MolProbity is a structure-validation web service that provides broad-spectrum solidly based evaluation of model quality at both the global and local levels for both proteins and nucleic acids. It relies heavily on the power and sensitivity provided by optimized hydrogen placement and all-atom contact analysis, complemented by updated versions of covalent-geometry and torsion-angle criteria. Some of the local corrections can be performed automatically in MolProbity and all of the diagnostics are presented in chart and graphical forms that help guide manual rebuilding. X-ray crystallography provides a wealth of biologically important molecular data in the form of atomic three-dimensional structures of proteins, nucleic acids and increasingly large complexes in multiple forms and states. Advances in automation, in everything from crystallization to data collection to phasing to model building to refinement, have made solving a structure using crystallo­graphy easier than ever. However, despite these improvements, local errors that can affect biological interpretation are widespread at low resolution and even high-resolution structures nearly all contain at least a few local errors such as Ramachandran outliers, flipped branched protein side chains and incorrect sugar puckers. It is critical both for the crystallographer and for the end user that there are easy and reliable methods to diagnose and correct these sorts of errors in structures. MolProbity is the authors' contribution to helping solve this problem and this article reviews its general capabilities, reports on recent enhancements and usage, and presents evidence that the resulting improvements are now beneficially affecting the global database.

/pdf/molprobity-all-atom-structure-validation-for-macromolecular-55t3n3noll.pdf

MolProbity: all-atom structure validation for macromolecular crystallography

J. Appl. Cryst.の発刊に際して

Preface.- Contributors.- List of Abbreviations.- Section 1: Basic Principles: Introduction.-Sources of Heavy Metals and Metalloids in Soils.- Chemistry of Heavy Metals and Metalloids in Soils.- Methods for the Determination of Heavy Metals and Metalloids in Soils.- Effects of Heavy Metals and Metalloids on Soil Organisms.- Soil-Plant Relationships of Heavy Metals and Metalloids.- Heavy Metals and Metalloids as Micronutrients for Plants and Animals.-Critical Loads of Heavy Metals for Soils.- Section 2: Key Heavy Metals And Metalloids: Arsenic.- Cadmium.- Chromium and Nickel.- Cobalt and Manganese.- Copper.-Lead.- Mercury.- Selenium.- Zinc.- Section 3: Other Heavy Metals And Metalloids Of Potential Environmental Significance: Antimony.- Barium.- Gold.- Molybdenum.- Silver.- Thallium.- Tin.- Tungsten.- Uranium.- Vanadium.- Glossary of Specialized Terms.- Index.

Heavy metals in soils : trace metals and metalloids in soils and their bioavailability

Hypertension 66 (20.3%) 24 (24.2%) 30 (16.3%) NS Diabetes 20 (6.2%) 7 (7.1%) 10 (5.4%) NS Excess weight 78 (24%) 27 (27.3%) 44 (23.9%) NS Smokers 64 (19.7%) 17 (17.2%) 35 (19.0%) NS Age >50 years 137 (42.2%) 54 (54.5%) 67 (36.4%) <0.02 Kidney disease 7 (2.2%) 1 (1%) 5 (2.7%) NS Family history, DM 102 (31.4%) 28 (28.3%) 66 (35.9%) NS

Conflict of interest statement. None declared.

Aminoacyl-tRNAs are substrates for translation and are pivotal in determining how the genetic code is interpreted as amino acids. The function of aminoacyl-tRNA synthesis is to precisely match amino acids with tRNAs containing the corresponding anticodon. This is primarily achieved by the direct attachment of an amino acid to the corresponding tRNA by an aminoacyl-tRNA synthetase, although intrinsic proofreading and extrinsic editing are also essential in several cases. Recent studies of aminoacyl-tRNA synthesis, mainly prompted by the advent of whole genome sequencing and the availability of a vast body of structural data, have led to an expanded and more detailed picture of how aminoacyl-tRNAs are synthesized. This article reviews current knowledge of the biochemical, structural, and evolutionary facets of aminoacyl-tRNA synthesis.

Aminoacyl-tRNA synthesis.

In bacteria, the binding of a single protein, the initiation factor sigma, to a multi-subunit RNA polymerase core enzyme results in the formation of a holoenzyme, the active form of RNA polymerase essential for transcription initiation. Here we report the crystal structure of a bacterial RNA polymerase holoenzyme from Thermus thermophilus at 2.6 A resolution. In the structure, two amino-terminal domains of the sigma subunit form a V-shaped structure near the opening of the upstream DNA-binding channel of the active site cleft. The carboxy-terminal domain of sigma is near the outlet of the RNA-exit channel, about 57 A from the N-terminal domains. The extended linker domain forms a hairpin protruding into the active site cleft, then stretching through the RNA-exit channel to connect the N- and C-terminal domains. The holoenzyme structure provides insight into the structural organization of transcription intermediate complexes and into the mechanism of transcription initiation.

