PDBsum entry: 1gdt

DNA binding protein/DNA

PDB-id

1gdt

	Biological unit* = asymmetric unit, as shown (as deduced by PQS*)


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DNA/RNA

Waters ×29

* Residue conservation analysis

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PDB id:

1gdt

Name:

DNA binding protein/DNA

Title:

Crystal structure of a site-specific recombinase, gamma- delta resolvase complexed with a 34 bp cleavage site

Structure:

Site i of res DNA. Chain: c. Synonym: crossover site or cleavage site. Engineered: yes. Site i of res DNA. Chain: d, f. Synonym: crossover site or cleavage site. Engineered: yes. Site i of res DNA.

Source:

Synthetic: yes. Escherichia coli. Organism_taxid: 562. Strain: strains that contain f episome. Gene: tnpr. Expressed in: escherichia coli. Expression_system_taxid: 562.

Biological unit:

Hexamer (from PQS)

UniProt:

Chains A, B: P03012 (TNR1_ECOLI)

Seq:

183 a.a.

Struc:

183 a.a.

Key:		PfamA domain
		Secondary structure			CATH domain

Resolution:

3.00Å

R-factor:

0.235

Authors:

W.Yang,T.A.Steitz

Key ref:

W.Yang and T.A.Steitz (1995). Crystal structure of the site-specific recombinase gamma delta resolvase complexed with a 34 bp cleavage site.. Cell, 82, 193-207. [PubMed id: 7628011] [DOI: 10.1016/0092-8674(95)90307-0]

Date:

11-Apr-95

Release date:

03-Apr-96

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Key reference

DOI no: 10.1016/0092-8674(95)90307-0 Cell 82:193-207 (1995)

PubMed id: 7628011

Crystal structure of the site-specific recombinase gamma delta resolvase complexed with a 34 bp cleavage site.

W.Yang, T.A.Steitz.

ABSTRACT

The structure of gamma delta resolvase complexed with a 34 bp substrate DNA has been determined at 3.0 A resolution. The DNA is sharply bent by 60 degrees toward the major groove and away from the resolvase catalytic domains at the recombination crossover point. The C-terminal one third of resolvase, which was disordered in the absence of DNA, forms an arm and a 3-helix DNA-binding domain on the opposite side of the DNA from the N-terminal domain. The arms wrap around the minor groove of the central 16 bp, and the DNA-binding domains interact with the major grooves near the outer boundaries of the binding site. The resolvase dimer is asymmetric, particularly in the arm region, implying a conformational adaptability that may be important for resolvase binding to different DNA sites in the synaptosome. It also raises the possibility of a sequential single-strand cleavage mechanism.

Literature references that cite this PDB file's key reference

PubMed id Reference

19002165 A.Keravala, S.Lee, B.Thyagarajan, E.C.Olivares, V.E.Gabrovsky, L.E.Woodard, and M.P.Calos (2009).
Mutational derivatives of PhiC31 integrase with increased efficiency and specificity.

Mol Ther, 17, 112-120.

19515935 A.R.McEwan, P.A.Rowley, and M.C.Smith (2009).
DNA binding and synapsis by the large C-terminal domain of phiC31 integrase.

Nucleic Acids Res, 37, 4764-4773.

19139398 C.Li, and C.D.Lu (2009).
Arginine racemization by coupled catabolic and anabolic dehydrogenases.

Proc Natl Acad Sci U S A, 106, 906-911.

19789272 F.J.Olorunniji, and W.M.Stark (2009).
The catalytic residues of Tn3 resolvase.

Nucleic Acids Res, 37, 7590-7602.

19515933 G.Dhar, M.M.McLean, J.K.Heiss, and R.C.Johnson (2009).
The Hin recombinase assembles a tetrameric protein swivel that exchanges DNA strands.

Nucleic Acids Res, 37, 4743-4756.

19282480 R.M.Gordley, C.A.Gersbach, and C.F.Barbas (2009).
Synthesis of programmable integrases.

Proc Natl Acad Sci U S A, 106, 5053-5058.

