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Structural Homologue (structural + homologue)

Distribution by Scientific Domains
Chemistry100%

Selected Abstracts

Structure of a putative ,-phosphoglucomutase (TM1254) from Thermotoga maritima

ACTA CRYSTALLOGRAPHICA SECTION F (ELECTRONIC), Issue 12 2009
Richard W. Strange
The structure of TM1254, a putative ,-phosphoglucomutase from T. maritima, was determined to 1.74,Å resolution in a high-throughput structural genomics programme. Diffraction data were obtained from crystals belonging to space group P22121, with unit-cell parameters a = 48.16, b = 66.70, c = 83.80,Å, and were refined to an R factor of 19.2%. The asymmetric unit contained one protein molecule which is comprised of two domains. Structural homologues were found from protein databases that confirmed a strong resemblance between TM1254 and members of the haloacid dehalogenase (HAD) hydrolase family. [source]

Effects of segment substitution on the structure and stability of immunoglobulin G binding domain of streptococcal protein G

BIOPOLYMERS, Issue 1 2005
Hai-Ning Du
Abstract Structural formation of segments plays pivotal roles in protein folding and stability, but how the segment influences the structural ensemble remains elusive. We engineered two hybrid proteins by replacing the central helical segment of immunoglobulin G binding domain of streptococcal protein G with an ,-helix or ,2 -strand element of a structural homologue, the immunoglobulin G binding domain of streptococcal protein L. The results show that substitution by the ,-helical sequence retains a folded structure predominantly with a three-stranded ,-sheet but slightly destabilizes the compact ensemble, while substitution by the ,2 -strand sequence completely destroys the structural formation. The finding implies that the local segment may influence the tertiary structure and overall stability, and the tertiary interactions may modulate structural formation of the segment, which might be considered when studying protein folding, prediction, design, and engineering. © 2005 Wiley Periodicals, Inc. Biopolymers 79: 9,17, 2005 This article was originally published online as an accepted preprint. The "Published Online" date corresponds to the preprint version. You can request a copy of the preprint by emailing the Biopolymers editorial office at biopolymers@wiley.com [source]

Preparation, crystallization and preliminary X-ray analysis of YjcG protein from Bacillus subtilis

ACTA CRYSTALLOGRAPHICA SECTION F (ELECTRONIC), Issue 5 2005
Dan Li
Bacillus subtilis YjcG is a functionally uncharacterized protein with 171 residues that has no structural homologue in the Protein Data Bank. However, it shows sequence homology to bacterial and archaeal 2,,5, RNA ligases. In order to identify its exact function via structural studies, the yjcG gene was amplified from B. subtilis genomic DNA and cloned into the expression vector pET21-DEST. The protein was expressed in a soluble form in Escherichia coli and was purified to homogeneity. Crystals suitable for X-ray analysis were obtained that diffracted to 2.3,Å and belonged to space group C2, with unit-cell parameters a = 99.66, b = 73.93, c = 61.77,Å, , = 113.56°. [source]

Evaluation of PSI-BLAST alignment accuracy in comparison to structural alignments

PROTEIN SCIENCE, Issue 11 2000
Iddo Friedberg
Abstract The PSI-BLAST algorithm has been acknowledged as one of the most powerful tools for detecting remote evolutionary relationships by sequence considerations only. This has been demonstrated by its ability to recognize remote structural homologues and by the greatest coverage it enables in annotation of a complete genome. Although recognizing the correct fold of a sequence is of major importance, the accuracy of the alignment is crucial for the success of modeling one sequence by the structure of its remote homologue. Here we assess the accuracy of PSI-BLAST alignments on a stringent database of 123 structurally similar, sequence-dissimilar pairs of proteins, by comparing them to the alignments defined on a structural basis. Each protein sequence is compared to a nonredundant database of the protein sequences by PSI-BLAST. Whenever a pair member detects its pair-mate, the positions that are aligned both in the sequential and structural alignments are determined, and the alignment sensitivity is expressed as the per-centage of these positions out of the structural alignment. Fifty-two sequences detected their pair-mates (for 16 pairs the success was bi-directional when either pair member was used as a query). The average percentage of correctly aligned residues per structural alignment was 43.5 ± 2.2%. Other properties of the alignments were also examined, such as the sensitivity vs. specificity and the change in these parameters over consecutive iterations. Notably, there is an improvement in alignment sensitivity over consecutive iterations, reaching an average of 50.9 + 2.5% within the five iterations tested in the current study. [source]