September 2008 issue
Cover illustration: Crystal packing of the c6-type cytochrome OmcF from Geobacter sulfurreducens (p. 919). Packing interactions are mediated via an extended Strep-tag II and linker sequence that forms the only connection between adjacent layers of protein within the crystal (3dp5).
Acta Cryst. (2008). D64, 909-918
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
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.
Acta Cryst. (2008). D64, 919-926
Crystal packing of the c6-type cytochrome OmcF from Geobacter sulfurreducens is mediated by an N-terminal Strep-tag II
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: OmcF, 3dp5, r3dp5sf
Acta Cryst. (2008). D64, 927-932
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.
Acta Cryst. (2008). D64, 933-940
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: Rieske-type ferredoxin, 3d89, r3d89sf
Acta Cryst. (2008). D64, 941-949
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: PCNA3, 2ijx, r2ijxsf; PCNA1–PCNA2, 2io4, r2io4sf; PCNA1–PCNA2–PCNA3, 2nti, r2ntisf
Acta Cryst. (2008). D64, 950-956
Structure of the C-terminal domain of the arginine repressor protein from Mycobacterium tuberculosis
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.
Acta Cryst. (2008). D64, 957-963
High-molecular-weight poly-γ-glutamic acid-based polymers have been synthesized, tested and adopted for protein crystallization.
Acta Cryst. (2008). D64, 964-970
The 1.5 Å structure of endo-1,3-β-glucanase from Streptomyces sioyaensis: evolution of the active-site structure for 1,3-β-glucan-binding specificity and hydrolysis
The 1.5 Å resolution crystal structure of the catalytic domain of S. sioyaensis endo-1,3-β-glucanase, a member of glycosyl hydrolase family 16, revealed an active-site cleft that was closed at one end for specific 1,3-β-glucan substrate binding.
PDB reference: endo-1,3-β-glucanase catalytic domain, 3dgt, r3dgtsf
Acta Cryst. (2008). D64, 971-976
Evaluation of the (haem)Fe—N∊2(HisF8) bond distances from haemoglobin structures deposited in the Protein Data Bank
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.
Acta Cryst. (2008). D64, 977-984
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
The structures of mouse DHFR holo enzyme and a ternary complex with NADPH and a potent inhibitor are described.
PDB references: dihydrofolate reductase complexes, 3d80, r3d80sf; 3d84, r3d84sf
Acta Cryst. (2008). D64, 985-992
The new crystal structures of viscotoxins A1 and B2 have been solved by sulfur-SAD phasing and ab initio direct methods, respectively.
PDB references: viscotoxin A1, 3c8p, r3c8psf; viscotoxin B2, 2v9b, r2v9bsf
Acta Cryst. (2008). D64, 993-999
Pseudo-merohedral twinning in crystals of the dihaem c-type cytochrome DHC2 from Geobacter sulfurreducens
Pseudo-merohedral twinning was detected in crystals of the dihaem c-type cytochrome DHC2 from G. sulfurreducens.
letters to the editor
Acta Cryst. (2008). D64, 1000-1002
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
Comment on Structural basis for cofactor-independent dioxygenation in vancomycin biosynthesis by Widboom et al. (2007), Nature (London), 447, 342–345.