Detection, delineation, measurement and display of cavities in macromolecular structures

Kleywegt, Gerard J.; Jones, Thomas A.

doi:10.1107/s0907444993011333

Cited by 968 publications

(774 citation statements)

References 10 publications

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Section: Dam-dna Nonspecific Interactionsmentioning

confidence: 99%

“…The only obvious differences involve side chain rotamers of several residues (Asn133, Lys134 and Asn135) involved in phosphate interactions. However, the orientations of the two molecules relative to the DNA helical axis are different: molecule A is rotated by ~20° relative to molecule B, resulting in a larger cavity 40 for molecule A (170 Å 3 ) vs. molecule B (30 Å 3 ) at the interface of protein and DNA. The smaller cavity and the larger buried surface area suggest that the binding mode of molecule B might be closer to a specific binding mode than that if molecule A.…”

Section: Dam-dna Nonspecific Interactionsmentioning

confidence: 99%

“…54). Contacts of buried surface were calculated using CONTACT 54 Cavity sizes were calculated using VOIDOO of RAVE 40 .…”

Section: Structure Determinationmentioning

confidence: 99%

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Structure of the bacteriophage T4 DNA adenine methyltransferase

Yang

Horton

Zhou

et al. 2003

Nat Struct Mol Biol

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DNA-adenine methylation at certain GATC sites plays a pivotal role in bacterial and phage gene expression as well as bacterial virulence. We report here the crystal structures of the bacteriophage T4Dam DNA adenine methyltransferase (MTase) in a binary complex with the methyl-donor product S-adenosyl-L-homocysteine (AdoHcy) and in a ternary complex with a synthetic 12-bp DNA duplex and AdoHcy. T4Dam contains two domains: a seven-stranded catalytic domain that harbors the binding site for AdoHcy and a DNA binding domain consisting of a five-helix bundle and a β-hairpin that is conserved in the family of GATC-related MTase orthologs. Unexpectedly, the sequence-specific T4Dam bound to DNA in a nonspecific mode that contained two Dam monomers per synthetic duplex, even though the DNA contains a single GATC site. The ternary structure provides a rare snapshot of an enzyme poised for linear diffusion along the DNA.DNA MTases catalyze methyl group transfer from donor S-adenosyl-L-methionine (AdoMet), producing S-adenosyl-L-homocysteine (AdoHcy) and methylated DNA. Although most prokaryote DNA MTases are components of restriction-modification systems, some MTases are not associated with cognate restriction enzymes, such as the Escherichia coli DNA adenine MTase (Dam). This enzyme methylates an exocyclic amino nitrogen (N6) of the adenine in GATC 1,2 . Dam MTase gene orthologs are widespread among enteric bacteria and their bacteriophages (see Fig. 1 legend). Dam methylation is not essential for the viability of E. coli, unless it is combined with certain other mutations 3 ; however, Dam is an essential gene in Vibrio cholerae and Yersinia pesudotuberculosis, at least under the tested growth conditions 4 . Dam methylation is essential for the virulence of Salmonella serovar typhimurium in a murine model of typhoid fever [5][6][7] . These observations COMPETING INTERESTS STATEMENTThe authors declare that they have no competing financial interests. NIH Public Access RESULTS Overall structure of DamThe monomeric Dam structure contains 9 β-strands and 11 α-helices (Fig. 1). The Nterminal region (residues 1-52) and C-terminal region (residues 149-259) come together, forming the catalytic domain (green in Figs. 1 and 2a) with a seven-stranded β-sheet, a characteristic feature of the class-I AdoMet-dependent MTases 28 . The N-terminal helices αZ and αA are located on one side of the β-sheet, and helices αC, αD1 and αD2 and αE are on the other side. Between strands β2 and β3 is a separate domain, which we designate as the target-recognition domain (TRD). TRD is composed of a five-helix bundle (αB1-αB5) (yellow in Figs. 1 and 2a) and a 25-residue segment containing a β-hairpin (β8 and β9) inserted between helices αB4 and αB5 (red). The overall dimensions of the molecule are 55 × 34 × 28 Å, with an open cleft located between the catalytic domain (green) and the TRD (yellow and red). Conserved residues and the effects of mutationsBased on the linear arrangement of conserved motifs in DNA MTases, T4Dam is classified in the...

