Citations in PubMed

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PDB ID Mentions in PubMed Central Article count: 10

Citations in PubMed

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PDB ID Mentions in PubMed Central

Data mentions are occurrences of PDB IDs in the full text articles from the PubMedCentral Open Access Subset of currently about 1 million articles. For each article, the sentences containing the PDB ID are listed. Article titles can be filtered by keywords and sorted by year.

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Synapsis and catalysis by activated Tn3 resolvase mutants.

(2008) Nucleic Acids Res 36

PubMed: 19015124 | PubMedCentral: PMC2602789 | DOI: 10.1093/nar/gkn885

( B ) Crystal structure of a synaptic tetramer of γδ resolvase with two cleaved site Is [1ZR4; ( 16 )], and on the right the orange resolvase subunit in the same orientation, showing r... sidues in spacefill as in (A), except that the following residues are mutant; A2, K56, S101, Y102, I103, Q124.

The structures of the site I synaptic intermediates [1ZR2, 1ZR4, 2GM4; ( 16 , 17 )] and of an activated variant catalytic domain without DNA [2GM5; ( 17 )] contain a tetrameric arrangement of the catalytic domains which is not found in any of the structures of wild-type resolvase [2RSL, 1GDR, 1GDT; ( 6 , 8 , 9 , 11 )] ( Figure 2 B).

Publication Year: 2008

The Hin recombinase assembles a tetrameric protein swivel that exchanges DNA strands.

(2009) Nucleic Acids Res 37

PubMed: 19515933 | PubMedCentral: PMC2724282 | DOI: 10.1093/nar/gkp466

An asymmetric tetramer structure of the catalytic domain of γδ resolvase has also been reported (PDB code 2GM5) in which one synapsed pair of subunits is in an alternative conformation... from that of the DNA bound tetramers in 1ZR4/2GM4 ( 11 ).

Tetrameric Hin models bound to a cleaved synaptic complex were derived from the crystal structures of resolvase (PDB code 1ZR4) and of a resolvase-Hin chimera (PDB code 2GM4) in which Hin residues 96–105 were substituted in place of resolvase ( 10 , 11 ).

MATERIALS AND METHODS Molecular models of Hin Hin closed tetramer conformation models were generated based on the γδ resolvase tetramer X-ray structures 2GM4 (3.5 Å) and 1ZR4 (3.4 Å) ( 10 , 11 ).

Model tetramers were generated by superimposing (LSQMAN) the DNA bound subunits onto the respective 2GM4 and 1ZR4 tetramers.

The final tetramer models of 2GM4 and 1ZR4 have no residues in the generously allowed or disallowed regions of the Ramachandran plot.

The Hin subunit models were docked onto DNA by aligning with the respective 2GM4 (chain B) and 1ZR4 (chain A) template structures using LSQMAN.

Alignment of backbone atoms of the 1ZR4 Hin model and resolvase tetramer give an overall RMSD of 3.1 Å and an RMSD of 0.8–1.1 Å over respective peptide chains from residues 1–134.

PDB derived from the 1ZR4 γδ resolvase tetramer) secondary structure elements (β strands, black arrows; α-helices, grey rectangles) are denoted above and below the resolvase and Hin sequences, respectively.

Publication Year: 2009

Regulatory mutations in Sin recombinase support a structure-based model of the synaptosome.

(2009) Mol Microbiol 74

PubMed: 19508283 | PubMedCentral: PMC2764113 | DOI: 10.1111/j.1365-2958.2009.06756.x

This model is based on the crystal structure of the γδ resolvase site I synaptic tetramer (pdb: 1ZR4): residues 1–119 of each subunit in the γδ resolvase tetram... r were replaced by segments of the Sin crystal structure (2R0Q, chain D).

, 2008 ), γδ resolvase (pdb: 1ZR4; Li et al .

Publication Year: 2009

The catalytic residues of Tn3 resolvase.

(2009) Nucleic Acids Res 37

PubMed: 19789272 | PubMedCentral: PMC2794168 | DOI: 10.1093/nar/gkp797

The second and third columns give the distance (Å) of the sidechain functional groups (nearest non-hydrogen atom) from the phosphorus atom of the scissile phosphate, in the two structures show... in Figure 2 B; the γδ resolvase dimer-site I structure 1GDT and the cleaved intermediate structure 1ZR4.

The E118 sidechains have moved apart in the structures of cleaved intermediates, e.g. 1ZR4, and are quite far from the scissile phosphates in all the structures, but they might be much closer to the DNA immediately prior to cleavage, and thus might have an accessory role in catalysis.

Right; crystal structure of a synaptic tetramer of a γδ resolvase activated mutant with two cleaved site Is [1ZR4 ( 22 ); smaller scale].

Structure analysis The following crystal structures which include serine recombinase catalytic domains are available: wild-type γδ resolvase [two structures, 2RSL and 1GDR, containing four structurally distinct subunits; ( 25–27 )]; a wild-type γδ resolvase dimer bound to site I DNA [1GDT; two distinct subunits; ( 24 )]; an activated mutant γδ resolvase N-terminal domain tetramer [2GM5; four distinct subunits; ( 23 )]; γδ resolvase mutants in synaptic complexes with cleaved site I DNA [three structures, with six distinct subunit forms; 1ZR2, 1ZR4 and 2GM4; ( 22 , 23 )]; a dimer of Sin recombinase bound to DNA [2R0Q; two distinct subunits ( 37 )]; the catalytic domain of TP901 integrase [3BVP; two distinct subunits ( 38 )]; the catalytic domain of a Clostridium recombinase [3G13; two distinct subunits ( 39 )]; and the catalytic domain of a Streptococcus recombinase [3GUV; one subunit ( 40 )].

Publication Year: 2009

Zinc-finger recombinase activities in vitro.

(2011) Nucleic Acids Res 39

PubMed: 21849325 | PubMedCentral: PMC3241657 | DOI: 10.1093/nar/gkr652

Molecular modelling Models of ZFRs bound to Z-sites with different core sequence lengths were built in PyMol ( 23 ) using crystal structures of a γδ resolvase dimer–DNA complex... [1GDT; ( 24 )], a synaptic γδ resolvase–DNA intermediate [1ZR4; ( 25 )] and a Zif268 zinc-finger domain–DNA complex [1AAY; ( 26 )].

The right panel shows a ZFR synaptic tetramer, built from four copies of 1AAY and the resolvase synaptic complex structure 1ZR4.

Publication Year: 2011

Crystal structure of an intermediate of rotating dimers within the synaptic tetramer of the G-segment invertase.

(2013) Nucleic Acids Res 41

PubMed: 23275567 | PubMedCentral: PMC3575834 | DOI: 10.1093/nar/gks1303

Generation of Gin homology model The amino acid sequence of Gin, accession number AAF01129, was provided to the EXPASY server and the SWISS-MODEL ( 36 ) tool for construction of homology models of Gin... using the synaptic structure of γδ resolvase (1ZR4) ( 8 ) or that of the Site I Dimer (1GDT) ( 15 ) as the template.

Publication Year: 2013

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