Doing the right things

Recent examples of the misrepresentation of biological helical structures in the popular media are identified and discussed.

Structure of the TRAF4 TRAF domain with a coiled-coil domain and its implications for the TRAF4 signalling pathway

TRAF4 is a unique family of TRAF, which participates in many ontogenic processes. The crystal structure of TRAF domain of TRAF4 was solved at 2.3 Å resolution.

X-ray crystallographic studies of family 11 xylanase Michaelis and product complexes: implications for the catalytic mechanism

X-ray structures of a family 11 xylanase with bound xylohexaose substrate or products revealed six sugar-binding subsites in the active site of the enzyme. Replacing amino acids near the catalytic glutamic acid 177 decreased the xylanase activity but increased the relative activity at alkaline pH.

Crystallographic snapshots of initial steps in the collapse of the calmodulin central helix

Novel bent conformations of the calmodulin central helix are presented. The structures may relate to the initial stages of structural collapse in calmodulin upon target-peptide binding.

The rotational order–disorder structure of the reversibly photoswitchable red fluorescent protein rsTagRFP

An analysis of the rotational order–disorder structure of the reversibly photoswitchable red fluorescent protein rsTagRFP is presented.

Structure and mechanism of a type III secretion protease, NleC

The crystal structure of NleC is reported at 1.55 Å resolution. In conjunction with biochemical analyses, the structure reveals that NleC is a member of the zincin zinc protease family and that the configuration of the NleC active site resembles that of the metzincin clan of metallopeptidases.

Lysine carboxylation: unveiling a spontaneous post-translational modification

A computational method for the prediction of lysine carboxylation (KCX) in protein structures is described. The method accurately identifies misreported KCXs and predicts previously unknown KCX sites.

The regulatory mechanism of the caspase 6 pro-domain revealed by crystal structure and biochemical assays

The regulatory mechanism of the caspase 6 pro-domain is revealed.

Structural characterization of new deoxycytidine kinase inhibitors rationalizes the affinity-determining moieties of the molecules

This article describes the structural and biochemical characterization of a new class of high-affinity and selective human deoxycytidine kinase inhibitors.

Structural basis for the broad specificity of a new family of amino-acid racemases

This work reports the crystal structure of BsrV, the broad spectrum racemase of Vibrio cholerae (1.15 Å resolution); unveils signature amino acids associated to its multispecificity and uses this signature sequence to identify a large family of BsrV-like multi-specific racemases in bacteria. Structural analyses of an additional Bsr confirmed the distinguishing features are conserved among Bsr-family members.

Atomic resolution crystal structure of glutaredoxin 1 from Plasmodium falciparum and comparison with other glutaredoxins

The structure of glutaredoxin 1 from P. falciparum has been determined at atomic resolution and its unique structural features have been dissected.

Breaking the indexing ambiguity in serial crystallography

In serial crystallography, it is demonstrated that the indexing mode of partial data sets can be established using correlation coefficients against other data sets and a clustering procedure. For 24 chiral space groups clustering can be performed in two dimensions, but in space groups P3, P3₁ and P3₂ clustering in three or four dimensions is required.

Towards accurate structural characterization of metal centres in protein crystals: the structures of Ni and Cu T₆ bovine insulin derivatives

The level of structural detail around the metal sites in Ni²⁺ and Cu²⁺ T₆ insulin derivatives was significantly improved by using a combination of single-crystal X-ray crystallography and X-ray absorption spectroscopy. Photoreduction and subsequent radiation damage of the Cu²⁺ sites in Cu insulin was followed by XANES spectroscopy.

The crystal structure and biochemical characterization of Kif15: a bifunctional molecular motor involved in bipolar spindle formation and neuronal development

The structural and biochemical study of Kif15 provides insight into this potential drug target and allows comparison with Eg5, a kinesin that partially shares the functions of Kif15.

Ligand placement based on prior structures: the guided ligand-replacement method

A new module, Guided Ligand Replacement (GLR), has been developed in Phenix to increase the ease and success rate of ligand placement when prior protein-ligand complexes are available.

Automating crystallographic structure solution and refinement of protein–ligand complexes

A software system for automated protein–ligand crystallography has been implemented in the Phenix suite. This significantly reduces the manual effort required in high-throughput crystallographic studies.

Structure of the FP domain of Fbxo7 reveals a novel mode of protein–protein interaction

The FP domain of the human F-box protein Fbxo7 adopts an α/β-fold structure that is similar to the FP domain of the human proteasome inhibitor PI31. However, the two FP domains show dramatic differences in the way that they mediate protein–protein interactions.

Atomic resolution view into the structure–function relationships of the human myelin peripheral membrane protein P2

The structure of the human myelin peripheral membrane protein P2 has been refined at 0.93 Å resolution. In combination with functional experiments in vitro, in vivo and in silico, the fine details of the structure–function relationships in P2 are emerging.

Structural enzymology of Helicobacter pylori methylthioadenosine nucleosidase in the futalosine pathway

Crystal structures of the H. pylori methylthioadenosine nucleosidase (MTAN) HpyMqnB have been solved in native and complexed forms, shedding light on substrate binding and the reaction mechanism.

Three-dimensional structure of a Streptomyces sviceus GNAT acetyltransferase with similarity to the C-terminal domain of the human GH84 O-GlcNAcase

The crystal structure of a bacterial acetyltransferase with 27% sequence identity to the C-terminal domain of human O-GlcNAcase has been solved at 1.5 Å resolution. This S. sviceus protein is compared with known GCN5-related acetyltransferases, adding to the diversity observed in this superfamily.

A novel mode of ferric ion coordination by the periplasmic ferric ion-binding subunit FbpA of an ABC-type iron transporter from Thermus thermophilus HB8

Crystal structures of FbpA from T. thermophilus (TtFbpA) in its apo and ferric ion-bound forms have been solved. TtFbpA shows the novel formation of a six-coordinated complex of ferric ion coordinated by three tyrosine residues, two monodentate bicarbonates and a water molecule.

A challenging interpretation of a hexagonally layered protein structure

The authors describe the structure determination of a hexagonally layered protein structure that suffered from a complicated combination of translational non-crystallographic symmetry and hemihedral twinning. This case serves as a reminder that broken crystallographic symmetry resulting from doubling of a unit-cell axis often requires a new choice of origin.