Citations in PubMed

Primary Citation PubMed: 7628011 Citations in PubMed

PDB ID Mentions in PubMed Central Article count: 22

Citations in PubMed

This linkout lists citations, indexed by PubMed, to the Primary Citation for this PDB ID.

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.

  • 3 per page
  • 5 per page
  • 10 per page
  • view all
  • Publication Year
  • Ascending
  • Descending

An overview of the structures of protein-DNA complexes.

(2000) Genome Biol 1

PubMed: 11104519 | PubMedCentral: PMC138832 | DOI: 10.1186/gb-2000-1-1-reviews001

Five enzymes also qualify on structural grounds for the HTH and other α helix groups: restriction endonuclease Fok I (PDB entry 1fok), γδ-resolvase (1gdt), Hin recombinase (1hc... ), Tc3 transposase (1tc3) and Cre recombinase (1crx).

Publication Year: 2000


Architecture of a serine recombinase-DNA regulatory complex.

(2008) Mol Cell 30

PubMed: 18439894 | PubMedCentral: PMC2428073 | DOI: 10.1016/j.molcel.2008.02.023

An initial model was constructed with selected secondary structural elements from the γδ resolvase-site I dimer structure (1GDT), and the register of the DNA was assigned by using the ... eavy atom positions.

Publication Year: 2008


Insights into protein-DNA interactions through structure network analysis.

(2008) PLoS Comput Biol 4

PubMed: 18773096 | PubMedCentral: PMC2518215 | DOI: 10.1371/journal.pcbi.1000170

Class 1 Class 2 Class 3 Class 4 Class 5 Class 6 Class 7 P-p clusters only P-S clusters only P-B clusters only P-p and P-S clusters (no P-B clusters) P-S and P-B clusters (no P-p clusters) P-p and P-B ... lusters (no P-S clusters) P-p, P-S, and P-B clusters are present Overlapping clusters Non-overlapping clusters Overlapping clusters Non-overlapping clusters Overlapping clusters Non-overlapping clusters Overlapping P-p, P-B, and P-S clusters Non-overlapping P-p, P-B, and P-S clusters P-p and P-S clusters overlap but not P-B clusters P-S and P-B clusters overlap but not P-p clusters P-p and P-B clusters overlap but not P-S clusters P-P, P-B and P-S clusters occur separately β-Hairpin β-Hairpin Zinc coordinating group Enzymes β-Hairpin β-Hairpin Other α-helices Others Helix turn helix – β-Hairpin β-Sheet Enzymes β-Hairpin 1cma- a 1azp- 1zaa- 1a31- 1ecr- 1bnz- 1ckt- 1ramA 1apl- 1bdt- 1d3u- 1bss- 1ihf- a Enzymes 1bf4- 1a35- 1xbr- a β-Sheet 1vkx- 1lli- Enzymes 1tgh- 1ipp- β-Sheet 7ice- Enzymes 1bhm- a Enzymes 1c9bB Zipper type Others 1cyq- Enzymes Helix turn helix 1vol- Helix turn helix 2dnj- 1dnk- 1bnk- 1cdw- 1an4- 1a3qA 1dctA 2bdp- 1tc3- Enzymes 3orc- 2rve- 1t7pA 1bpx- Enzymes 1hlo- a 1bf5-* 1rv5- 3ktq- 1a74- a Other α-helices 3bam- 1qss- 10mh- 1nfkA 4skn- Helix turn helix 1ssp- 1skn- Helix turn helix 1qsy- 1clq- Zinc coordinating group 5mht- 1fjl- a 1vas- Zipper type 6pax- 2bpf- 1pvi- a 1a1g- Helix turn helix Zinc coordinating group 3pvi- 1ysa- a Other α-helices 2ktq- 1tau- 1aay-* 1gdt- a 1cit- Helix turn helix 1b3t- a 2ssp- 2pvi- 1d66-* 1ignA a 1fok- Zinc coordinating group 4ktq- Other α-helices 1ubd-* 1rpe- 1hcr- a 1lat- Helix turn helix 1qrv- 1zme- 6cro- 1mnm- a 1akh- Zipper type Zinc coordinating group 1yrn- a 1hddC a 1an2- 2gli- a 3cro- a 1pdn- Zipper type Zinc coordinating group 3hddA 1a02- 1a6y- Other α-helices 1a0a- 1aoi- Zinc coordinating group 1glu- 1tsr- a 2nll- a These protein–DNA complexes are also present in DS3 (see Materials and Methods section).