19508283 S.J.Rowland, M.R.Boocock, A.L.McPherson, K.W.Mouw, P.A.Rice, and W.M.Stark (2009).
Regulatory mutations in Sin recombinase support a structure-based model of the synaptosome.

Mol Microbiol, 74, 282-298.

19015124 F.J.Olorunniji, J.He, S.V.Wenwieser, M.R.Boocock, and W.M.Stark (2008).
Synapsis and catalysis by activated Tn3 resolvase mutants.

Nucleic Acids Res, 36, 7181-7191.

18694512 J.H.Keith, C.A.Schaeper, T.S.Fraser, and M.J.Fraser (2008).
Mutational analysis of highly conserved aspartate residues essential to the catalytic core of the piggyBac transposase.

BMC Mol Biol, 9, 73.

18439894 K.W.Mouw, S.J.Rowland, M.M.Gajjar, M.R.Boocock, W.M.Stark, and P.A.Rice (2008).
Architecture of a serine recombinase-DNA regulatory complex.

Mol Cell, 30, 145-155.

PDB code: 2r0q

18834537 L.M.Iyer, S.Abhiman, and L.Aravind (2008).
A new family of polymerases related to superfamily A DNA polymerases and T7-like DNA-dependent RNA polymerases.

Biol Direct, 3, 39.

18689469 L.Zhang, X.Ou, G.Zhao, and X.Ding (2008).
Highly efficient in vitro site-specific recombination system based on streptomyces phage phiBT1 integrase.

J Bacteriol, 190, 6392-6397.

18689475 P.A.Rowley, and M.C.Smith (2008).
Role of the N-terminal domain of phiC31 integrase in attB-attP synapsis.

J Bacteriol, 190, 6918-6921.

17595300 G.Lerman, and B.E.Shakhnovich (2007).
Defining functional distance using manifold embeddings of gene ontology annotations.

Proc Natl Acad Sci U S A, 104, 11334-11339.

17478521 M.Gupta, R.Till, and M.C.Smith (2007).
Sequences in attB that affect the ability of phiC31 integrase to synapse and to activate DNA cleavage.

Nucleic Acids Res, 35, 3407-3419.

17098894 M.Han, M.Yagura, and T.Itoh (2007).
Specific interaction between the initiator protein (Rep) and origin of plasmid ColE2-P9.

J Bacteriol, 189, 1061-1071.

16740123 A.Bhardwaj, K.Welfle, R.Misselwitz, S.Ayora, J.C.Alonso, and H.Welfle (2006).
Conformation and stability of the Streptococcus pyogenes pSM19035-encoded site-specific beta recombinase, and identification of a folding intermediate.

Biol Chem, 387, 525-533.

16756503 N.D.Grindley, K.L.Whiteson, and P.A.Rice (2006).
Mechanisms of site-specific recombination.

Annu Rev Biochem, 75, 567-605.

16553879 S.J.Rowland, M.R.Boocock, and W.M.Stark (2006).
DNA bending in the Sin recombination synapse: functional replacement of HU by IHF.

Mol Microbiol, 59, 1730-1743.

16807292 S.Kamtekar, R.S.Ho, M.J.Cocco, W.Li, S.V.Wenwieser, M.R.Boocock, N.D.Grindley, and T.A.Steitz (2006).
Implications of structures of synaptic tetramers of gamma delta resolvase for the mechanism of recombination.

Proc Natl Acad Sci U S A, 103, 10642-10647.

PDB codes: 2gm4 2gm5

16629663 V.Adams, I.S.Lucet, F.E.Tynan, M.Chiarezza, P.M.Howarth, J.Kim, J.Rossjohn, D.Lyras, and J.I.Rood (2006).
Two distinct regions of the large serine recombinase TnpX are required for DNA binding and biological function.

Mol Microbiol, 60, 591-601.

15768032 D.L.Daniels, and W.I.Weis (2005).
Beta-catenin directly displaces Groucho/TLE repressors from Tcf/Lef in Wnt-mediated transcription activation.

Nat Struct Mol Biol, 12, 364-371.

