An ArsR-like transcriptional factor recognizes a conserved sequence motif and positively regulates the expression of phoP in mycobacteria

2011 ◽  
Vol 411 (4) ◽  
pp. 726-731 ◽  
Author(s):  
Chun-Hui Gao ◽  
Min Yang ◽  
Zheng-Guo He
Keyword(s):  
Transcriptional Factor ◽  
Sequence Motif ◽  
Conserved Sequence

scholarly journals The Crystal Structure of Shikimate Dehydrogenase (AroE) Reveals a Unique NADPH Binding Mode

2003 ◽  
Vol 185 (14) ◽  
pp. 4144-4151 ◽  
Author(s):  
Sheng Ye ◽  
Frank von Delft ◽  
Alexei Brooun ◽  
Mark W. Knuth ◽  
Ronald V. Swanson ◽  
...  
Keyword(s):  
Catalytic Domain ◽  
Binding Pocket ◽  
Binding Mode ◽  
Sequence Motif ◽  
Binary Complex ◽  
Shikimate Dehydrogenase ◽  
Conserved Residues ◽  
Conserved Sequence ◽  
Nicotinamide Mononucleotide ◽  
Reversible Reduction

ABSTRACT Shikimate dehydrogenase catalyzes the NADPH-dependent reversible reduction of 3-dehydroshikimate to shikimate. We report the first X-ray structure of shikimate dehydrogenase from Haemophilus influenzae to 2.4-Å resolution and its complex with NADPH to 1.95-Å resolution. The molecule contains two domains, a catalytic domain with a novel open twisted α/β motif and an NADPH binding domain with a typical Rossmann fold. The enzyme contains a unique glycine-rich P-loop with a conserved sequence motif, GAGGXX, that results in NADPH adopting a nonstandard binding mode with the nicotinamide and ribose moieties disordered in the binary complex. A deep pocket with a narrow entrance between the two domains, containing strictly conserved residues primarily contributed by the catalytic domain, is identified as a potential 3-dehydroshikimate binding pocket. The flexibility of the nicotinamide mononucleotide portion of NADPH may be necessary for the substrate 3-dehydroshikimate to enter the pocket and for the release of the product shikimate.

Functional importance of a conserved sequence motif in FhaC, a prototypic member of the TpsB/Omp85 superfamily

FEBS Journal ◽  
2010 ◽  
Vol 277 (22) ◽  
pp. 4755-4765 ◽  
Author(s):  
Anne-Sophie Delattre ◽  
Bernard Clantin ◽  
Nathalie Saint ◽  
Camille Locht ◽  
Vincent Villeret ◽  
...  
Keyword(s):  
Sequence Motif ◽  
Functional Importance ◽  
Conserved Sequence

A nuclear factor that binds to a conserved sequence motif in transcriptional control elements of immunoglobulin genes

Nature ◽  
1986 ◽  
Vol 319 (6049) ◽  
pp. 154-158 ◽  
Author(s):  
Harinder Singh ◽  
Ranjan Sen ◽  
David Baltimore ◽  
Phillip A. Sharp
Keyword(s):  
Transcriptional Control ◽  
Sequence Motif ◽  
Nuclear Factor ◽  
Immunoglobulin Genes ◽  
Conserved Sequence

scholarly journals Viral DNA Synthesis Defects in Assembly-Competent Rous Sarcoma Virus CA Mutants

2001 ◽  
Vol 75 (1) ◽  
pp. 242-250 ◽  
Author(s):  
Tina M. Cairns ◽  
Rebecca C. Craven
Keyword(s):  
Dna Synthesis ◽  
Rous Sarcoma Virus ◽  
Virus Assembly ◽  
Virus Infectivity ◽  
Sequence Motif ◽  
Viral Dna ◽  
Conserved Sequence ◽  
Rous Sarcoma ◽  
Core Proteins ◽  
Sarcoma Virus