Publication Year: 2008


Synapsis and catalysis by activated Tn3 resolvase mutants.

(2008) Nucleic Acids Res 36

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

( A ) Crystal structure of a wild-type γδ resolvase dimer bound to site I [1GDT; ( 11 )].

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


Small local variations in B-form DNA lead to a large variety of global geometries which can accommodate most DNA-binding protein motifs.

(2009) BMC Struct Biol 9

PubMed: 19393049 | PubMedCentral: PMC2687451 | DOI: 10.1186/1472-6807-9-24

Cfit Lfit Cfit/Lfit Value Position 1KX5 30 15.1 10.5 51.9 A 10 A 11 A 12 126.7 0.77 37.9 0.6 20.0 0.03 C 0.1 1J59 28 25.3 16.2 66.5 T 9 G 10 A 11 98.5 0.85 47.2 0.7 21.4 0.03 C -41.9 1RUN 28 30.4 17.1... 71.1 T 9 G 10 A 11 109.7 0.85 47.8 0.6 22.2 0.03 C -50.6 1CGP 26 19.1 18.9 65.9 G 7 T 8 G 9 72.4 0.86 48.2 0.8 17.9 0.04 C -51.1 1BL0 20 10.5 6.1 25.0 A 6 G 7 C 8 38.8 0.94 47.0 0.7 3.6 0.19 C -68.9 1HLV 19 10.0 7.6 30.1 G 15 G 16 G 17 39.3 0.95 54.6 0.6 3.3 0.18 C -129.0 1APL 18 11.8 7.3 33.0 A 16 C 17 G 18 3.7 0.99 NA 4.9 0.9 5.44 L NA 1K78 23 9.1 3.2 15.6 T 19 G 20 G 21 15.9 1.00 NA 2.4 1.0 2.40 L NA 4CRX 32 11.8 12.2 56.5 A 17 T 18 G 19 76.3 0.82 NA 3.4 9.1 0.37 U NA 1GDT 32 15.4 13.0 60.3 T 14 T 15 A 16 40.2 0.87 NA 1.6 14.5 0.11 U NA 1MNM 23 11.8 7.8 26.8 G 13 A 14 A 15 58.7 0.89 NA 1.7 5.4 0.31 U NA 1JE8 18 23.0 13.0 49.6 T 2 A 3 C 4 56.9 0.93 NA 1.1 5.0 0.22 U NA 1DDN 23 8.8 4.4 19.1 T 13 T 14 A 15 36.0 0.95 NA 7.7 2.5 3.08 U NA 1L3L 18 9.0 5.9 19.7 C 14 A 15 C 16 32.5 0.96 NA 1.5 1.6 0.94 U NA 1U78 23 10.6 12.3 51.1 T 10 A 11 G 12 41.3 0.97 NA 1.4 19.6 0.07 U NA 1Z9C 24 10.0 5.9 23.9 T 11 A 12 T 13 3.4 0.97 NA 6.1 2.0 3.05 U NA 1H88 23 7.4 4.5 16.8 C 8 A 9 A 10 12.3 0.98 NA 1.6 7.8 0.21 U NA 1D5Y 18 8.9 5.7 21.6 C 15 A 16 A 17 10.6 0.98 NA 2.6 2.0 1.30 U NA 1K61 18 8.8 6.1 22.3 T 4 A 5 A 6 6.6 0.99 NA 1.3 7.1 0.18 U NA 1DU0 18 6.3 4.0 15.2 C 15 C 16 T 17 10.1 0.99 NA 0.6 2.9 0.21 U NA 1RIO 25 14.8 8.7 34.1 C 8 C 9 G 10 16.1 0.99 NA 0.6 2.7 0.22 U NA 6PAX 22 11.8 7.1 25.6 A 8 C 9 G 10 20.4 0.99 NA 0.6 2.1 0.29 U NA 2HDD 18 10.7 5.4 23.3 T 12 C 13 C 14 22.9 0.99 NA 1.2 1.8 0.67 U NA 1HDD 18 10.9 4.1 19.9 G 3 C 4 C 5 1.9 0.99 NA 2.6 1.4 1.86 U NA 3HDD 18 6.5 3.7 14.4 G 8 T 9 A 10 8.3 0.99 NA 3.0 1.4 2.14 U NA 1JT0 26 10.4 5.9 22.1 A 23 T 24 A 25 29.8 0.99 NA 9.1 1.1 8.27 U NA 1F4K 19 7.9 5.1 20.2 T 3 G 4 A 5 24.8 1.00 NA 0.8 2.4 0.33 U NA 1MDM 23 9.2 4.7 20.8 A 6 G 7 A 8 15.6 1.00 NA 1.7 1.1 1.55 U NA 1HF0 20 10.5 7.3 30.7 T 6 G 7 A 8 28.6 1.01 NA 1.4 0.9 1.56 U NA The calculation of successive bending angles, end-to-end bending angle, d/l local , Radius of Curvature (ROC), RMSD for circle fit (Cfit) and line fit (Lfit) and torsion angle for out-of-plane component of bending have been described in the 'Methods' section.