15542858 I.S.Lucet, F.E.Tynan, V.Adams, J.Rossjohn, D.Lyras, and J.I.Rood (2005).
Identification of the structural and functional domains of the large serine recombinase TnpX from Clostridium perfringens.

J Biol Chem, 280, 2503-2511.

15822102 J.L.Jiménez (2005).
Does structural and chemical divergence play a role in precluding undesirable protein interactions?

Proteins, 59, 757-764.

15980165 M.Nöllmann, O.Byron, and W.M.Stark (2005).
Behavior of Tn3 resolvase in solution and its interaction with res.

Biophys J, 89, 1920-1931.

16077726 P.A.Rice (2005).
Resolving integral questions in site-specific recombination.

Nat Struct Mol Biol, 12, 641-643.

15813731 S.J.Rowland, M.R.Boocock, and W.M.Stark (2005).
Regulation of Sin recombinase by accessory proteins.

Mol Microbiol, 56, 371-382.

15994378 W.Li, S.Kamtekar, Y.Xiong, G.J.Sarkis, N.D.Grindley, and T.A.Steitz (2005).
Structure of a synaptic gammadelta resolvase tetramer covalently linked to two cleaved DNAs.

Science, 309, 1210-1215.

PDB codes: 1zr2 1zr4

14763971 M.E.Burke, P.H.Arnold, J.He, S.V.Wenwieser, S.J.Rowland, M.R.Boocock, and W.M.Stark (2004).
Activating mutations of Tn3 resolvase marking interfaces important in recombination catalysis and its regulation.

Mol Microbiol, 51, 937-948.

15306021 V.Adams, I.S.Lucet, D.Lyras, and J.I.Rood (2004).
DNA binding properties of TnpX indicate that different synapses are formed in the excision and integration of the Tn4451 family.

Mol Microbiol, 53, 1195-1207.

12837939 A.Akopian, J.He, M.R.Boocock, and W.M.Stark (2003).
Chimeric recombinases with designed DNA sequence recognition.

Proc Natl Acad Sci U S A, 100, 8688-8691.

11809893 A.Das, C.Mandal, A.Dasgupta, T.Sengupta, and H.K.Majumder (2002).
An insight into the active site of a type I DNA topoisomerase from the kinetoplastid protozoan Leishmania donovani.

Nucleic Acids Res, 30, 794-802.

PDB code: 1juw

12228710 H.Yang, P.D.Jeffrey, J.Miller, E.Kinnucan, Y.Sun, N.H.Thoma, N.Zheng, P.L.Chen, W.H.Lee, and N.P.Pavletich (2002).
BRCA2 function in DNA binding and recombination from a BRCA2-DSS1-ssDNA structure.

Science, 297, 1837-1848.

PDB codes: 1iyj 1miu 1mje

11972771 M.C.Smith, and H.M.Thorpe (2002).
Diversity in the serine recombinases.

Mol Microbiol, 44, 299-307.

11994145 S.J.Rowland, W.M.Stark, and M.R.Boocock (2002).
Sin recombinase from Staphylococcus aureus: synaptic complex architecture and transposon targeting.

Mol Microbiol, 44, 607-619.

11847127 T.K.Chiu, C.Sohn, R.E.Dickerson, and R.C.Johnson (2002).
Testing water-mediated DNA recognition by the Hin recombinase.

EMBO J, 21, 801-814.

PDB codes: 1ijw 1jj6 1jj8 1jko 1jkp 1jkq 1jkr

12198117 U.Narendra, L.Zhu, B.Li, J.Wilken, and M.A.Weiss (2002).
Sex-specific gene regulation. The Doublesex DM motif is a bipartite DNA-binding domain.

J Biol Chem, 277, 43463-43473.

11812835 C.R.Sclimenti, B.Thyagarajan, and M.P.Calos (2001).
Directed evolution of a recombinase for improved genomic integration at a native human sequence.

Nucleic Acids Res, 29, 5044-5051.

