X-ray structure of T4 endonuclease VII: a DNA junction resolvase with a novel fold and unusual domain-swapped dimer architecture

Raaijmakers, H.C.A.; Vix, Olivier; Törö, I; Gölz, Stefan; Kemper, Börries; Suck, Dietrich

doi:10.1093/emboj/18.6.1447

Cited by 127 publications

(97 citation statements)

References 53 publications

Supporting

Mentioning

Contrasting

Unclassified

Order By: Relevance

“…4). The three x-ray structures published [Escherichia coli RuvC (5), bacteriophage T4 endonuclease VII (6), and phage T7 endonuclease I (7)] show three unrelated protein folds, emphasizing the diversity of this class of enzymes. Although all of the junction-resolving enzymes catalyze the hydrolysis of the phosphodiester backbone by utilizing a metalactivated hydroxyl ion, they differ significantly in their means of recognition and manipulation of the four-way DNA junction substrate.…”

mentioning

confidence: 99%

Structure of Hjc, a Holliday junction resolvase, from Sulfolobus solfataricus

Bond

Kvaratskhelia

Richard

et al. 2001

Proc. Natl. Acad. Sci. U.S.A.

View full text Add to dashboard Cite

The 2.15-Å structure of Hjc, a Holliday junction-resolving enzyme from the archaeon Sulfolobus solfataricus, reveals extensive structural homology with a superfamily of nucleases that includes type II restriction enzymes. Hjc is a dimer with a large DNA-binding surface consisting of numerous basic residues surrounding the metal-binding residues of the active sites. Residues critical for catalysis, identified on the basis of sequence comparisons and site-directed mutagenesis studies, are clustered to produce two active sites in the dimer, about 29 Å apart, consistent with the requirement for the introduction of paired nicks in opposing strands of the four-way DNA junction substrate. Hjc displays similarity to the restriction endonucleases in the way its specific DNA-cutting pattern is determined but uses a different arrangement of nuclease subunits. Further structural similarity to a broad group of metal͞phosphate-binding proteins, including conservation of active-site location, is observed. A high degree of conservation of surface electrostatic character is observed between Hjc and T4-phage endonuclease VII despite a complete lack of structural homology. A model of the Hjc-Holliday junction complex is proposed, based on the available functional and structural data.

show abstract

mentioning

confidence: 99%

Structure of Hjc, a Holliday junction resolvase, from Sulfolobus solfataricus

Bond

Kvaratskhelia

Richard

et al. 2001

Proc. Natl. Acad. Sci. U.S.A.

View full text Add to dashboard Cite

show abstract

“…1 and 3, can contribute to DNA repair and explain ''homing'' of intron DNA (15,18,19). Most of the proteins involved in these pathways have been biochemically characterized in exquisite detail (2,12,(20)(21)(22)(23)(24)(25)(26)(27)(28)(29)(30)(31)(32)(33)(34)(35).…”

mentioning

confidence: 99%

Two recombination-dependent DNA replication pathways of bacteriophage T4, and their roles in mutagenesis and horizontal gene transfer

Mosig

Gewin

Luder

et al. 2001

Proc. Natl. Acad. Sci. U.S.A.

View full text Add to dashboard Cite

. In wild-type T4, timing of these pathways is integrated with the developmental program and related to transcription and packaging of DNA. In primase mutants, which are defective in origin-dependent lagging-strand DNA synthesis, the late pathway can bypass the lack of primers for lagging-strand DNA synthesis. The exquisitely regulated synthesis of endo VII, and of two proteins from its gene, explains the delay of recombination-dependent DNA replication in primase (as well as topoisomerase) mutants, and the temperature-dependence of the delay. Other proteins (e.g., the singlestranded DNA binding protein and the products of genes 46 and 47) are important in all recombination pathways, but they interact differently with other proteins in different pathways. These homologous recombination pathways contribute to evolution because they facilitate acquisition of any foreign DNA with limited sequence homology during horizontal gene transfer, without requiring transposition or site-specific recombination functions. Partial heteroduplex repair can generate what appears to be multiple mutations from a single recombinational intermediate. The resulting sequence divergence generates barriers to formation of viable recombinants. The multiple sequence changes can also lead to erroneous estimates in phylogenetic analyses.The purpose of looking back is not, of course, merely to obtain satisfaction from reflecting on past triumphs; rather, it is to discover as many clues as possible to the likely developments of the future.Glenn T. Seaborg T he tight interrelationship between homologous recombination and DNA replication was first evident in T4 and the related T-even phages. Because DNA of T4 and its host E. coli differ in base composition and modifications and because the host DNA is rapidly degraded after phage infection, molecular aspects of T4 replication and recombination could be readily investigated by biochemical, biophysical, and genetic methods. Early characterization of mutations in most essential genes (1) and the almost complete dependence of replication and recombination on phage-encoded proteins (2) allowed analyses of recombination and replication proteins, as well as ''reality checks'' of results obtained with genetic and biochemical methods (3). The following idiosyncrasies of T4 chromosomes revealed the importance of DNA ends and recombination-dependent DNA replication. Ends of T4 chromosomes are cut during packaging from branched concatemers, which are generated by recombination-dependent replication. A ''headful mechanism'' packages a complete genome and Ϸ3% DNA repeated at each end as ''terminal redundancy,'' thereby generating the random circular permutation of chromosomal ends (4). Some smaller T4 particles, formed because of assembly errors, package incomplete genomes whose ends are also randomly circularly permuted (5). Multifactor crosses revealed stimulation of recombination by their DNA ends, regardless of map positions (5, 6). Moreover, different segregation patterns of alleles in patch vs. splice re...