In some of these structures (CRE recombinase protein (4CRX), γδ resolvase-DNA complex (1GDT)), bending appears to be a result of large kinks at one or two steps in the duplex, as is evident from the higher maximum bending angle values obtained for these structures.

Publication Year: 2009


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

The model for the Hin dimer [ Figure 2 B, panel (i)] based on the γδ resolvase dimer catalytic domain [PDB code 1GDT; ( 12 )] and C-terminal Hin DNA binding domain crystal structures [... esidues 139–190, PDB code 1IJW; ( 26 )] has been described previously ( 9 , 31 ).

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

The WT dimer is thought to bind in a similar ‘closed’ conformation at site I, as seen in the crystal structure of WT γδ resolvase bound at site I (pdb: 1GDT; Yang and S... eitz, 1995 ).

Publication Year: 2009


DNA-binding residues and binding mode prediction with binding-mechanism concerned models.

(2009) BMC Genomics 10 Suppl 3

PubMed: 19958487 | PubMedCentral: PMC2788376 | DOI: 10.1186/1471-2164-10-S3-S23

Table 5 Dataset of 253 TF-DNA complexes for DNA-binding residues prediction 253 TF-DNA Complexes 1A02:F 1A02:J 1A0A:A 1A0A:B 1A6Y:A 1A6Y:B 1AKH:A 1AKH:B 1AM9:A 1AM9:B 1AM9:C 1AM9:D 1AN2:A 1AN4:A 1AN4:... 1APL:C 1APL:D 1AU7:A 1AU7:B 1B01:A 1B01:B 1B72:B 1B8I:B 1BDT:A 1BDT:B 1BDT:C 1BDT:D 1BDV:A 1BDV:B 1BDV:C 1BDV:D 1BY4:A 1BY4:B 1BY4:C 1BY4:D 1C0W:A 1C0W:B 1C0W:C 1C0W:D 1CF7:A 1CF7:B 1CGP:A 1CGP:B 1CMA:A 1CMA:B 1CQT:A 1D5Y:A 1D5Y:B 1D5Y:C 1D5Y:D 1D66:A 1D66:B 1DDN:A 1DDN:B 1DDN:C 1DDN:D 1DSZ:A 1DSZ:B 1DU0:A 1DU0:B 1EA4:A 1EA4:B 1EA4:D 1EA4:E 1EA4:F 1EA4:G 1EA4:H 1EA4:J 1EA4:K 1EA4:L 1F2I:G 1F2I:H 1F2I:I 1F2I:J 1F2I:K 1F2I:L 1F5T:A 1F5T:B 1F5T:C 1F5T:D 1FJL:A 1FJL:B 1FJL:C 1FOS:E 1FOS:F 1FOS:G 1FOS:H 1G2D:C 1G2D:F 1G2F:C 1G2F:F 1GDT:A 1GDT:B 1H88:A 1H88:B 1H89:A 1H89:B 1H8A:A 1H8A:B 1H9T:A 1H9T:B 1HCQ:A 1HCQ:B 1HDD:C 1HDD:D 1HF0:A 1HF0:B 1HJB:A 1HJB:B 1HJB:D 1HJB:E 1HLO:A 1HLO:B 1HW2:A 1HW2:B 1HWT:C 1HWT:D 1HWT:G 1HWT:H 1IO4:A 1IO4:B 1JGG:A 1JGG:B 1JNM:A 1JNM:B 1JT0:A 1JT0:B 1JT0:C 1JT0:D 1JWL:A 1JWL:B 1K61:A 1K61:B 1K61:C 1K61:D 1KB2:A 1KB2:B 1KB4:A 1KB4:B 1KB6:A 1KB6:B 