Crystal structure of a bacterial RNA polymerase holoenzyme at 2.6 A resolution

Structural Basis for Transcription Regulation by Alarmone ppGpp

https://www.uab.edu/medicine/biochem/images/Biochemistry/Vassylyev/PDF/Structural%20Basis%20for%20Double-Sieve%20Discrimination%20of%20L-Valine%20from%20L-Isoleucine%20and%20L-Threonine%20by%20the%20Complex%20of%20tRNAVal%20and%20Valyl-tRNA%20Synthetase.pdf

Structural basis for double-sieve discrimination of L-valine from L-isoleucine and L-threonine by the complex of tRNA(Val) and valyl-tRNA synthetase.

Aminoacyl-tRNA synthetases catalyze the formation of an aminoacyl-AMP from an amino acid and ATP, prior to the aminoacyl transfer to tRNA. A subset of aminoacyl-tRNA synthetases, including glutamyl-tRNA synthetase (GluRS), have a regulation mechanism to avoid aminoacyl-AMP formation in the absence of tRNA. In this study, we determined the crystal structure of the 'non-productive' complex of Thermus thermophilus GluRS, ATP and L-glutamate, together with those of the GluRS.ATP, GluRS.tRNA.ATP and GluRS.tRNA.GoA (a glutamyl-AMP analog) complexes. In the absence of tRNA(Glu), ATP is accommodated in a 'non-productive' subsite within the ATP-binding site, so that the ATP alpha-phosphate and the glutamate alpha-carboxyl groups in GluRS. ATP.Glu are too far from each other (6.2 A) to react. In contrast, the ATP-binding mode in GluRS.tRNA. ATP is dramatically different from those in GluRS.ATP.Glu and GluRS.ATP, but corresponds to the AMP moiety binding mode in GluRS.tRNA.GoA (the 'productive' subsite). Therefore, tRNA binding to GluRS switches the ATP-binding mode. The interactions of the three tRNA(Glu) regions with GluRS cause conformational changes around the ATP-binding site, and allow ATP to bind to the 'productive' subsite.

/pdf/atp-binding-by-glutamyl-trna-synthetase-is-switched-to-the-2anivld6he.pdf

ATP binding by glutamyl‐tRNA synthetase is switched to the productive mode by tRNA binding

A crystal structure of bacterial RNA polymerase (RNAP) bound to the transcription inhibitor Gfh1 reveals the mechanism of inhibition by Gfh1 and shows RNAP in a novel 'ratcheted' conformation. The authors propose that the conformation they observe could be relevant for other stages of transcription such as translocation of the polymerase along DNA. A crystal structure of bacterial RNA polymerase (RNAP) bound to the transcription inhibitor Gfh1 reveals the mechanism of inhibition by Gfh1 and an alternative ratcheted state of RNAP. The multi-subunit DNA-dependent RNA polymerase (RNAP) is the principal enzyme of transcription for gene expression. Transcription is regulated by various transcription factors. Gre factor homologue 1 (Gfh1), found in the Thermus genus, is a close homologue of the well-conserved bacterial transcription factor GreA, and inhibits transcription initiation and elongation by binding directly to RNAP1,2,3,4,5,6,7,8. The structural basis of transcription inhibition by Gfh1 has remained elusive, although the crystal structures of RNAP and Gfh1 have been determined separately6,7,8,9. Here we report the crystal structure of Thermus thermophilus RNAP complexed with Gfh1. The amino-terminal coiled-coil domain of Gfh1 fully occludes the channel formed between the two central modules of RNAP; this channel would normally be used for nucleotide triphosphate (NTP) entry into the catalytic site. Furthermore, the tip of the coiled-coil domain occupies the NTP β-γ phosphate-binding site. The NTP-entry channel is expanded, because the central modules are ‘ratcheted’ relative to each other by ∼7°, as compared with the previously reported elongation complexes. This ‘ratcheted state’ is an alternative structural state, defined by a newly acquired contact between the central modules. Therefore, the shape of Gfh1 is appropriate to maintain RNAP in the ratcheted state. Simultaneously, the ratcheting expands the nucleic-acid-binding channel, and kinks the bridge helix, which connects the central modules. Taken together, the present results reveal that Gfh1 inhibits transcription by preventing NTP binding and freezing RNAP in the alternative structural state. The ratcheted state might also be associated with other aspects of transcription, such as RNAP translocation and transcription termination.

Shun-ichi Sekine

Papers

Crystal structure of a bacterial RNA polymerase holoenzyme at 2.6 A resolution

Structural Basis for Transcription Regulation by Alarmone ppGpp

Structural basis for double-sieve discrimination of L-valine from L-isoleucine and L-threonine by the complex of tRNA(Val) and valyl-tRNA synthetase.

ATP binding by glutamyl‐tRNA synthetase is switched to the productive mode by tRNA binding

Crystal structure of bacterial RNA polymerase bound with a transcription inhibitor protein