Biological Crystallography

 

Acta Cryst. (2008). D64, 909-918  [ doi:10.1107/S0907444908019513 ]

Structures of the wild-type and activated catalytic domains of Brachydanio rerio Polo-like kinase 1 (Plk1): changes in the active-site conformation and interactions with ligands

R. A. Elling, R. V. Fucini and M. J. Romanowski

Synopsis: Crystal structures of ligand-free wild-type and activated zebrafish Plk1 kinase domains reveal the organization of the secondary structural elements around the active site. The cocrystal structure of wild-type Plk1 with ADP documents the hydrolysis of ATP and reveals the autophosphorylation site, while the cocrystal structure of the activated kinase domain with wortmannin, a covalent inhibitor of the PI3 kinase, shows the binding mode of the small molecule to the enzyme and could facilitate the design of more potent Plk1 inhibitors.

PDB references: 3d5u, 3d5v, 3d5w and 3d5x

Online 13 August 2008

 

Acta Cryst. (2008). D64, 919-926  [ doi:10.1107/S0907444908021306 ]

Crystal packing of the c₆-type cytochrome OmcF from Geobacter sulfurreducens is mediated by an N-terminal Strep-tag II

P. Lukat, M. Hoffmann and O. Einsle

Synopsis: The structure of the Strep-tag II-tagged monohaem c-type cytochrome OmcF from G. sulfurreducens was determined by Fe SAD on a rotating-anode X-ray source. Packing analysis reveals that the N-terminal Strep-tag II is the exclusive mediator of crystal contacts along the c axis, providing crystal contacts to three monomers simultaneously.

PDB reference: 3dp5

Online 13 August 2008

 

Acta Cryst. (2008). D64, 927-932  [ doi:10.1107/S0907444908021641 ]

Structure of the thioredoxin-like domain of yeast glutaredoxin 3

L. M. Gibson, N. N. Dingra, C. E. Outten and L. Lebioda

Synopsis: Yeast Grx3 is involved in iron-responsive transcription regulation. The single active site thiol of the thioredoxin-like domain is in a flexible surface loop as suggested by its partial disorder.

PDB reference: 3d6i

Online 13 August 2008

 

Acta Cryst. (2008). D64, 933-940  [ doi:10.1107/S0907444908021653 ]

X-ray structure of a soluble Rieske-type ferredoxin from Mus musculus

E. J. Levin, N. L. Elsen, K. D. Seder, J. G. McCoy, B. G. Fox and G. N. Phillips Jr

Synopsis: The X-ray crystal structure of a soluble Rieske ferredoxin from M. musculus was solved at 2.07 Å resolution, revealing an iron-sulfur cluster-binding domain with similar architecture to the Rieske-type domains of bacterial aromatic dioxygenases. The ferredoxin was also shown to be capable of accepting electrons from both eukaryotic and prokaryotic oxidoreductases.

PDB reference: 3d89

Online 13 August 2008

 

Acta Cryst. (2008). D64, 941-949  [ doi:10.1107/S0907444908021665 ]

Structures of monomeric, dimeric and trimeric PCNA: PCNA-ring assembly and opening

V. Hlinkova, G. Xing, J. Bauer, Y. J. Shin, I. Dionne, K. R. Rajashankar, S. D. Bell and H. Ling

Synopsis: Crystal structures of three PCNA homologues from Sulfolobus solfataricus have been determined in different oligomeric states. The structural features in different assemblies present a molecular model for clamp-ring forming and opening.

PDB references: 2ijx, 2io4 and 2nti

Online 13 August 2008

 

Acta Cryst. (2008). D64, 950-956  [ doi:10.1107/S0907444908021513 ]

Structure of the C-terminal domain of the arginine repressor protein from Mycobacterium tuberculosis

L. T. Cherney, M. M. Cherney, C. R. Garen, G. J. Lu and M. N. G. James

Synopsis: The structure of the core domain of the arginine repressor protein from M. tuberculosis has been determined with (1.85 Å resolution) and without (2.15 Å resolution) the arginine corepressor bound. Three additional arginine molecules have been found to bind to the core domain hexamer at high (0.2 M) arginine concentration.