1KU7:A 1L3L:A 1L3L:B 1L3L:C 1L3L:D 1LAT:A 1LAT:B 1LB2:A 1LE8:A 1LE8:B 1LLI:A 1LLI:B 1LLM:C 1LMB:3 1LMB:4 1MDY:A 1MDY:C 1MDY:D 1MEY:C 1MEY:F 1MJM:A 1MJM:B 1MJP:A 1MJP:B 1MNM:C 1MNM:D 1NKP:A 1NKP:B 1NKP:D 1NKP:E 1NLW:A 1NLW:B 1NLW:D 1NLW:E 1P47:A 1P47:B 1PAR:A 1PAR:B 1PAR:C 1PAR:D 1PER:L 1PER:R 1PUF:A 1PUF:B 1PYI:A 1PYI:B 1QP9:A 1QP9:B 1QP9:C 1QP9:D 1R0N:A 1RPE:L 1RPE:R 1TF6:A 1TF6:D 1TRO:A 1TRO:C 1TRO:E 1TRO:G 1TRR:A 1TRR:B 1TRR:D 1TRR:E 1TRR:G 1TRR:H 1TRR:J 1TRR:K 1YRN:A 1YRN:B 1YSA:C 1YSA:D 1ZME:C 1ZME:D 2DRP:A 2DRP:D 2HAP:C 2HAP:D 2HDD:A 2HDD:B 2NLL:A 2NLL:B 2OR1:L 2OR1:R 2PRT:A 2QL2:A 2QL2:B 2QL2:C 2QL2:D 2R5Y:A 2R5Y:B 3BPY:A 3CBB:A 3CBB:B 3CO6:C 3COQ:A 3COQ:B 3D0A:A 3D0A:B 3D0A:C 3D0A:D 3DFX:A 3DFX:B 3DZY:A 3DZY:D 3E00:A 3E00:D 3EXJ:A 3EXJ:B 3EXL:A 3HDD:A 3HDD:B 9ANT:A Defining the DNA-binding residue Previous research used various distance cut-offs from 3.5 Å to 6 Å to define DNA-binding residues between proteins and DNA [ 6 - 10 , 14 , 40 , 42 ].

Publication Year: 2009


The catalytic residues of Tn3 resolvase.

(2009) Nucleic Acids Res 37

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

In the crystal structures, the carboxamide sidechain of Q19 is within H-bonding distance of the main-chain amino and carboxyl groups of R8, as well as the sidechain of another active site residue R68 ... in 1GDT), so its role might be structural, to orient the R8 and R68 residues appropriately in the active site.

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 )].

( B ) Left; crystal structure of a wild-type γδ resolvase dimer bound to site I [1GDT ( 24 )].

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 shown in Figure 2 B; the γδ resolvase dimer-site I structure 1GDT and the cleaved intermediate structure 1ZR4.

Publication Year: 2009


Precise targeted integration by a chimaeric transposase zinc-finger fusion protein.

(2010) Nucleic Acids Res 38

PubMed: 19965773 | PubMedCentral: PMC2831304 | DOI: 10.1093/nar/gkp1068

Linker L3 (inset rainbow cylinders; from PDB ID: 1GDT) would have to stretch 40 Å and 46 Å (dotted lines) from the predicted C-termini of ISY100 transposase (blue) to the N-terminus of... Zif268 (red sphere).

