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PDBsum entry 1en7

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protein metals Protein-protein interface(s) links
Hydrolase PDB id
1en7
Jmol
Contents
Protein chains
157 a.a. *
Metals
_CA ×3
_ZN ×2
Waters ×73
* Residue conservation analysis
PDB id:
1en7
Name: Hydrolase
Title: Endonuclease vii (endovii) from phage t4
Structure: Recombination endonuclease vii. Chain: a, b. Synonym: protein gp49. Engineered: yes. Other_details: one zn bound to cys 23,26,58,61 of each chain ca liganded to asp40 and asn 62
Source: Enterobacteria phage t4. Organism_taxid: 10665. Gene: gp49. Expressed in: escherichia coli bl21. Expression_system_taxid: 511693.
Biol. unit: Dimer (from PQS)
Resolution:
2.40Å     R-factor:   0.239     R-free:   0.308
Authors: H.Raaijmakers,O.Vix,I.Toro,D.Suck
Key ref:
H.Raaijmakers et al. (1999). X-ray structure of T4 endonuclease VII: a DNA junction resolvase with a novel fold and unusual domain-swapped dimer architecture. EMBO J, 18, 1447-1458. PubMed id: 10075917 DOI: 10.1093/emboj/18.6.1447
Date:
07-Feb-99     Release date:   07-Feb-00    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chains
Pfam   ArchSchema ?
P13340  (END7_BPT4) -  Recombination endonuclease VII
Seq:
Struc:
157 a.a.
157 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Gene Ontology (GO) functional annotation 
  GO annot!
  Biological process     metabolic process   2 terms 
  Biochemical function     hydrolase activity     4 terms  

 

 
DOI no: 10.1093/emboj/18.6.1447 EMBO J 18:1447-1458 (1999)
PubMed id: 10075917  
 
 
X-ray structure of T4 endonuclease VII: a DNA junction resolvase with a novel fold and unusual domain-swapped dimer architecture.
H.Raaijmakers, O.Vix, I.Törõ, S.Golz, B.Kemper, D.Suck.
 
  ABSTRACT  
 
Phage T4 endonuclease VII (Endo VII), the first enzyme shown to resolve Holliday junctions, recognizes a broad spectrum of DNA substrates ranging from branched DNAs to single base mismatches. We have determined the crystal structures of the Ca2+-bound wild-type and the inactive N62D mutant enzymes at 2.4 and 2.1 A, respectively. The Endo VII monomers form an elongated, highly intertwined molecular dimer exhibiting extreme domain swapping. The major dimerization elements are two pairs of antiparallel helices forming a novel 'four-helix cross' motif. The unique monomer fold, almost completely lacking beta-sheet structure and containing a zinc ion tetrahedrally coordinated to four cysteines, does not resemble any of the known junction-resolving enzymes, including the Escherichia coli RuvC and lambda integrase-type recombinases. The S-shaped dimer has two 'binding bays' separated by approximately 25 A which are lined by positively charged residues and contain near their base residues known to be essential for activity. These include Asp40 and Asn62, which function as ligands for the bound calcium ions. A pronounced bipolar charge distribution suggests that branched DNA substrates bind to the positively charged face with the scissile phosphates located near the divalent cations. A model for the complex with a four-way DNA junction is presented.
 
  Selected figure(s)  
 
Figure 2.
Figure 2 Structure of the wild-type Endo VII dimer. (A) Ribbon plot representation produced with MOLSCRIPT (Kraulis, 1991) in two perpendicular views (one of them in stereo) with the individual monomers colored red and green. The bound zinc and calcium ions are shown as blue and yellow spheres, respectively. Indicated in ball and stick representation are the side chains of D40 and N62 liganding the calcium as well as the nearby E65. (B) Stereo representation of the four-helix cross region showing the hydrophobic residues. They form an extended hydrophobic core representing the major dimerization element of the Endo VII dimer. (C) Electrostatic surface representation of the Endo VII dimer. The two opposite faces of the dimer, viewed approximately along the dyad, show a distinctly different charge distribution. The predominantly positively charged face shown on the right (indicated by the blue color) also contains the bound calcium ion and residues known to be essential for activity. The figure was produced with GRASP (Nicholls et al., 1991) with the scale ranging from -10 (red) to +17 (blue).
Figure 4.
Figure 4 Model of a four-way DNA junction–Endo VII complex. Two perpendicular views are shown, one approximately along the molecular 2-fold axis of the Endo VII dimer (left), the other one rotated 90° around a vertical axis (right). The Endo VII dimer (represented by a green ribbon) is docked onto the minor groove side of a four-way DNA junction (shown in a space-filled representation) corresponding to the antiparallel stacked X structure (von Kitzing et al., 1990). The continuous strands are colored purple, the crossing strands light and dark blue. The scissile phosphates, two and three bases 3' of the point of strand exchange on the crossing strands, are highlighted in yellow; the calcium ions at the active sites of Endo VII are shown as golden spheres. Minor groove contacts with residues exposed on the central helices as well as major groove contacts with basic residues located in the C-terminal domains can be formed.
 