11114897 O.Z.Nanassy, and K.T.Hughes (2001).
Hin recombinase mutants functionally disrupted in interactions with Fis.

J Bacteriol, 183, 28-35.

11069650 H.M.Thorpe, S.E.Wilson, and M.C.Smith (2000).
Control of directionality in the site-specific recombination system of the Streptomyces phage phiC31.

Mol Microbiol, 38, 232-241.

10898790 L.Zhu, J.Wilken, N.B.Phillips, U.Narendra, G.Chan, S.M.Stratton, S.B.Kent, and M.A.Weiss (2000).
Sexual dimorphism in diverse metazoans is regulated by a novel class of intertwined zinc fingers.

Genes Dev, 14, 1750-1764.

PDB code: 1lpv

11104519 N.M.Luscombe, S.E.Austin, H.M.Berman, and J.M.Thornton (2000).
An overview of the structures of protein-DNA complexes.

Genome Biol, 1, REVIEWS001.

10026283 K.Nadassy, S.J.Wodak, and J.Janin (1999).
Structural features of protein-nucleic acid recognition sites.

Biochemistry, 38, 1999-2017.

10493576 M.Young, K.Kirshenbaum, K.A.Dill, and S.Highsmith (1999).
Predicting conformational switches in proteins.

Protein Sci, 8, 1752-1764.

10064606 P.H.Arnold, D.G.Blake, N.D.Grindley, M.R.Boocock, and W.M.Stark (1999).
Mutants of Tn3 resolvase which do not require accessory binding sites for recombination activity.

EMBO J, 18, 1407-1414.

10585967 P.Hindmarsh, and J.Leis (1999).
Retroviral DNA integration.

Microbiol Mol Biol Rev, 63, 836.

10476039 S.Minakhina, G.Kholodii, S.Mindlin, O.Yurieva, and V.Nikiforov (1999).
Tn5053 family transposons are res site hunters sensing plasmidal res sites occupied by cognate resolvases.

Mol Microbiol, 33, 1059-1068.

10690407 T.Komano (1999).
Shufflons: multiple inversion systems and integrons.

Annu Rev Genet, 33, 171-191.

9663657 C.C.Liu, R.Hühne, J.Tu, E.Lorbach, and P.Dröge (1998).
The resolvase encoded by Xanthomonas campestris transposable element ISXc5 constitutes a new subfamily closely related to DNA invertases.

Genes Cells, 3, 221-233.

9705513 C.E.Peña, J.M.Kahlenberg, and G.F.Hatfull (1998).
The role of supercoiling in mycobacteriophage L5 integrative recombination.

Nucleic Acids Res, 26, 4012-4018.

9600906 D.M.Tanenbaum, Y.Wang, S.P.Williams, and P.B.Sigler (1998).
Crystallographic comparison of the estrogen and progesterone receptor's ligand binding domains.

Proc Natl Acad Sci U S A, 95, 5998-6003.

PDB code: 1a52

9576912 H.M.Thorpe, and M.C.Smith (1998).
In vitro site-specific integration of bacteriophage DNA catalyzed by a recombinase of the resolvase/invertase family.

Proc Natl Acad Sci U S A, 95, 5505-5510.

9722507 M.Hartung, and B.Kisters-Woike (1998).
Cre mutants with altered DNA binding properties.

J Biol Chem, 273, 22884-22891.

9774480 M.Lehmann, T.Siegmund, K.G.Lintermann, and G.Korge (1998).
The pipsqueak protein of Drosophila melanogaster binds to GAGA sequences through a novel DNA-binding domain.

J Biol Chem, 273, 28504-28509.

9691026 O.Z.Nanassy, and K.T.Hughes (1998).
In vivo identification of intermediate stages of the DNA inversion reaction catalyzed by the Salmonella Hin recombinase.

Genetics, 149, 1649-1663.

9518483 R.E.Dickerson (1998).
DNA bending: the prevalence of kinkiness and the virtues of normality.

Nucleic Acids Res, 26, 1906-1926.

9732277 S.K.Merickel, M.J.Haykinson, and R.C.Johnson (1998).
Communication between Hin recombinase and Fis regulatory subunits during coordinate activation of Hin-catalyzed site-specific DNA inversion.

