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A K Aggarwal

Publications and source records attributed to A K Aggarwal.

At least 73 records · Page 4Linked to original sources
PubMed1995

Structure and function of restriction endonucleases.

Structures of two restriction endonucleases, BamHI and PvuII, were reported in the past year. This doubles the number of restriction endonuclease structures now known from two to four, and enables a comparative analysis of their structures and modes of DNA recognition. Despite a lack of sequence homology between the enzymes, BamHI turns out to resemble EcoRI, and PvuII turns out to resemble EcoRV. The active-site regions are structurally similar in all four enzymes, but their mechanisms of cleavage may differ.

Deoxyribonucleases, Type II Site-Specific↗
PubMed1994

Crystallization and preliminary X-ray analysis of restriction endonuclease BamHI-DNA complex.

Restriction endonuclease BamHI from Bacillus amyloliquefaciens has been co-crystallized with a 12 bp DNA fragment that encompasses its recognition site. The co-crystals diffract to at least 1.95 A resolution and belong to space group P2(1)2(1)2(1). The unit cell parameters are a = 108.8 A, b = 81.9 A, c = 68.8 A, consistent with one complex in the crystallographic asymmetric unit. The direction of the DNA appears to be along the b axis. In order to achieve end to end stacking of DNA, the complex must lie on the screw axis along b. A self-rotation function has determined the directions of the non-crystallographic 2-fold axes.

Base Sequence↗
PubMed1994

Structure of restriction endonuclease bamhi phased at 1.95 A resolution by MAD analysis.

BACKGROUND: Type II restriction endonucleases recognize DNA sequences that vary between four to eight base pairs, and require only Mg2+ as a cofactor to catalyze the hydrolysis of DNA. Their protein sequences display a surprising lack of similarity, and no recurring structural motif analogous to the helix-turn-helix or the zinc finger of transcription factors, has yet been discovered. RESULTS: We have determined the crystal structure of restriction endonuclease BamHI at 1.95 A resolution. The structure was solved by combining phase information derived from multi-wavelength X-ray data by algebraic and maximum likelihood methods. The BamHI subunit consists of a central beta-sheet with alpha-helices on both sides. The dimer configuration reveals a large cleft which could accommodate B-form DNA. Mutants of the enzyme that are deficient in cleavage are located at or near the putative DNA-binding cleft. BamHI and endonuclease EcoRI share a common core motif (CCM) consisting of five beta-strands and two helices. It remains to be determined if other restriction enzymes also contain the CCM. CONCLUSIONS: The structure of BamHI provides the first clear evidence that there may be substantial structural homology amongst restriction enzymes, even though it is undetectable at the sequence level.

Amino Acid Sequence↗
PubMed1994

Structure of restriction endonuclease BamHI and its relationship to EcoRI.

Type II restriction endonucleases are characterized by the remarkable specificity with which they cleave specific DNA sequences. Surprisingly, their protein sequences are in most cases unrelated, and no recurring structural motif has yet been identified. We have determined the structure of restriction endonuclease BamHI at 1.95 A resolution. BamHI shows striking resemblance to the structure of endonuclease EcoRI (refs 3, 4), despite the lack of sequence similarity between them. We also observe some curious differences between the two structures, and propose an evolutionary scheme that may explain them. The active site of BamHI is structurally similar to the active sites of EcoRI and EcoRV (ref. 5), but the mechanism by which BamHI activates a water molecule for nucleophilic attack may be different.

Binding Sites↗
PubMed1991

Overexpression, purification and crystallization of BamHI endonuclease.

The type II restriction endonuclease BamHI has been expressed in E. coli, producing 100-fold more enzyme than the wild type Bacillus amyloliquefaciens H strain. This high yield has facilitated purification to homogeneity of large amounts of the enzyme, along with its crystallization in a form which diffracts to at least 1.9 A in X-ray analysis.

Bacillus↗
PubMed1990

Conserved residues make similar contacts in two repressor-operator complexes.

Comparison of a lambda repressor-operator complex and a 434 repressor-operator complex reveals that three conserved residues in the helix-turn-helix (HTH) region make similar contacts in each of the crystallographically determined structures. These conserved residues and their interactions with phosphodiester oxygens help establish a frame of reference within which other HTH residues make contacts that are critical for site-specific recognition. Such "positioning contacts" may be important conserved features within families of HTH proteins. In contrast, the structural comparisons appear to rule out any simple "recognition code" at the level of detailed side chain-base pair interactions.

Amino Acid Sequence↗
PubMed1988

Recognition of a DNA operator by the repressor of phage 434: a view at high resolution.

The repressors of temperate bacteriophages such as 434 and lambda control transcription by binding to a set of DNA operator sites. The different affinity of repressor for each of these sites ensures efficient regulation. High-resolution x-ray crystallography was used to study the DNA-binding domain of phage 434 repressor in complex with a synthetic DNA operator. The structure shows recognition of the operator by direct interactions with base pairs in the major groove, combined with the sequence-dependent ability of DNA to adopt the required conformation on binding repressor. In particular, a network of three-centered bifurcated hydrogen bonds among base pairs in the operator helps explain why 434 repressor prefers certain sites over others. These bonds, which stabilize the conformation of the bound DNA, can form only with certain sequences.

Base Composition↗
PubMed1985

Nucleic acid binding drugs. Part XIII. Molecular motion in a drug-nucleic acid model system: thermal motion analysis of a proflavine-dinucleoside crystal structure.

The high-resolution crystal structure of the intercalation complex between proflavine and cytidylyl-3',5'-guanosine (CpG) has been studied by thermalmotion analysis. This has provided information on the translational and librational motions of individual groups in the complex. Many of these motions are similar to, though of larger magnitude than in uncomplexed dinucleosides. Pronounced librational effects were observed along the base pairs and in the plane of the drug chromophore.

Acridines↗
PubMed1984

Dissociation of the locomotor and hypotensive effects of adenosine analogues in the rat.

Rats implanted with chronic indwelling cannulae were injected in the lateral cerebral ventricle with two adenosine analogues and the effects on spontaneous locomotor activity and blood pressure recorded. Both analogues produced dose-related decreases in locomotor activity, with 5'-N-ethylcarboxamidoadenosine (NECA) exhibiting slightly more potent depressant activity than (-)-N-(1-methyl-2-phenylethyl)adenosine (L-phenylisopropyladenosine) (L-PIA). NECA and L-PIA also produced dose-related reductions in blood pressure but the threshold dose for hypotensive activity was 10-100-fold higher than the dose required for depression of spontaneous locomotor activity. The depression of locomotor activity and the hypotensive effect of both analogues were antagonized by parenteral injections of caffeine. These results show that the hypoactive and hypotensive effects of adenosine analogues can be dissociated and that methylxanthines probably exert an antagonism of central adenosine receptors in the rat.

Adenosine↗