Biological Crystallography

 

Acta Cryst. (2009). D65, 733-743  [ doi:10.1107/S0907444909011482 ]

Removing the invariant salt bridge of parvalbumin increases flexibility in the AB-loop structure

F. Hoh, A. Cavé, M.-P. Strub, J.-L. Banères and A. Padilla

Synopsis: The structure of R75A-mutant rat parvalbumin solved by molecular replacement points out the role of the Arg75-Glu81 salt bridge in attaching the nonbinding AB domain to the rest of the protein core.

PDB reference: 3f45

Online 10 July 2009

 

Acta Cryst. (2009). D65, 744-750  [ doi:10.1107/S0907444909012773 ]

Structure of endoglucanase Cel9A from the thermoacidophilic Alicyclobacillus acidocaldarius

J. H. Pereira, R. Sapra, J. V. Volponi, C. L. Kozina, B. Simmons and P. D. Adams

Synopsis: Here, the crystal structure of an endoglucanase, Cel9A, from Alicyclobacillus acidocaldarius (Aa_Cel9A) is reported which displays a modular architecture composed of an N-terminal Ig-like domain connected to the catalytic domain. This paper describes the overall structure and the detailed contacts between the two modules.

PDB reference: 3ez8

Online 10 July 2009

 

Acta Cryst. (2009). D65, 751-757  [ doi:10.1107/S0907444909013936 ]

Inhibitory properties and X-ray crystallographic study of the binding of AR-101, AR-102 and iclaprim in ternary complexes with NADPH and dihydrofolate reductase from Staphylococcus aureus

C. Oefner, S. Parisi, H. Schulz, S. Lociuro and G. E. Dale

Synopsis: The binding modes of DHFR inhibitors AR-101, AR-102 and iclaprim have been analysed and compared. The X-ray crystallographic data explain the binding modes of all molecules well and can be used to rationalize the equipotent affinity of AR-101, AR-102 and iclaprim, which is also reflected in their antibacterial properties.

PDB references: 3fy8, 3fy9, 3fyv and 3fyw

Online 10 July 2009

 

Acta Cryst. (2009). D65, 758-766  [ doi:10.1107/S0907444909014711 ]

A description of the structural determination procedures of a gap junction channel at 3.5 Å resolution

M. Suga, S. Maeda, S. Nakagawa, E. Yamashita and T. Tsukihara

Synopsis: The structural determination procedures of a gap junction channel at 3.5 Å resolution are described, including the preparation of crystals, intensity data collection, data processing, phasing and structural refinement.

PDB reference: 2zw3

Online 10 July 2009

 

Acta Cryst. (2009). D65, 767-776  [ doi:10.1107/S0907444909015601 ]

Structure of the putative thioesterase protein TTHA1846 from Thermus thermophilus HB8 complexed with coenzyme A and a zinc ion

T. Hosaka, K. Murayama, M. Kato-Murayama, A. Urushibata, R. Akasaka, T. Terada, M. Shirouzu, S. Kuramitsu and S. Yokoyama

Synopsis: The 1.9 Å resolution crystal structure of TTHA1846 from T. thermophilus HB8 complexed with coenzyme A and zinc ion is reported. The putative function of TTHA1846 and the inhibitory role played by the zinc ion in its activity are discussed.

PDB reference: 2cye

Online 10 July 2009

 

Acta Cryst. (2009). D65, 777-785  [ doi:10.1107/S090744490901600X ]

The three-dimensional structure of MAP kinase p38: different features of the ATP-binding site in p38 compared with p38

S. B. Patel, P. M. Cameron, S. J. O'Keefe, B. Frantz-Wattley, J. Thompson, E. A. O'Neill, T. Tennis, L. Liu, J. W. Becker and G. Scapin

Synopsis: The structure of the C119S,C162S double mutant of human MAP-kinase p38 has been solved and refined to 2.05 Å resolution. A comparison of the structures of p38 and p38 shows that they are highly similar overall but that there are small conformational differences that could be exploited in order to achieve drug selectivity.

PDB references: 3gc7, 3gc8 and 3gc9

Online 10 July 2009

 

Acta Cryst. (2009). D65, 786-795  [ doi:10.1107/S0907444909015935 ]

Adaptability and selectivity of human peroxisome proliferator-activated receptor (PPAR) pan agonists revealed from crystal structures

T. Oyama, K. Toyota, T. Waku, Y. Hirakawa, N. Nagasawa, J. Kasuga, Y. Hashimoto, H. Miyachi and K. Morikawa

Synopsis: The structures of the ligand-binding domains (LBDs) of human peroxisome proliferator-activated receptors (PPAR, PPAR and PPAR) in complexes with a pan agonist, an / dual agonist and a PPAR-specific agonist were determined. The results explain how each ligand is recognized by the PPAR LBDs at an atomic level.

PDB references: 2znn, 2zno, 2znp and 2znq

Online 10 July 2009

 

Acta Cryst. (2009). D65, 796-803  [ doi:10.1107/S0907444909017260 ]

Structure of the methyltransferase domain from the Modoc virus, a flavivirus with no known vector

A. M. Jansson, E. Jakobsson, P. Johansson, V. Lantez, B. Coutard, X. de Lamballerie, T. Unge and T. A. Jones

Synopsis: The structure of Modoc virus NS5 methyltransferase reveals structural conservation between methyltransferases in different flaviviral evolutionary groups. These findings support the choice of the Modoc virus as a model for flaviviral studies.