  The above figures are reprinted from an Open Access publication published by Macmillan Publishers Ltd: EMBO J (1999, 18, 1447-1458) copyright 1999.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference Google scholar

  PubMed id Reference
18160275 A.C.Déclais, and D.M.Lilley (2008).
New insight into the recognition of branched DNA structure by junction-resolving enzymes.
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18283539 J.Hanus, M.Kalinowska-Herok, and P.Widlak (2008).
The major apoptotic endonuclease DFF40/CAD is a deoxyribose-specific and double-strand-specific enzyme.
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18953336 W.Yang (2008).
An equivalent metal ion in one- and two-metal-ion catalysis.
  Nat Struct Mol Biol, 15, 1228-1231.  
17499273 A.Jakubauskas, J.Giedriene, J.M.Bujnicki, and A.Janulaitis (2007).
Identification of a single HNH active site in type IIS restriction endonuclease Eco31I.
  J Mol Biol, 370, 157-169.  
17873859 C.Biertümpfel, W.Yang, and D.Suck (2007).
Crystal structure of T4 endonuclease VII resolving a Holliday junction.
  Nature, 449, 616-620.
PDB codes: 2qnc 2qnf
17785455 M.Saravanan, K.Vasu, S.Ghosh, and V.Nagaraja (2007).
Dual role for Zn2+ in maintaining structural integrity and inducing DNA sequence specificity in a promiscuous endonuclease.
  J Biol Chem, 282, 32320-32326.  
16470805 C.H.Lu, Y.S.Lin, Y.C.Chen, C.S.Yu, S.Y.Chang, and J.K.Hwang (2006).
The fragment transformation method to detect the protein structural motifs.
  Proteins, 63, 636-643.  
17029241 I.A.Cymerman, A.Obarska, K.J.Skowronek, A.Lubys, and J.M.Bujnicki (2006).
Identification of a new subfamily of HNH nucleases and experimental characterization of a representative member, HphI restriction endonuclease.
  Proteins, 65, 867-876.  
16434744 L.G.Doudeva, H.Huang, K.C.Hsia, Z.Shi, C.L.Li, Y.Shen, Y.S.Cheng, and H.S.Yuan (2006).
Crystal structural analysis and metal-dependent stability and activity studies of the ColE7 endonuclease domain in complex with DNA/Zn2+ or inhibitor/Ni2+.
  Protein Sci, 15, 269-280.
PDB codes: 1zns 1znv
16575941 P.A.Khuu, A.R.Voth, F.A.Hays, and P.S.Ho (2006).
The stacked-X DNA Holliday junction and protein recognition.
  J Mol Recognit, 19, 234-242.  
15596505 A.Merlino, M.A.Ceruso, L.Vitagliano, and L.Mazzarella (2005).
Open interface and large quaternary structure movements in 3D domain swapped proteins: insights from molecular dynamics simulations of the C-terminal swapped dimer of ribonuclease A.
  Biophys J, 88, 2003-2012.  
16055542 J.Chahine, and M.S.Cheung (2005).
Computational studies of the reversible domain swapping of p13suc1.
  Biophys J, 89, 2693-2700.  
16154091 N.McGregor, S.Ayora, S.Sedelnikova, B.Carrasco, J.C.Alonso, P.Thaw, and J.Rafferty (2005).
The structure of Bacillus subtilis RecU Holliday junction resolvase and its role in substrate selection and sequence-specific cleavage.
  Structure, 13, 1341-1351.
PDB code: 1zp7
14747998 B.Japelj, J.P.Waltho, and R.Jerala (2004).
Comparison of backbone dynamics of monomeric and domain-swapped stefin A.
  Proteins, 54, 500-512.  
15479781 C.L.Middleton, J.L.Parker, D.J.Richard, M.F.White, and C.S.Bond (2004).
Substrate recognition and catalysis by the Holliday junction resolving enzyme Hje.