Genes Dev, 12, 2803-2816.

9759484 S.Verma, and F.Eckstein (1998).
Modified oligonucleotides: synthesis and strategy for users.

Annu Rev Biochem, 67, 99.

9578550 T.S.Heuer, and P.O.Brown (1998).
Photo-cross-linking studies suggest a model for the architecture of an active human immunodeficiency virus type 1 integrase-DNA complex.

Biochemistry, 37, 6667-6678.

9187646 A.Mondragón (1997).
Solving the cis/trans paradox in the Int family of recombinases.

Nat Struct Biol, 4, 427-429.

9348666 B.Hallet, and D.J.Sherratt (1997).
Transposition and site-specific recombination: adapting DNA cut-and-paste mechanisms to a variety of genetic rearrangements.

FEMS Microbiol Rev, 21, 157-178.

9194184 B.Pan, Z.Deng, D.Liu, S.Ghosh, and G.P.Mullen (1997).
Secondary and tertiary structural changes in gamma delta resolvase: comparison of the wild-type enzyme, the I110R mutant, and the C-terminal DNA binding domain in solution.

Protein Sci, 6, 1237-1247.

9082984 H.J.Kwon, R.Tirumalai, A.Landy, and T.Ellenberger (1997).
Flexibility in DNA recombination: structure of the lambda integrase catalytic core.

Science, 276, 126-131.

PDB code: 1ae9

9214634 K.Myung, D.M.He, S.E.Lee, and E.A.Hendrickson (1997).
KARP-1: a novel leucine zipper protein expressed from the Ku86 autoantigen locus is implicated in the control of DNA-dependent protein kinase activity.

EMBO J, 16, 3172-3184.

9228950 M.Cai, R.Zheng, M.Caffrey, R.Craigie, G.M.Clore, and A.M.Gronenborn (1997).
Solution structure of the N-terminal zinc binding domain of HIV-1 integrase.

Nat Struct Biol, 4, 567-577.

PDB codes: 1wja 1wjb 1wjc 1wjd

9242914 N.L.Craig (1997).
Target site selection in transposition.

Annu Rev Biochem, 66, 437-474.

9336450 P.J.Artymiuk, T.A.Ceska, D.Suck, and J.R.Sayers (1997).
Prokaryotic 5'-3' exonucleases share a common core structure with gamma-delta resolvase.

Nucleic Acids Res, 25, 4224-4229.

9782776 R.E.Dickerson, and T.K.Chiu (1997).
Helix bending as a factor in protein/DNA recognition.

Biopolymers, 44, 361-403.

8759784 J.C.Alonso, S.Ayora, I.Canosa, F.Weise, and F.Rojo (1996).
Site-specific recombination in gram-positive theta-replicating plasmids.

FEMS Microbiol Lett, 142, 1.

8702660 M.D.Andrake, and A.M.Skalka (1996).
Retroviral integrase, putting the pieces together.

J Biol Chem, 271, 19633-19636.

8557624 S.Cal, and B.A.Connolly (1996).
The EcoRV modification methylase causes considerable bending of DNA upon binding to its recognition sequence GATATC.

J Biol Chem, 271, 1008-1015.

8599941 Z.Wang, and P.Dröge (1996).
Differential control of transcription-induced and overall DNA supercoiling by eukaryotic topoisomerases in vitro.

EMBO J, 15, 581-589.

7588641 M.R.Boocock, X.Zhu, and N.D.Grindley (1995).
Catalytic residues of gamma delta resolvase act in cis.

EMBO J, 14, 5129-5140.

7552718 R.Craigie (1995).
Resolving a resolvase.

Nat Struct Biol, 2, 607-609.

The most recent references are shown first. Citation data come partly from CiteXplore and partly from an automated harvesting procedure. Note that this is likely to be only a partial list as not all journals are covered by either method. However, we are continually building up the citation data so more and more references will be included with time. Where a reference describes a PDB structure, the PDB code is shown on the right.