Publication Year: 2010


Identification of new homologs of PD-(D/E)XK nucleases by support vector machines trained on data derived from profile-profile alignments.

(2011) Nucleic Acids Res 39

PubMed: 20961958 | PubMedCentral: PMC3045609 | DOI: 10.1093/nar/gkq958

PD-(D/E)XK and HtH domains in DUF2887 proteins appear to be connected via a long α-helix, much like the arrangement of catalytic and HtH domains in γδ-resolvase [( 38 ); PDB id... 1gdt].

Publication Year: 2011


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 model is built from the resolvase–DNA structure 1GDT and two copies of the Zif268 domain–DNA structure 1AAY.

( A ) Crystal structure (1GDT) of a γδ resolvase dimer bound to DNA ( res site I).

( A ) Structure of the ‘arm’ region of resolvase (residues 120–148 are shown) bound to DNA (data are from the crystal structure 1GDT).

Publication Year: 2011


Re-visiting protein-centric two-tier classification of existing DNA-protein complexes.

(2012) BMC Bioinformatics 13

PubMed: 22800292 | PubMedCentral: PMC3472317 | DOI: 10.1186/1471-2105-13-165

Table 1 Representatives for previous families 54 existing families (Thornton classification) representatives were selected and were validated using Jack-knifing Group Families Representative(s) HTH &#... 000a0;     Cro & repressor 1LMB   Homeodomain 1FJL, 1HDD, 6PAX   LacI repressor 1WET   Endonuclease Fok1 1FOK   Gamma Delta resolvase 1GDT   Hin recombinase 1HCR   RAP1 family 1IGN   Prd paired domain 1PDN   Tc3 transposase 1TC3   Trp repressor 1TRR   Diptheria tox repressor 1DDN   Transcription factor IIB 1D3U   Interferon regulatory 2IRF   Catabolite gene activator protein 1RUO   Transcription factor 1CF7, 3HTS   Ets domain 1BC8 Zinc Co-ordinating       β-β-α zinc finger 1ZAA   Harmone Nuclear Receptor 2NLL   Loop sheet helix 1TSR   GAL4 type 1ZME Zipper type       Leucine Zipper 1YSA   Helix loop helix 1AN2 Other-α Helix       Pappilomavirus 1 E2 2BOP   Histone 1AOI   EBNA1 nuclear protein 1B3T   Skn-1 transcription factor 1SKN   Cre Recombinase 1CRX   High Mobility Group 1QRV   MADS box 1MNM β-Sheet       TATA box binding 1YTB β-Hairpin/Ribbon       MetJ repressor 1CMA   Tus replication terminator 1ECR   Integration host factor 1IHF   Transcription Factor T-domain 1XBR   Hyperthermophile DNA 1AZP   Arc repressor 1PAR Other       ReI homology 1SVC   Stat protein 1BF5 Enzyme       Methyltransferase 6MHT   Endonuclease PvuII 3PVI   Endonuclease ecorV 1RVA   Endonuclease ecorI 1QPS   Endonuclease BamHI 3BAM   Enonuclease V 1VAS   Dnase I 2DNJ   DNA mismatch endonuclease 1CW0   DNA polymerase β 1BPY   DNA Polymerase I 2BDP   DNA Polymerase T7 1T7P,1CLQ   HIV Reverse Transcriptase 2HMI   Uracil DNA glycosylase 1SSP   3-Methyladenine DNA glycosylase 1BNK   Homing endonuclease 1A73, 1BP7   TopoisomeraseI 1A31 For all the 59 selected representatives, PSI-BLAST profiles were again built against dummy database using the earlier profile creation parameters (as described in Methods).

Publication Year: 2012


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


A comprehensive approach to zinc-finger recombinase customization enables genomic targeting in human cells.

(2013) Nucleic Acids Res 41

PubMed: 23393187 | PubMedCentral: PMC3616721 | DOI: 10.1093/nar/gkt071

Model was generated from crystal structures of the γδ resolvase and Aart zinc-finger protein (PDB IDs: 1GDT and 2I13, respectively).

