An RNA degradosome assembly in Caulobacter crescentus.

Nucleic Acids Res. 2010 Oct 15. [Epub ahead of print]

Authors: Hardwick SW, Chan VS, Broadhurst RW, Luisi BF.

In many bacterial species, the multi-enzyme RNA degradosome assembly makes key contributions to RNA metabolism. Powering the turnover of RNA and the processing of structural precursors, the RNA degradosome has differential activities on a spectrum of transcripts and contributes to gene regulation at a global level. Here, we report the isolation and characterization of an RNA degradosome assembly from the α-proteobacterium Caulobacter crescentus, which is a model organism for studying morphological development and cell-cycle progression.

Molecular recognition between Escherichia coli enolase and ribonuclease E.

Acta Crystallogr D Biol Crystallogr. 2010 Sep;66(Pt 9):1036-40. Epub 2010 Aug 13.

Authors: Nurmohamed S, McKay AR, Robinson CV, Luisi BF.

In Escherichia coli and many other bacterial species, the glycolytic enzyme enolase is a component of the multi-enzyme RNA degradosome, an assembly that is involved in RNA processing and degradation. Enolase is recruited into the degradosome through interactions with a small recognition motif located within the degradosome-scaffolding domain of RNase E. Here, the crystal structure of enolase bound to its cognate site from RNase E (residues 823-850) at 1.9 A resolution is presented. The structure suggests that enolase may help to organize an adjacent conserved RNA-binding motif in RNase E.

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An ancient anion-binding structural module in RNA and DNA helicases.

Proteins. 2010 Jun;78(8):1900-8.

Authors: Milner-White EJ, Pietras Z, Luisi BF.

RNA and DNA helicases manipulate or translocate along single strands of nucleic acids by grasping them using a conserved structural motif. We have examined the available crystal structures of helicases of the two principal superfamilies, SF1 and SF2, and observed that the most conserved interactions with the nucleic acid occur between the phosphosugar backbone of a trinucleotide and the three strand-helix loops within a (beta-strand/alpha-helix)(3) structural module.

The use of novel organic gels and hydrogels in protein crystallization

J Appl Crystallogr. 2010 Feb;43(1):58-63. Epub 6 Jan 2010.

Authors: Pietras Z, Lin HT, Surade S, Luisi BF, Slattery O, Pos KM and Moreno A.

The use of an organic solvent-based gel prepared from polyethylene oxide and a polyvinyl alcohol hydrogel for protein crystallization was investigated. The preparation, properties and application of the gels for protein crystallization are described, and the advantages and limitations of the approach are discussed. The gels are compared with agar, which is a popular aqueous gel used for protein crystallization. The growth behaviour and diffraction quality of crystals prepared in these gel media were evaluated for two model soluble proteins, thaumatin and lysozyme, and for two bacterial membrane proteins, TolC and AcrB.

The regulatory protein RraA modulates RNA-binding and helicase activities of the E. coli RNA degradosome.

RNA 2010 Mar;16(3):553-62. Epub 2010 Jan 27.

Authors: Górna MW, Pietras Z, Tsai YC, Callaghan AJ, Hernández H, Robinson CV, Luisi BF.

The Escherichia coli endoribonuclease RNase E is an essential enzyme having key roles in mRNA turnover and the processing of several structured RNA precursors, and it provides the scaffold to assemble the multienzyme RNA degradosome. The activity of RNase E is inhibited by the protein RraA, which can interact with the ribonuclease's degradosome-scaffolding domain. Here, we report that RraA can bind to the RNA helicase component of the degradosome (RhlB) and the two RNA-binding sites in the degradosome-scaffolding domain of RNase E. In the presence of ATP, the helicase can facilitate the exchange of RraA for RNA stably bound to the degradosome. Our data suggest that RraA can affect multiple components of the RNA degradosome in a dynamic, energy-dependent equilibrium. The multidentate interactions of RraA impede the RNA-binding and ribonuclease activities of the degradosome and may result in complex modulation and rerouting of degradosome activity.

Crystal structure of DNA-PKcs reveals a large open-ring cradle comprised of HEAT repeats.

Nature. 2009 Dec 20;

Authors: Sibanda BL, Chirgadze DY, Blundell TL

Broken chromosomes arising from DNA double-strand breaks result from endogenous events such as the production of reactive oxygen species during cellular metabolism, as well as from exogenous sources such as ionizing radiation. Left unrepaired or incorrectly repaired they can lead to genomic changes that may result in cell death or cancer. DNA-dependent protein kinase (DNA-PK), a holoenzyme that comprises the DNA-PK catalytic subunit (DNA-PKcs) and the heterodimer Ku70/Ku80, has a major role in non-homologous end joining-the main pathway in mammals used to repair double-strand breaks. DNA-PKcs is a serine/threonine protein kinase comprising a single polypeptide chain of 4,128 amino acids and belonging to the phosphatidylinositol-3-OH kinase (PI(3)K)-related protein family. DNA-PKcs is involved in the sensing and transmission of DNA damage signals to proteins such as p53, setting off events that lead to cell cycle arrest. It phosphorylates a wide range of substrates in vitro, including Ku70/Ku80, which is translocated along DNA. Here we present the crystal structure of human DNA-PKcs at 6.6 A resolution, in which the overall fold is clearly visible, to our knowledge, for the first time. The many alpha-helical HEAT repeats (helix-turn-helix motifs) facilitate bending and allow the polypeptide chain to fold into a hollow circular structure. The carboxy-terminal kinase domain is located on top of this structure, and a small HEAT repeat domain that probably binds DNA is inside. The structure provides a flexible cradle to promote DNA double-strand-break repair.

PMID: 20023628 [PubMed - as supplied by publisher]

A new version of the CREDO database has been released today comprising 41,691 protein-ligand complexes from the PDB.

New features include:

• All contacts up to 6A are now stored
• A new Variations tables has been added containing mutation information from dbSNP, EnsEMBL, OMIM and COSMIC
• The Ligands table now contains an ism field to store isomeric SMILES (very useful for heteropeptides)
• The LigandRing and ResidueRing tables now contain an is_hetero_aromatic field
• FragmentProperties now contains all descriptors from OEMolProp
• Several improvements to the CREDO API

For instructions on how to download and install the CREDO database, please go to the CREDO website.

A new version of the CREDO database has been released including 40,091 PDB structures. New features include:

• Ring interaction geometries have been implemented according to Chakrabarti, P. & Bhattacharyya, R. Geometry of nonbonded interactions involving planar groups in proteins. Progress in Biophysics and Molecular Biology 95, 83-137 (2007).
• New RECAP rules have been introduced to better fragment biomolecules, e.g. breaking of phosphate bonds and cleavage of sulphates.
• New flags for residues have been introduced to label mutated and modified amino acids (through sequence-to-structure mapping)
• SCOP version 1.75
• Structural interaction fingerprints are now available on a UniProt residue level and SIFt clusters part of the public version.
• Donor-Pi, Cation-Pi as well as Carbon-Pi atom-ring interactions are now available in dedicated tables (from which the Contacts table can be updated).
• SCOP- and UniProt-based SIFt clustering

For instructions on how to download and install the CREDO database, please go to the CREDO website.

Atomic interactions and profile of small molecules disrupting protein-protein interfaces: the TIMBAL database.

Chem Biol Drug Des. 2009 Nov;74(5):457-67

Authors: Higueruelo AP, Schreyer A, Bickerton GR, Pitt WR, Groom CR, Blundell TL