  Nucleic Acids Res, 32, 5442-5451.
PDB codes: 1ob8 1ob9
14962381 K.C.Hsia, K.F.Chak, P.H.Liang, Y.S.Cheng, W.Y.Ku, and H.S.Yuan (2004).
DNA binding and degradation by the HNH protein ColE7.
  Structure, 12, 205-214.
PDB code: 1pt3
15190054 M.J.Maté, and C.Kleanthous (2004).
Structure-based analysis of the metal-dependent mechanism of H-N-H endonucleases.
  J Biol Chem, 279, 34763-34769.
PDB codes: 1v13 1v14 1v15
15103625 M.Stehr, and Y.Lindqvist (2004).
NrdH-redoxin of Corynebacterium ammoniagenes forms a domain-swapped dimer.
  Proteins, 55, 613-619.
PDB code: 1r7h
14691243 P.Mehta, K.Katta, and S.Krishnaswamy (2004).
HNH family subclassification leads to identification of commonality in the His-Me endonuclease superfamily.
  Protein Sci, 13, 295-300.  
15140887 R.Guan, E.L.Malchiodi, Q.Wang, P.Schuck, and R.A.Mariuzza (2004).
Crystal structure of the C-terminal peptidoglycan-binding domain of human peptidoglycan recognition protein Ialpha.
  J Biol Chem, 279, 31873-31882.
PDB codes: 1sk3 1sk4
15133049 S.Okubo, F.Hara, Y.Tsuchida, S.Shimotakahara, S.Suzuki, H.Hatanaka, S.Yokoyama, H.Tanaka, H.Yasuda, and H.Shindo (2004).
NMR structure of the N-terminal domain of SUMO ligase PIAS1 and its interaction with tumor suppressor p53 and A/T-rich DNA oligomers.
  J Biol Chem, 279, 31455-31461.
PDB code: 1v66
15520813 Y.Liu, and S.C.West (2004).
Happy Hollidays: 40th anniversary of the Holliday junction.
  Nat Rev Mol Cell Biol, 5, 937-944.  
12628932 A.C.Déclais, J.M.Fogg, A.D.Freeman, F.Coste, J.M.Hadden, S.E.Phillips, and D.M.Lilley (2003).
The complex between a four-way DNA junction and T7 endonuclease I.
  EMBO J, 22, 1398-1409.  
12881435 C.L.Li, L.I.Hor, Z.F.Chang, L.C.Tsai, W.Z.Yang, and H.S.Yuan (2003).
DNA binding and cleavage by the periplasmic nuclease Vvn: a novel structure with a known active site.
  EMBO J, 22, 4014-4025.
PDB codes: 1ouo 1oup
12626685 E.S.Miller, E.Kutter, G.Mosig, F.Arisaka, T.Kunisawa, and W.Rüger (2003).
Bacteriophage T4 genome.
  Microbiol Mol Biol Rev, 67, 86.  
14563836 F.A.Hays, J.Watson, and P.S.Ho (2003).
Caution! DNA crossing: crystal structures of Holliday junctions.
  J Biol Chem, 278, 49663-49666.  
12623012 F.Rousseau, J.W.Schymkowitz, and L.S.Itzhaki (2003).
The unfolding story of three-dimensional domain swapping.
  Structure, 11, 243-251.  
11972790 G.J.Sharples, E.L.Bolt, and R.G.Lloyd (2002).
RusA proteins from the extreme thermophile Aquifex aeolicus and lactococcal phage r1t resolve Holliday junctions.
  Mol Microbiol, 44, 549-559.  
12169615 J.G.Lawrence, G.F.Hatfull, and R.W.Hendrix (2002).
Imbroglios of viral taxonomy: genetic exchange and failings of phenetic approaches.
  J Bacteriol, 184, 4891-4905.  
12093751 J.M.Hadden, A.C.Déclais, S.E.Phillips, and D.M.Lilley (2002).
Metal ions bound at the active site of the junction-resolving enzyme T7 endonuclease I.
  EMBO J, 21, 3505-3515.
PDB codes: 1m0d 1m0i
11839489 M.E.Newcomer (2002).
Protein folding and three-dimensional domain swapping: a strained relationship?
  Curr Opin Struct Biol, 12, 48-53.  
12441392 M.J.Sui, L.C.Tsai, K.C.Hsia, L.G.Doudeva, W.Y.Ku, G.W.Han, and H.S.Yuan (2002).
Metal ions and phosphate binding in the H-N-H motif: crystal structures of the nuclease domain of ColE7/Im7 in complex with a phosphate ion and different divalent metal ions.
