scholarly journals NMR structure of HI0004, a putative essential gene product from Haemophilus influenzae, and comparison with the X-ray structure of an Aquifex aeolicus homolog

2005 ◽  
Vol 14 (2) ◽  
pp. 424-430 ◽  
Author(s):  
D. C. Yeh
Keyword(s):  
Haemophilus Influenzae ◽  
Gene Product ◽  
Essential Gene ◽  
Nmr Structure ◽  
Aquifex Aeolicus ◽  
X Ray

scholarly journals Letter to the Editor: NMR assignment of the hypothetical protein HI0004 from Haemophilus influenzae – a putative essential gene product

2004 ◽  
Vol 29 (1) ◽  
pp. 101-102 ◽  
Author(s):  
Deok Cheon Yeh ◽  
James F. Parsons ◽  
Lisa M. Parsons ◽  
Fang Liu ◽  
Edward Eisenstein ◽  
...  
Keyword(s):  
Haemophilus Influenzae ◽  
Gene Product ◽  
Nmr Assignment ◽  
Essential Gene ◽  
Hypothetical Protein ◽  
Letter To The Editor

X-ray vs. NMR structure of N-terminal domain of δ-subunit of RNA polymerase

2014 ◽  
Vol 187 (2) ◽  
pp. 174-186 ◽  
Author(s):  
Gabriel Demo ◽  
Veronika Papoušková ◽  
Jan Komárek ◽  
Pavel Kadeřávek ◽  
Olga Otrusinová ◽  
...  
Keyword(s):  
Rna Polymerase ◽  
Nmr Structure ◽  
X Ray ◽  
Terminal Domain

NMR structure of bucandin, a neurotoxin from the venom of the Malayan krait (Bungarus candidus)

2001 ◽  
Vol 360 (3) ◽  
pp. 539-548 ◽  
Author(s):  
Allan M. TORRES ◽  
R. Manjunatha KINI ◽  
Nirthanan SELVANAYAGAM ◽  
Philip W. KUCHEL
Keyword(s):  
Solution Structure ◽  
Pharmacological Action ◽  
Nmr Structure ◽  
Side Chains ◽  
X Ray ◽  
Nmr Study ◽  
C Terminus ◽  
Mean Structure ◽  
Β Sheets ◽  
Β Sheet

A high-resolution solution structure of bucandin, a neurotoxin from Malayan krait (Bungarus candidus), was determined by 1H-NMR spectroscopy and molecular dynamics. The average backbone root-mean-square deviation for the 20 calculated structures and the mean structure is 0.47 Å (1 Å = 0.1nm) for all residues and 0.24 Å for the well-defined region that spans residues 23–58. Secondary-structural elements include two antiparallel β-sheets characterized by two and four strands. According to recent X-ray analysis, bucandin adopts a typical three-finger loop motif and yet it has some peculiar characteristics that set it apart from other common α-neurotoxins. The presence of a fourth strand in the second antiparallel β-sheet had not been observed before in three-finger toxins, and this feature was well represented in the NMR structure. Although the overall fold of the NMR structure is similar to that of the X-ray crystal structure, there are significant differences between the two structures that have implications for the pharmacological action of the toxin. These include the extent of the β-sheets, the conformation of the region spanning residues 42–49 and the orientation of some side chains. In comparison with the X-ray structure, the NMR structure shows that the hydrophobic side chains of Trp27 and Trp36 are stacked together and are orientated towards the tip of the middle loop. The NMR study also showed that the two-stranded β-sheet incorporated in the first loop, as defined by residues 1–22, and the C-terminus from Asn59, is probably flexible relative to the rest of the molecule. On the basis of the dispositions of the hydrophobic and hydrophilic side chains, the structure of bucandin is clearly different from those of cytotoxins.

scholarly journals A presumptive helicase (MOT1 gene product) affects gene expression and is required for viability in the yeast Saccharomyces cerevisiae.

1992 ◽  
Vol 12 (4) ◽  
pp. 1879-1892 ◽  
Author(s):  
J L Davis ◽  
R Kunisawa ◽  
J Thorner
Keyword(s):  
Saccharomyces Cerevisiae ◽  
Gene Product ◽  
Essential Gene ◽  
Single Gene ◽  
Temperature Sensitive ◽  
Yeast Saccharomyces Cerevisiae ◽  
Sequence Element ◽  
Cis Acting ◽  
Upstream Activating Sequence ◽  
Identical Manner

Exposure of a haploid yeast cell to mating pheromone induces transcription of a set of genes. Induction is mediated through a cis-acting DNA sequence found upstream of all pheromone-responsive genes. Although the STE12 gene product binds specifically to this sequence element and is required for maximum levels of both basal and induced transcription, not all pheromone-responsive genes are regulated in an identical manner. To investigate whether additional factors may play a role in transcription of these genes, a genetic screen was used to identify mutants able to express pheromone-responsive genes constitutively in the absence of Ste12. In this way, we identified a recessive, single gene mutation (mot1, for modifier of transcription) which increases the basal level of expression of several, but not all, pheromone-responsive genes. The mot1-1 allele also relaxes the requirement for at least one other class of upstream activating sequence and enhances the expression of another gene not previously thought to be involved in the mating pathway. Cells carrying mot1-1 grow slowly at 30 degrees C and are inviable at 38 degrees C. The MOT1 gene was cloned by complementation of this temperature-sensitive lethality. Construction of a null allele confirmed that MOT1 is an essential gene. MOT1 residues on chromosome XVI and encodes a large protein of 1,867 amino acids which contains all seven of the conserved domains found in known and putative helicases. The product of MOT1 is strikingly homologous to the Saccharomyces cerevisiae SNF2/SW12 and RAD54 gene products over the entire helicase region.