PDB references: 3bue, 2zfz and 3cag

Online 13 August 2008

 

Acta Cryst. (2008). D64, 957-963  [ doi:10.1107/S0907444908021616 ]

High-molecular-weight polymers for protein crystallization: poly--glutamic acid-based precipitants

T.-C. Hu, J. Korczynska, D. K. Smith and A. M. Brzozowski

Synopsis: High-molecular-weight poly--glutamic acid-based polymers have been synthesized, tested and adopted for protein crystallization.

Online 13 August 2008

 

Acta Cryst. (2008). D64, 964-970  [ doi:10.1107/S0907444908021550 ]

The 1.5 Å structure of endo-1,3--glucanase from Streptomyces sioyaensis: evolution of the active-site structure for 1,3--glucan-binding specificity and hydrolysis

T.-Y. Hong, Y.-Y. Hsiao, M. Meng and T. T. Li

Synopsis: The 1.5 Å resolution crystal structure of the catalytic domain of S. sioyaensis endo-1,3--glucanase, a member of glycosyl hydrolase family 16, revealed an active-site cleft that was closed at one end for specific 1,3--glucan substrate binding.

PDB reference: 3dgt

Online 13 August 2008

 

Acta Cryst. (2008). D64, 971-976  [ doi:10.1107/S0907444908022208 ]

Evaluation of the (haem)Fe-N²(HisF8) bond distances from haemoglobin structures deposited in the Protein Data Bank

F. A. V. Seixas, T. D. Santini, V. P. Moura and E. Á. Gandra

Synopsis: The bond distances that bind the haem group to the globin molecule in the crystallographic structures of haemoglobins deposited in the Protein Data Bank were evaluated by comparison with the same bond distance determined using EXAFS and X-ray absorption techniques.

Online 13 August 2008

 

Acta Cryst. (2008). D64, 977-984  [ doi:10.1107/S0907444908022348 ]

Structural analysis of a holoenzyme complex of mouse dihydrofolate reductase with NADPH and a ternary complex with the potent and selective inhibitor 2,4-diamino-6-(2'-hydroxydibenz[b,f]azepin-5-yl)methylpteridine

V. Cody, J. Pace and A. Rosowsky

Synopsis: The structures of mouse DHFR holo enzyme and a ternary complex with NADPH and a potent inhibitor are described.

PDB references: 3d80 and 3d84

Online 13 August 2008

 

Acta Cryst. (2008). D64, 985-992  [ doi:10.1107/S0907444908022646 ]

Structures of viscotoxins A1 and B2 from European mistletoe solved using native data alone

A. Pal, J. É. Debreczeni, M. Sevvana, T. Gruene, B. Kahle, A. Zeeck and G. M. Sheldrick

Synopsis: The new crystal structures of viscotoxins A1 and B2 have been solved by sulfur-SAD phasing and ab initio direct methods, respectively.

PDB references: 3c8p and 2v9b

Online 13 August 2008

 

Acta Cryst. (2008). D64, 993-999  [ doi:10.1107/S0907444908019197 ]

Pseudo-merohedral twinning in crystals of the dihaem c-type cytochrome DHC2 from Geobacter sulfurreducens

D. Heitmann and O. Einsle

Synopsis: Pseudo-merohedral twinning was detected in crystals of the dihaem c-type cytochrome DHC2 from G. sulfurreducens.

Online 13 August 2008

 

Acta Cryst. (2008). D64, 1000-1002  [ doi:10.1107/S0907444908022002 ]

Not so clear on oxygen. Comment on Structural basis for cofactor-independent dioxygenation in vancomycin biosynthesis by Widboom et al. (2007), Nature (London), 447, 342-345

B. Stec and K. A. Stieglitz

Synopsis: Comment on Structural basis for cofactor-independent dioxygenation in vancomycin biosynthesis by Widboom et al. (2007), Nature (London), 447, 342-345.

Online 13 August 2008