show abstract

“…[17][18][19][20][21][22]27,32,23 The ␤␤␣-metal binding motif is characterized by one ␣-helix and an antiparallel ␤-sheet, which are separated from each other by a variable length of intervening sequences from 9 to 36. This motif usually binds to divalent metal ions like Zn or Mg.…”

Section: Results and Discussion The ␤␤␣-Metal Motifmentioning

confidence: 99%

“…Table II lists the top ranking hits of proteins and the corresponding structure-aligned sequences. We list only the representative proteins of the protein families, which are colicin E9 (ColE9), 34 the periplasmic nuclease Vvn, 22 the HNH homing endonuclease I-HmuI, 35 the His-Cys box endonuclease I-PpoI, 18 the endonucleases such as Serratia nuclease, 17 CAD/DFF40, 32 the T4 Endo VII, 20 and HIV integrase (IN). 36 The lengths of the intervening sequence between the two ␤-strands vary from 2 to 39.…”

Section: Results and Discussion The ␤␤␣-Metal Motifmentioning

confidence: 99%

“…The motif sequences are usually much less conserved than those of the first type, and the RMS distances of the motif residues from the consensus template are more widely distributed. Examples are the ␤␤␣-metal binding motif, [17][18][19][20][21][22][23] the treble clef finger motif, 24 and the helix-turn-helix motif. 25 Figure 1 shows a typical ␤␤␣-metal binding motif.…”

Section: Introductionmentioning

confidence: 99%

See 1 more Smart Citation

The fragment transformation method to detect the protein structural motifs

Lin

Chen

et al. 2006

Proteins

View full text Add to dashboard Cite

To identify functional structural motifs from protein structures of unknown function becomes increasingly important in recent years due to the progress of the structural genomics initiatives. Although certain structural patterns such as the Asp-His-Ser catalytic triad are easy to detect because of their conserved residues and stringently constrained geometry, it is usually more challenging to detect a general structural motifs like, for example, the ␤␤␣-metal binding motif, which has a much more variable conformation and sequence. At present, the identification of these motifs usually relies on manual procedures based on different structure and sequence analysis tools. In this study, we develop a structural alignment algorithm combining both structural and sequence information to identify the local structure motifs. We applied our method to the following examples: the ␤␤␣-metal binding motif and the treble clef motif. The ␤␤␣-metal binding motif plays an important role in nonspecific DNA interactions and cleavage in host defense and apoptosis. The treble clef motif is a zinc-binding motif adaptable to diverse functions such as the binding of nucleic acid and hydrolysis of phosphodiester bonds. Our results are encouraging, indicating that we can effectively identify these structural motifs in an automatic fashion. Our method may provide a useful means for automatic functional annotation through detecting structural motifs associated with particular functions. Proteins 2006;63:636 -643.

show abstract

X-ray structure of T4 endonuclease VII: a DNA junction resolvase with a novel fold and unusual domain-swapped dimer architecture

Cited by 127 publications

References 53 publications

Structure of Hjc, a Holliday junction resolvase, from Sulfolobus solfataricus

Structure of Hjc, a Holliday junction resolvase, from Sulfolobus solfataricus

Two recombination-dependent DNA replication pathways of bacteriophage T4, and their roles in mutagenesis and horizontal gene transfer

The fragment transformation method to detect the protein structural motifs

Contact Info

Product

Resources

About