  Protein Sci, 11, 2947-2957.
PDB code: 1mz8
12021428 Y.Liu, and D.Eisenberg (2002).
3D domain swapping: as domains continue to swap.
  Protein Sci, 11, 1285-1299.  
11557808 B.S.Chevalier, and B.L.Stoddard (2001).
Homing endonucleases: structural and functional insight into the catalysts of intron/intein mobility.
  Nucleic Acids Res, 29, 3757-3774.  
11331763 C.S.Bond, M.Kvaratskhelia, D.Richard, M.F.White, and W.N.Hunter (2001).
Structure of Hjc, a Holliday junction resolvase, from Sulfolobus solfataricus.
  Proc Natl Acad Sci U S A, 98, 5509-5514.
PDB code: 1hh1
11251805 G.J.Sharples (2001).
The X philes: structure-specific endonucleases that resolve Holliday junctions.
  Mol Microbiol, 39, 823-834.  
11459968 G.Mosig, J.Gewin, A.Luder, N.Colowick, and D.Vo (2001).
Two recombination-dependent DNA replication pathways of bacteriophage T4, and their roles in mutagenesis and horizontal gene transfer.
  Proc Natl Acad Sci U S A, 98, 8306-8311.  
11165501 J.M.Bujnicki, M.Radlinska, and L.Rychlewski (2001).
Polyphyletic evolution of type II restriction enzymes revisited: two independent sources of second-hand folds revealed.
  Trends Biochem Sci, 26, 9.  
11483577 L.Aravind, and E.V.Koonin (2001).
Prokaryotic homologs of the eukaryotic DNA-end-binding protein Ku, novel domains in the Ku protein and prediction of a prokaryotic double-strand break repair system.
  Genome Res, 11, 1365-1374.  
11500367 M.Cai, Y.Huang, R.Ghirlando, K.L.Wilson, R.Craigie, and G.M.Clore (2001).
Solution structure of the constant region of nuclear envelope protein LAP2 reveals two LEM-domain structures: one binds BAF and the other binds DNA.
  EMBO J, 20, 4399-4407.
PDB code: 1gjj
11292843 N.V.Grishin (2001).
Treble clef finger--a functionally diverse zinc-binding structural motif.
  Nucleic Acids Res, 29, 1703-1714.  
11726496 S.Ceschini, A.Keeley, M.S.McAlister, M.Oram, J.Phelan, L.H.Pearl, I.R.Tsaneva, and T.E.Barrett (2001).
Crystal structure of the fission yeast mitochondrial Holliday junction resolvase Ydc2.
  EMBO J, 20, 6601-6611.
PDB code: 1kcf
10760268 B.F.Eichman, J.M.Vargason, B.H.Mooers, and P.S.Ho (2000).
The Holliday junction in an inverted repeat DNA sequence: sequence effects on the structure of four-way junctions.
  Proc Natl Acad Sci U S A, 97, 3971-3976.
PDB codes: 1dcv 1dcw
10944205 D.M.Lilley, and M.F.White (2000).
Resolving the relationships of resolving enzymes.
  Proc Natl Acad Sci U S A, 97, 9351-9353.  
11071943 H.Daiyasu, K.Komori, S.Sakae, Y.Ishino, and H.Toh (2000).
Hjc resolvase is a distantly related member of the type II restriction endonuclease family.
  Nucleic Acids Res, 28, 4540-4543.  
10982859 L.Aravind, K.S.Makarova, and E.V.Koonin (2000).
SURVEY AND SUMMARY: holliday junction resolvases and related nucleases: identification of new families, phyletic distribution and evolutionary trajectories.
  Nucleic Acids Res, 28, 3417-3432.  
11123916 S.Schöttler, W.Wende, V.Pingoud, and A.Pingoud (2000).
Identification of Asp218 and Asp326 as the principal Mg2+ binding ligands of the homing endonuclease PI-SceI.
  Biochemistry, 39, 15895-15900.  
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 codes are shown on the right.