PDB references: 2wa1 and 2wa2

Online 10 July 2009

 

Acta Cryst. (2009). D65, 804-813  [ doi:10.1107/S0907444909017314 ]

Hyperstability and crystal structure of cytochrome c₅₅₅ from hyperthermophilic Aquifex aeolicus

M. Obuchi, K. Kawahara, D. Motooka, S. Nakamura, M. Yamanaka, T. Takeda, S. Uchiyama, Y. Kobayashi, T. Ohkubo and Y. Sambongi

Synopsis: The crystal structure of A. aeolicus cytochrome c₅₅₅ (AA c₅₅₅) has been determined at 1.15 Å resolution. A unique helix structure is revealed which might be responsible for the high stability of AA c₅₅₅.

PDB reference: 2zxy

Online 17 July 2009

 

Acta Cryst. (2009). D65, 814-822  [ doi:10.1107/S090744490901779X ]

Structure of aminopeptidase N from Escherichia coli complexed with the transition-state analogue aminophosphinic inhibitor PL250

M.-C. Fournié-Zaluski, H. Poras, B. P. Roques, Y. Nakajima, K. Ito and T. Yoshimoto

Synopsis: The structure of an APN-aminophosphinic inhibitor complex is reported.

PDB reference: 2zxg

Online 17 July 2009

 

Acta Cryst. (2009). D65, 823-831  [ doi:10.1107/S0907444909017958 ]

Characterization of gadolinium complexes for SAD phasing in macromolecular crystallography: application to CbpF

R. Molina, M. Stelter, R. Kahn and J. A. Hermoso

Synopsis: In SAD phasing, the efficacy of cocrystallization versus soaking in the binding of the different Gd complexes, their mode of interaction and a comparative study using synchrotron radiation and rotating-anode generator, were tested.

Online 17 July 2009

 

Acta Cryst. (2009). D65, 832-838  [ doi:10.1107/S0907444909018344 ]

Structure of ristocetin A in complex with a bacterial cell-wall mimetic

V. Nahoum, S. Spector and P. J. Loll

Synopsis: The crystal structure of the complex between ristocetin A and the cell-wall peptide mimetic N-acetyl-lysine-D-alanine-D-alanine has been solved. Structural details explaining the anticooperativity of the antibiotic have been identified.

Online 17 July 2009

 

Acta Cryst. (2009). D65, 839-846  [ doi:10.1107/S0907444909018253 ]

Structure of the C-terminal domain of nsp4 from feline coronavirus

I. Manolaridis, J. A. Wojdyla, S. Panjikar, E. J. Snijder, A. E. Gorbalenya, H. Berglind, P. Nordlund, B. Coutard and P. A. Tucker

Synopsis: The structure of the cytosolic C-terminal domain of nonstructural protein 4 from feline coronavirus has been determined and analyzed.

PDB reference: 3gzf

Online 17 July 2009

 

Acta Cryst. (2009). D65, 847-857  [ doi:10.1107/S0907444909018666 ]

Biochemical and structural characterization of residue 96 mutants of Plasmodium falciparum triosephosphate isomerase: active-site loop conformation, hydration and identification of a dimer-interface ligand-binding site

P. Gayathri, M. Banerjee, A. Vijayalakshmi, H. Balaram, P. Balaram and M. R. N. Murthy

Synopsis: In order to probe the role of residue 96, three P. falciparum triosephosphate isomerase mutants, F96S, F96H and F96W, were biochemically and structurally characterized. The studies show that Phe96 and Ser73 are important for maintaining the optimal hydration of the active site required for ligand binding. A new binding site for the ligand at the dimer interface has also been identified.

PDB references: 2vfd, 2vfe, 2vff, 2vfg, 2vfh and 2vfi

Online 17 July 2009

 

Acta Cryst. (2009). D65, 858-871  [ doi:10.1107/S0907444909018745 ]

Structure of the Calx- domain of the integrin 4 subunit: insights into function and cation-independent stability

N. Alonso-García, A. Inglés-Prieto, A. Sonnenberg and J. M. de Pereda

Synopsis: The crystal structure of the Calx- domain of integrin 64 at 1.48 Å resolution provides the first example of a non-calcium-binding Calx- domain.

PDB references: 3fq4, 3h6a and 3fso

Online 17 July 2009

 

Acta Cryst. (2009). D65, 872-874  [ doi:10.1107/S0907444909017855 ]

Cross-linking of protein crystals as an aid in the generation of binary protein-ligand crystal complexes, exemplified by the human PDE10a-papaverine structure

O. A. Andersen, D. L. Schönfeld, I. Toogood-Johnson, B. Felicetti, C. Albrecht, T. Fryatt, M. Whittaker, D. Hallett and J. Barker

Synopsis: The crystal structure of PDE10a in complex with papaverine was generated by ligand soaking of protein crystals that were cross-linked by glutaraldehyde.

PDB reference: 2wey

Online 17 July 2009

 

Acta Cryst. (2009). D65, 875-879  [ doi:10.1107/S0907444909018800 ]

New kinase regulation mechanism found in HipBA: a bacterial persistence switch

A. Evdokimov, I. Voznesensky, K. Fennell, M. Anderson, J. F. Smith and D. A. Fisher

Synopsis: The structure of the HipBA complex from E. coli has been solved using the SAD technique applied to a mercury derivative. A novel HipA activation mechanism is proposed and an intriguing tryptophan-binding pocket on the surface of the protein is described.

PDB reference: 2wiu

Online 17 July 2009