Regulation of Capsule Synthesis and Cell Motility in Salmonella enterica by the Essential Gene igaA

Genetics ◽  
2002 ◽  
Vol 162 (4) ◽  
pp. 1513-1523
Author(s):  
David A Cano ◽  
Gustavo Domínguez-Bernal ◽  
Alberto Tierrez ◽  
Francisco Garcia-del Portillo ◽  
Josep Casadesús
Keyword(s):  
Cell Motility ◽  
Gene Product ◽  
Regulatory Network ◽  
Salmonella Enterica ◽  
Essential Gene ◽  
Fibroblast Cells ◽  
Null Mutant ◽  
Functional Interaction ◽  
Cells In Culture ◽  
System A

Abstract Mutants of Salmonella enterica carrying the igaA1 allele, selected as able to overgrow within fibroblast cells in culture, are mucoid and show reduced motility. Mucoidy is caused by derepression of wca genes (necessary for capsule synthesis); these genes are regulated by the RcsC/YojN/RcsB phosphorelay system and by the RcsA coregulator. The induction of wca expression in an igaA1 mutant is suppressed by mutations in rcsA and rcsC. Reduced motility is caused by lowered expression of the flagellar master operon, flhDC, and is suppressed by mutations in rcsB or rcsC, suggesting that mutations in the igaA gene reduce motility by activating the RcsB/C system. A null igaA allele can be maintained only in an igaA+/igaA merodiploid, indicating that igaA is an essential gene. Lethality is suppressed by mutations in rcsB, rcsC, and yojN, but not in rcsA, suggesting that the viability defect of an igaA null mutant is mediated by the RcsB/RcsC system, independently of RcsA (and therefore of the wca genes). Because all the defects associated with igaA mutations are suppressed by mutations that block the RcsB/RcsC system, we propose a functional interaction between the igaA gene product and either the Rcs regulatory network or one of its regulated products.

Crystal structure of Aquifex aeolicus gene product Aq1627: a putative phosphoglucosamine mutase reveals a unique C-terminal end-to-end disulfide linkage

2017 ◽  
Vol 13 (7) ◽  
pp. 1370-1376
Author(s):  
Upasana Sridharan ◽  
Seiki Kuramitsu ◽  
Shigeyuki Yokoyama ◽  
Thirumananseri Kumarevel ◽  
Karthe Ponnuraj
Keyword(s):  
Crystal Structure ◽  
Gene Product ◽  
Aquifex Aeolicus ◽  
Disulfide Linkage ◽  
Hyperthermophilic Bacterium ◽  
End To End

The crystal structure of Aq1627 protein from Aquifex aeolicus, a hyperthermophilic bacterium has been solved, which reveals a unique end-to-end disulfide linkage.

scholarly journals PTA1, an essential gene of Saccharomyces cerevisiae affecting pre-tRNA processing.

1992 ◽  
Vol 12 (9) ◽  
pp. 3843-3856 ◽  
Author(s):  
J P O'Connor ◽  
C L Peebles
Keyword(s):  
Saccharomyces Cerevisiae ◽  
Gene Product ◽  
Genomic Library ◽  
Essential Gene ◽  
Growth Defect ◽  
Temperature Sensitive ◽  
Putative Open Reading Frame ◽  
Reading Frame ◽  
Trna Processing ◽  
Chromosome I

We have identified an essential Saccharomyces cerevisiae gene, PTA1, that affects pre-tRNA processing. PTA1 was initially defined by a UV-induced mutation, pta1-1, that causes the accumulation of all 10 end-trimmed, intron-containing pre-tRNAs and temperature-sensitive but osmotic-remedial growth. pta1-1 does not appear to be an allele of any other known gene affecting pre-tRNA processing. Extracts prepared from pta1-1 strains had normal pre-tRNA splicing endonuclease activity. pta1-1 was suppressed by the ochre suppressor tRNA gene SUP11, indicating that the pta1-1 mutation creates a termination codon within a protein reading frame. The PTA1 gene was isolated from a genomic library by complementation of the pta1-1 growth defect. Episome-borne PTA1 directs recombination to the pta1-1 locus. PTA1 has been mapped to the left arm of chromosome I near CDC24; the gene was sequenced and could encode a protein of 785 amino acids with a molecular weight of 88,417. No other protein sequences similar to that of the predicted PTA1 gene product have been identified within the EMBL or GenBank data base. Disruption of PTA1 near the carboxy terminus of the putative open reading frame was lethal. Possible functions of the PTA1 gene product are discussed.

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