coiled-coil structure of NSP4 of rotavirus

A. R. Chacko, P. H. Zwart, R. J. Read, E. J. Dodson, C. D. Rao and K. Suguna

Synopsis: An account of the detection of severe diffraction anisotropy, rotational pseudosymmetry and twinning during the refinement of the rotaviral nonstructural protein NSP4 and a description of corrections for these factors leading to successful refinement of the structure are presented.

Online 18 October 2012


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Acta Cryst. (2012). D68, 1549-1557  [ doi:10.1107/S090744491203853X ]

Structure of the corrinoid:coenzyme M methyltransferase MtaA from Methanosarcina mazei

A. Hoeppner, F. Thomas, A. Rueppel, R. Hensel, W. Blankenfeldt, P. Bayer and A. Faust

Synopsis: The structures of a substrate-free but Zn2+-bound state of MtaA and its complex with substrate (coenzyme M) and Zn2+ are reported. MtaA is one of the three subunits of the methanol-coenzyme M-methyltransferase complex of M. mazei responsible for the conversion of methanol to methylated coenzyme M.

PDB references: 4ay7 and 4ay8

Online 18 October 2012


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Acta Cryst. (2012). D68, 1558-1569  [ doi:10.1107/S0907444912038486 ]

Structure analysis of geranyl pyrophosphate methyltransferase and the proposed reaction mechanism of SAM-dependent C-methylation

O. Ariyawutthiphan, T. Ose, A. Minami, S. Sinde, M. Tsuda, Y.-G. Gao, M. Yao, H. Oikawa and I. Tanaka

Synopsis: The hexameric crystal structure of geranyl pyrophosphate methyltransferase in complex with bona fide substrate provides the first model of enzymatic C-methylation of an isoprenoid pyrophosphate.

PDB references: 4f84, 4f85 and 4f86

Online 18 October 2012


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Acta Cryst. (2012). D68, 1570-1577  [ doi:10.1107/S0907444912038826 ]

Structural characterization of a modification subunit of a putative type I restriction enzyme from Vibrio vulnificus YJ016

S.-Y. Park, H.-J. Lee, J.-M. Song, J. Sun, H.-J. Hwang, K. Nishi and J.-S. Kim

Synopsis: An HsdM structure of a putative type I restriction enzyme was revealed, which shows a close enzymatic relationship with N6 DNA TaqI methyltransferase.

PDB reference: 3ufb

Online 18 October 2012


short communications


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Acta Cryst. (2012). D68, 1578-1583  [ doi:10.1107/S0907444912037900 ]

Alteration of fluorescent protein spectroscopic properties upon cryoprotection

D. von Stetten, G. O. Batot, M. Noirclerc-Savoye and A. Royant

Synopsis: The cryoprotecting agent ethylene glycol is shown to affect the structural and spectroscopic properties of cyan fluorescent proteins, shedding new light on fluorescent protein dynamics.

PDB reference: 4as8

Online 18 October 2012


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Acta Cryst. (2012). D68, 1584-1587  [ doi:10.1107/S0907444912038152 ]

Nanoflow electrospinning serial femtosecond crystallography

R. G. Sierra, H. Laksmono, J. Kern, R. Tran, J. Hattne, R. Alonso-Mori, B. Lassalle-Kaiser, C. Glöckner, J. Hellmich, D. W. Schafer, N. Echols, R. J. Gildea, R. W. Grosse-Kunstleve, J. Sellberg, T. A. McQueen, A. R. Fry, M. M. Messerschmidt, A. Miahnahri, M. M. Seibert, C. Y. Hampton, D. Starodub, N. D. Loh, D. Sokaras, T.-C. Weng, P. H. Zwart, P. Glatzel, D. Milathianaki, W. E. White, P. D. Adams, G. J. Williams, S. Boutet, A. Zouni, J. Messinger, N. K. Sauter, U. Bergmann, J. Yano, V. K. Yachandra and M. J. Bogan

Synopsis: A low flow rate liquid microjet method for delivery of hydrated protein crystals to X-ray lasers is presented. Linac Coherent Light Source data demonstrates serial femtosecond protein crystallography with micrograms, a reduction of sample consumption by orders of magnitude.

Online 18 October 2012


obituaries


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Acta Cryst. (2012). D68, 1588-1590  [ doi:10.1107/S0907444912042965 ]

Professor Dame Louise Napier Johnson (26 September 1940-25 September 2012)

T. L. Blundell

Synopsis: Obituary for Professor Dame Louise Napier Johnson.

Online 19 October 2012


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