Dataset Information

(NZ)CH...O contacts assist crystallization of a ParB-like nuclease.

ABSTRACT: The major bottleneck for determination of 3 D structures of proteins using X-rays is the production of diffraction quality crystals. Often proteins are subjected to chemical modification to improve the chances of crystallizationHere, we report the successful crystallization of a nuclease employing a reductive methylation protocol. The key to crystallization was the successful introduction of 44 new cohesive (NZ) CH...O contacts (3.2-3.7 A) by the addition of 2 methyl groups to the side chain amine nitrogen (NZ) of 9 lysine residues of the nuclease. The new contacts dramatically altered the crystallization properties of the protein, resulting in crystals that diffracted to 1.2 A resolution. Analytical ultracentrifugation analysis and thermodynamics results revealed a more compact protein structure with better solvent exclusion of buried Trp residues in the folded state of the methylated protein, assisting crystallization.In this study, introduction of novel cohesive (NZ)CH...O contacts by reductive methylation resulted in the crystallization of a protein that had previously resisted crystallization in spite of extensive purification and crystallization space screening. Introduction of (NZ)CH...O contacts could provide a solution to crystallization problems for a broad range of protein targets.

SUBMITTER: Shaw N

PROVIDER: S-EPMC1940005 | biostudies-literature | 2007 Jul

REPOSITORIES: biostudies-literature

ACCESS DATA

Publications

(NZ)CH...O contacts assist crystallization of a ParB-like nuclease.

Shaw Neil N Cheng Chongyun C Tempel Wolfram W Chang Jessie J Ng Joseph J Wang Xin-Yu XY Perrett Sarah S Rose John J Rao Zihe Z Wang Bi-Cheng BC Liu Zhi-Jie ZJ

BMC structural biology 20070707

<h4>Background</h4>The major bottleneck for determination of 3 D structures of proteins using X-rays is the production of diffraction quality crystals. Often proteins are subjected to chemical modification to improve the chances of crystallization<h4>Results</h4>Here, we report the successful crystallization of a nuclease employing a reductive methylation protocol. The key to crystallization was the successful introduction of 44 new cohesive (NZ) CH...O contacts (3.2-3.7 A) by the addition of 2 ...[more]

PMID: 17617922

Similar Datasets

Project description:BackgroundSea urchins are studied as model organisms for developmental and systems biology and also produce highly valued food products. Evechinus chloroticus (Kina) is a sea urchin species that is indigenous to New Zealand. It is the type member of the Evechinus genus based on its morphological characteristics. Previous research has focused on identifying physical factors affecting commercial roe quality of E. chloroticus, but there is almost no genetic information available for E. chloroticus. E. chloroticus is the only species in its genus and has yet to be subject to molecular phylogenetic analysis.ResultsIn this study we performed a de novo transcriptome assembly of Illumina sequencing data. A total of 123 million 100 base length paired-end reads were generated using RNA-Seq libraries from a range of E. chloroticus tissues from two individuals obtained from Fiordland, New Zealand. The assembly resulted in a set of 75,002 transcripts with an accepted read coverage and length, of which 24,655 transcripts could be functionally annotated using protein similarity. Transcripts could be further annotated with Gene Ontology, KEGG Orthology and InterPro terms. With this sequence data we could perform the first phylogenetic analysis of E. chloroticus to other species of its family using multiple genes. When sequences for the mitochondrial nitrogen dehydrogenase genes were compared, E. chloroticus remained outside of a family level clade, which indicated E. chloroticus is indeed a genetically distinct genus within its family.ConclusionsThis study has produced a large set of E. chloroticus transcripts/proteins along with functional annotations, vastly increasing the amount of genomic data available for this species. This provides a resource for current and future studies on E. chloroticus, either to increase its commercial value, or its use as a model organism. The phylogenetic results provide a basis for further analysis of relationships between E. chloroticus, its family members, and its evolutionary history.

Dataset Information

(NZ)CH...O contacts assist crystallization of a ParB-like nuclease.

Publications

(NZ)CH...O contacts assist crystallization of a ParB-like nuclease.

Similar Datasets

OmicsDI is part of the ELIXIR infrastructure