( E ) Interactions between the γδ resolvase dimer and DNA at (left) the dinucleotide core, (middle) positions 6, 5 and 4 and (right) positions 10, 9, 8 and 7 (PDB ID: 1GDT).

( B ) (Top) Structure of the γδ resolvase in complex with DNA (PDB ID: 1GDT).

Publication Year: 2013


Attachment site recognition and regulation of directionality by the serine integrases.

(2013) Nucleic Acids Res 41

PubMed: 23821671 | PubMedCentral: PMC3783163 | DOI: 10.1093/nar/gkt580

Models of synaptic complexes The full-length int– attP complex model was constructed by superposing base pairs 1–5 onto the corresponding base pairs in each half-site of the γ&... x003b4;-resolvase/ res site I complex (pdb 1GDT) and introduction of phosphodiester linkages at the crossover site.

Publication Year: 2013


Multiple interfaces between a serine recombinase and an enhancer control site-specific DNA inversion.

(2013) Elife 2

PubMed: 24151546 | PubMedCentral: PMC3798978 | DOI: 10.7554/eLife.01211

Yang W , Steitz TA , 1995 , Crystal structure of the site-specific recombinase gamma delta resolvase complexed with a 34 bp cleavage site , http://www.rcsb.org/pdb/explore/explore.do?structureId=1gdt ... Publicly available at RCSB Protein Data Bank.

Invertasome modeling Hin structural models of the DNA-bound dimers (based on PDB ID: 1GDT , Yang and Steitz, 1995 ), pre-cleaved tetramer (based on PDB ID: 3BVP , Yuan et al., 2008 ), and cleaved tetramer (based on PDB ID: 1ZR4 , Li et al., 2005 ) combined with the Hin DBD-DNA structure (PDB ID: 1IJW ) have been described previously ( Dhar et al., 2009a , 2009b ; Heiss et al., 2011 ).

Publication Year: 2013


Expanding the zinc-finger recombinase repertoire: directed evolution and mutational analysis of serine recombinase specificity determinants.

(2014) Nucleic Acids Res 42

PubMed: 24452803 | PubMedCentral: PMC3985619 | DOI: 10.1093/nar/gkt1389

( A ) (Top) Crystal structure of the γδ resolvase dimer bound to target DNA (PDB ID: 1GDT) ( 20 ).

Inert residues are shown in yellow (PDB ID: 1GDT) ( 20 ).

Publication Year: 2014


Enhancing the specificity of recombinase-mediated genome engineering through dimer interface redesign.

(2014) J Am Chem Soc 136

PubMed: 24611715 | PubMedCentral: PMC3985937 | DOI: 10.1021/ja4130059

Model shows the structure of an engineered ZFR, generated from the crystal structures of the γδ resolvase 46 and Aart zinc-finger protein 70 (PDB IDs: 1GDT and 2I13, respectively).

Publication Year: 2014


A proposed mechanism for IS607-family serine transposases.

(2013) Mob DNA 4

PubMed: 24195768 | PubMedCentral: PMC4058570 | DOI: 10.1186/1759-8753-4-24

(a) Inactive dimer: WT γδ resolvase dimer bound to its cognate crossover site (PDBid 1gdt) [ 26 ].

Publication Year: 2013


PubMed ID is not available.

Published in 2014

PubMedCentral: PMC4139171

(A) (Top) Three-dimensional model of the ZFR dimer (blue and orange) in complex with DNA (gray), adapted from Gaj et al. 60 (PDB IDs: 1GDT and 2I13, respectively).

Publication Year: 2014


PubMed ID is not available.

Published in 2015

PubMedCentral: PMC4513852

Left, Hin dimer- hixL structure modeled from the γδ resolvase catalytic domain and helix E (PDB: 1GDT) and Hin DNA binding domain (PDB: 1IJW).

(B) Hin dimer model (based on PDB: 1GDT), (C) Hin tetramer model (based on PDB: 1ZR4), (D) resolvase dimer (PDB: 1GDT), (E) γδ resolvase tetramer (PDB: 1ZR4), (F) Gin tetramer (PDB: 3UJ3) and (G) TP901 integrase tetramer intermediate PDB: 3BVP).

Publication Year: 2015