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At least 595 records · Page 33Linked to original sources
PubMed1999

A newly identified, essential catalytic residue in a critical secondary structure element in the integrase family of site-specific recombinases is conserved in a similar element in eucaryotic type IB topoisomerases.

The integrase family of site-specific recombinases catalyzes conservative rearrangements between defined segments of DNA. A highly conserved tetrad (RHRY) of catalytic residues is essential for this process. This tetrad is dispersed in two motifs in the linear sequence, but is configured appropriately in the catalytic pocket to execute the strand cleavage and rejoining reactions. A third conserved motif has been identified in the Xer subgroup of the integrase family. Mutational analysis of 12 conserved residues in this motif in the XerD protein from Salmonella typhimurium led to the identification of an essential fifth catalytic residue (lysine 172) which is implicated in strand cleavage or exchange. This lysine residue occupies part of the turn of an antiparallel beta-hairpin which forms one side of the catalytic cleft in XerD, and is found at similar positions among evolutionarily diverse integrase family members. Related antiparallel beta-hairpins are present in eucaryotic type IB topoisomerase enzymes which also contain a critical lysine residue in the turn of the hairpin. In both the integrase family and eucaryotic type IB topoisomerases, the catalytic lysine residues are in close contact with the substrates and may play similar roles in influencing the reactivity of the phosphotyrosine intermediates formed during reactions catalyzed by both enzymes.

Amino Acid Sequence↗
PubMed1986

RNA structural elements for expression in Escherichia coli. Alpha 1-antitrypsin synthesis using translation control elements based on the cII ribosome-binding site of phage lambda.

Analysis of a series of lambda cII::alpha 1-antitrypsin (alpha 1AT) gene fusions of different sizes showed that increased alpha 1AT expression correlated with the stabilisation of a particular computer-predicted RNA secondary structure. Moreover, significant synthesis of unfused alpha 1AT was achieved by reconstruction of this conformation to permit interaction between the upstream region of the ribosome-binding site and the first part of the alpha 1AT coding sequence. This high-level expression was dependent upon certain silent point mutations in the coding sequence, indicating that RNA primary and secondary structure determinants can operate in concert to dictate the efficiency of protein synthesis.

Bacteriophage lambda↗
PubMed2000

Studies on the interaction of REST4 with the cholinergic repressor element-1/neuron restrictive silencer element.

REST4 is a neuron specific truncated form of the transcription factor REST/NRSE derived by alternative splicing. REST4 was previously shown to block the repressor activity of REST/NRSF by forming a hetero-oligomer, Shimojo et al. [Mol. Cell. Biol. 19 (1999) 6788-6795]. A series of deletion mutants have now been used to characterize REST4 in terms of its structure and DNA binding. REST4 was found to be O-glycosylated between between residues 87 and 152. Binding of REST4 to the cholinergic RE-1/NRSE was approximately 1/10 to 1/20 as strong as full length REST/NRSF. DNA binding was enhanced by deletion of the first 86 residues and was found to require all four of the C-terminal zinc fingers as well as a twelve amino acid sequence preceding the first of these zinc fingers. REST4 can form homo-oligomers, however only the monomer was found to bind to DNA. REST4 binds to the 3' sequence of the cholinergic NRSE suggesting an anti-parallel orientation of the protein to the DNA.

Alternative Splicing↗
PubMed1997

La autoantigen binding to a 5' cis-element of rubella virus RNA correlates with element function in vivo.

Rubella virus genomic RNA contains a 5' stem-loop (5'(+) SL) which is required for efficient translation and replication. The La autoantigen previously was shown to bind this RNA sequence in vitro. Results reported here demonstrate that this cellular RNA-binding protein binds to the RV 5' SL RNA with sufficient specificity for the binding to occur in the presence of excess total cellular RNA. Further, the affinity of purified La for the RV sequence is similar to its affinity for known cellular substrates. To address the functional significance of La binding, mutant forms of the RV 5'(+) SL were analysed which bind La weaker or stronger than the native form. These three forms of the RV 5' SL were incorporated into RV-luciferase constructs which expressed luciferase activity in transient transfection. The level of expression from each construct correlated with the ability of its RV sequence to bind La. The detection of La/RV RNA complexes in infected cells further supported the physiological relevance of this interaction. Possible implications of autoantigen La interaction with RV RNA for rubella virus pathology and vaccine associated adverse reactions are discussed.

Animals↗
PubMed1999

Element-Element Bonds. IX.(1) Structures of Tetrakis(trifluoromethyl)diphosphane and -diarsane: Experimental and Theoretical Investigations.

X-ray structure determinations of tetrakis(trifluoromethyl)diphosphane (2c, mp -82 degrees C, triclinic, P&onemacr;; Z = 1, a = 529.7(3) pm, b = 681.6(2) pm, c = 802.8(3) pm, alpha = 108.58(1) degrees, beta = 99.66(1) degrees, gamma = 103.29(1) degrees, wR2 = 0.204) and -diarsane (3c, mp -52 degrees C, monoclinic, P2(1)/c; Z = 2, a = 769.5(3) pm, b = 750.0(3) pm, c = 960.7(2) pm, beta = 105.26(1) degrees, wR2 = 0.115), both at -100(3) degrees C, reveal the molecules to adopt the trans conformation in the solid. Compared with the tetramethyl derivatives, the E-E (224.6(2)/246.3(1) pm, E = P, As) and E-C (188.3(4)/201.3(7) pm) bonds are elongated by 4.5/4.8 pm and 3.4/3.4 pm, respectively. From gas electron diffraction studies of diphosphane 2c a mixture of 85(10)% trans and 15(10)% gauche conformers can be deduced; diarsane 3c shows the trans form exclusively. The molecular parameters (E-E, 224.8(11)/245.2(6); E-C, 189.6(4)/ 201.2(4) pm) agree excellently with those determined for the crystalline state. As a result of quantum chemical calculations at Hartree-Fock and hybrid density functional levels of theory using 6-311+G basis sets, the gauche conformer of hydrazine derivative 1c and the trans conformer of diarsane 3c are clearly lowest in energy. However, for diphosphane 2c the gauche and not the trans form is found to be slightly more stable. Variations of calculated E-E and E-C bond lengths are analyzed and compared with corresponding values of the parent compounds E(2)H(4) (1a to 3a) as well as the tetramethyl derivatives 1b to 3b.

Journal Article↗