ABSTRACT The major structural protein of the retroviral core (CA) contains a conserved sequence motif shared with the CA-like proteins of distantly related transposable elements. The function of this major region of homology (MHR) has not been defined, in part due to the baffling array of phenotypes in mutants of several viruses and the yeast TY3. This report describes new mutations in the CA protein of Rous sarcoma virus (RSV) that were designed to test whether these different phenotypes might indicate distinct functional subdomains in the MHR. A comparison of 25 substitutions at 10 positions in the RSV conserved motif argues against this possibility. Most of the replacements destroyed virus infectivity, although either of two lethal phenotypes was obtained depending on the residue introduced. At most of the positions, one or more replacements (generally the more conservative substitutions) caused a severe replication defect without having any obvious effects on virus assembly, budding, Gag-Pol and genome incorporation, or protein processing. The mutant particles exhibited a defect in endogenous viral DNA synthesis and showed increased sensitivity of the core proteins to detergent, indicating that the mutations interfere with the formation and/or activity of the virion core. The distribution of these mutations across the MHR, with no evidence of clustering, suggests that the entire region is important for a critical postbudding function. In contrast, a second class of lethal substitutions (those that destroyed virus assembly and release) consists of alterations that are expected to cause severe effects on protein structure by disruption either of the hydrophobic core of the CA carboxyl-terminal domain or of the hydrogen bond network that stabilizes the domain. We suggest that this duality of phenotypes is consistent with a role for the MHR in the maturation process that links the two parts of the life cycle.

scholarly journals Genera specific distribution of DEAD-box RNA helicases in cyanobacteria

2021 ◽  
Vol 7 (3) ◽  
Author(s):  
Denise S. Whitford ◽  
Brendan T. Whitman ◽  
George W. Owttrim
Keyword(s):  
Phylogenetic Analysis ◽  
Rna Helicase ◽  
Evolutionary Divergence ◽  
Sequence Motif ◽  
Rna Helicases ◽  
Homologous Proteins ◽  
Content Type ◽  
Conserved Sequence ◽  
Link Type ◽  
Dead Box

Although RNA helicases are essentially ubiquitous and perform roles in all stages of RNA metabolism, phylogenetic analysis of the DEAD (Asp-Glu-Ala-Asp)-box RNA helicase family in a single phylum has not been performed. Here, we performed a phylogenetic analysis on DEAD-box helicases from all currently available cyanobacterial genomes, comprising a total of 362 helicase protein sequences from 280 strains. DEAD-box helicases belonging to three distinct clades were observed. Two clades, the CsdA (cold shock DEAD-box A)-like and RhlE (RNA helicase E)-like helicases, cluster with the homologous proteins from Escherichia coli . The third clade, the CrhR (cyanobacterial RNA helicase Redox)-like helicases, is unique to cyanobacteria and characterized by a conserved sequence motif in the C-terminal extension. Restricted distribution is observed across cyanobacterial diversity with respect to both helicase type and strain. CrhR-like and CsdA-like helicases essentially never occur together, while RhlE always occurs with either a CrhR-like or CsdA-like helicase. CrhR-like and RhlE-like proteins occurred in filamentous cyanobacteria of the orders Nostocales , Oscillatoriales and Synechococcales . Similarly, CsdA- and RhlE-like proteins are restricted to unicellular cyanobacteria of the genera Cyanobium and Synechococcus . In addition, the unexpected occurrence of RhlE in two Synechococcus strains suggests recent acquisition and evolutionary divergence. This study, therefore, raises physiological and evolutionary questions as to why DEAD-box RNA helicases encoded in cyanobacterial lineages display restricted distributions, suggesting niches that require either CrhR or CsdA RNA helicase activity but not both. Extensive conservation of gene synteny surrounding the previously described rimO–crhR operon is also observed, indicating a role in the maintenance of photosynthesis. The analysis provides insights into the evolution, origin and dissemination of sequences within a single gene family to yield divergent functional roles.

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