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Section: Dam-dna Nonspecific Interactionsmentioning

confidence: 99%

Section: Dam-dna Nonspecific Interactionsmentioning

confidence: 99%

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Structure of the bacteriophage T4 DNA adenine methyltransferase

Yang

Horton

Zhou

et al. 2003

Nat Struct Mol Biol

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“…Buckle et al (1996) used the program VOID00 (Kleywegt & Jones. 1994) with a probe radius of 0.8 A ; those of Varadarajan and Richards (1992) used a Voronoi analysis.…”

Section: Valine 149 To Alaninementioning

confidence: 99%

The response of T4 lysozyme to large‐to‐small substitutions within the core and its relation to the hydrophobic effect

et al. 1998

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To further examine the structural and thermodynamic basis of hydrophobic stabilization in proteins, all of the bulky non-polar residues that are buried or largely buried within the core of T4 lysozyme were substituted with alanine. In 25 cases, including eight reported previously, it was possible to determine the crystal structures of the variants. The structures of four variants with double substitutions were also determined. In the majority of cases the "large-to-small" substitutions lead to internal cavities. In other cases declivities or channels open to the surface were formed. In some cases the structural changes were minimal (mainchain shifts 5 0.3 A); in other cases mainchain atoms moved up to 2 A.In the case of Ile 29 -+ Ala the structure col!apsed to such a degree that the volume of the putative cavity was zero. Crystallographic analysis suggests that the occupancy of the engineered cavities by solvent is usually low. The mutants Val 149 4 Ala (V149A) and Met 6 -+ Ala (M6A), however, are exceptions and have, respectively, one and two well-ordered water molecules within the. cavity. The Val 149 -+ Ala substitution allows the solvent molecule to hydrogen bond to polar atoms that are occluded in the wild-type molecule. Similarly, the replacement of Met 6 with alanine allows the two solvent molecules to hydrogen bond to each other and to polar atoms on the protein. Except for Val 149 -+ Ala the loss of stability of all the cavity mutants can be rationalized as a combination of two terms. The first is a constant for a given class of substitution (e.g., -2.1 kcal/mol for all Leu + Ala substitutions) and can be considered as the difference between the free energy of transfer of leucine and alanine from solvent to the core of the protein. The second term can be considered as the energy cost of forming the cavity and is consistent with a numerical value of 22 cal mol" k 3 . Physically, this term is due to the loss of van der Waal's interactions between the bulky sidechain that is removed and the atoms that form the wall of the cavity. The overall results are consistent with the prior rationalization of Leu + Ala mutants in T4 lysozyme by Eriksson et al. (Eriksson et al., 1992, Science 255:178-183).

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“…Although of similar areas (20–30 Å 2 ), the open triangular apertures of 2 resultantly present a less equilateral surface than 1 . Void volumes, calculated using VOIDOO,16 revealed cavities of 282 Å 3 for 1 and 423 Å 3 for 2 . These volumes are approximately ten times larger than those of the M II 4 L 4 tetrahedra formed from the same triamines using 2‐formylpyridine 17…”

mentioning

confidence: 99%

Peripheral Templation Generates an M^II₆L₄ Guest‐Binding Capsule

Rizzuto

Ronson

et al. 2016

Angew Chem Int Ed

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Pseudo‐octahedral MII 6L4 capsules result from the subcomponent self‐assembly of 2‐formylphenanthroline, threefold‐symmetric triamines, and octahedral metal ions. Whereas neutral tetrahedral guests and most of the anions investigated were observed to bind within the central cavity, tetraphenylborate anions bound on the outside, with one phenyl ring pointing into the cavity. This binding configuration is promoted by the complementary arrangement of the phenyl rings of the intercalated guest between the phenanthroline units of the host. The peripherally bound, rapidly exchanging tetraphenylborate anions were found to template an otherwise inaccessible capsular structure in a manner usually associated with slow‐exchanging, centrally bound agents. Once formed, this cage was able to bind guests in its central cavity.

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Detection, delineation, measurement and display of cavities in macromolecular structures

Abstract: A computer program,

Cited by 968 publications

References 10 publications

Structure of the bacteriophage T4 DNA adenine methyltransferase

Structure of the bacteriophage T4 DNA adenine methyltransferase

The response of T4 lysozyme to large‐to‐small substitutions within the core and its relation to the hydrophobic effect

Peripheral Templation Generates an M^II₆L₄ Guest‐Binding Capsule

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Detection, delineation, measurement and display of cavities in macromolecular structures

Abstract: A computer program,

Cited by 968 publications

References 10 publications

Structure of the bacteriophage T4 DNA adenine methyltransferase

Structure of the bacteriophage T4 DNA adenine methyltransferase

The response of T4 lysozyme to large‐to‐small substitutions within the core and its relation to the hydrophobic effect

Peripheral Templation Generates an MII6L4 Guest‐Binding Capsule

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Peripheral Templation Generates an M^II₆L₄ Guest‐Binding Capsule