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PDBsum entry 1dmu

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protein dna_rna ligands metals links
Hydrolase/DNA PDB id
1dmu
Jmol
Contents
Protein chain
299 a.a.
DNA/RNA
Ligands
BME
Metals
_CA ×4
Waters ×255
PDB id:
1dmu
Name: Hydrolase/DNA
Title: Crystal structure of the restriction endonuclease bgli (E.C.3.1.21.4) bound to its DNA recognition sequence
Structure: DNA (5'- d( Ap Tp Cp Gp Cp Cp Tp Ap Ap Tp Ap Gp Gp Cp Gp Ap T)-3'). Chain: f. Engineered: yes. Bgli restriction endonuclease. Chain: a. Engineered: yes
Source: Synthetic: yes. Other_details: contains DNA recognition sequence of bgli. Bacillus subtilis. Organism_taxid: 1423. Expressed in: escherichia coli. Expression_system_taxid: 562
Biol. unit: Tetramer (from PDB file)
Resolution:
2.20Å     R-factor:   0.177     R-free:   0.239
Authors: M.Newman,K.Lunnen,G.Wilson,J.Greci,I.Schildkraut, S.E.V.Phillips
Key ref:
M.Newman et al. (1998). Crystal structure of restriction endonuclease BglI bound to its interrupted DNA recognition sequence. EMBO J, 17, 5466-5476. PubMed id: 9736624 DOI: 10.1093/emboj/17.18.5466
Date:
15-Dec-99     Release date:   18-Dec-99    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
O68557  (T2B1_BACIU) -  Type-2 restriction enzyme BglI
Seq:
Struc:
299 a.a.
299 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Enzyme reactions 
   Enzyme class: E.C.3.1.21.4  - Type Ii site-specific deoxyribonuclease.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: Endonucleolytic cleavage of DNA to give specific double-stranded fragments with terminal 5'-phosphates.
      Cofactor: Mg(2+)
 Gene Ontology (GO) functional annotation 
  GO annot!
  Biological process     nucleic acid phosphodiester bond hydrolysis   3 terms 
  Biochemical function     hydrolase activity     5 terms  

 

 
DOI no: 10.1093/emboj/17.18.5466 EMBO J 17:5466-5476 (1998)
PubMed id: 9736624  
 
 
Crystal structure of restriction endonuclease BglI bound to its interrupted DNA recognition sequence.
M.Newman, K.Lunnen, G.Wilson, J.Greci, I.Schildkraut, S.E.Phillips.
 
  ABSTRACT  
 
The crystal structure of the type II restriction endonuclease BglI bound to DNA containing its specific recognition sequence has been determined at 2.2 A resolution. This is the first structure of a restriction endonuclease that recognizes and cleaves an interrupted DNA sequence, producing 3' overhanging ends. BglI is a homodimer that binds its specific DNA sequence with the minor groove facing the protein. Parts of the enzyme reach into both the major and minor grooves to contact the edges of the bases within the recognition half-sites. The arrangement of active site residues is strikingly similar to other restriction endonucleases, but the co-ordination of two calcium ions at the active site gives new insight into the catalytic mechanism. Surprisingly, the core of a BglI subunit displays a striking similarity to subunits of EcoRV and PvuII, but the dimer structure is dramatically different. The BglI-DNA complex demonstrates, for the first time, that a conserved subunit fold can dimerize in more than one way, resulting in different DNA cleavage patterns.
 
  Selected figure(s)  
 
Figure 1.
Figure 1 Sequence of the 17 base pair DNA fragment used in the BglI -DNA complex. Recognition half-sites are boxed. The sites of cleavage are indicated by arrows. The position of the crystallographic two-fold is shown and the symmetry related strand is indicated by #. To avoid crystallographic disorder, an A:A mismatch was incorporated at the centre of the oligonucleotide.
Figure 5.
Figure 5 The active site of BglI. (A) Comparison of the active sites of BglI and EcoRV. Both views are in a similar orientation and show similar regions of the structures. The central -sheet is green with an -helix ( 4 in BglI and B in EcoRV) is purple. Only five bases of a single strand of DNA are shown for clarity, with the sugar -phosphate backbone in red. Active site residues and the active site phosphate are shown as a ball-and-stick representation. Calcium ion positions for the BglI -DNA complex are shown as cyan spheres. (B) Stereo view of the co-ordination geometry of the Ca^2+ ions in the active site of BglI. Active site residues are shown as a ball-and-stick representation. Only a small segment of the DNA phosphate backbone on either side of the scissile phosphodiester bond is shown. DNA bases have been omitted for clarity. Calcium ions are shown as cyan spheres. Atoms co-ordinated to the calcium ions are shown connected by solid grey lines. (C) The active site of the 3' -5' exonuclease domain of DNA polymerase I (PDB code 1kfs) shown as a ball-and-stick representation. Divalent cations, shown as cyan spheres, are Zn2+ at position 1 and Mg2+ at position 2. The attacking water molecule is not shown. Produced using MOLSCRIPT (Kraulis, 1991) and RASTER3D (Merritt and Murphy, 1994).
 
  The above figures are reprinted from an Open Access publication published by Macmillan Publishers Ltd: EMBO J (1998, 17, 5466-5476) copyright 1998.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
21428944 S.E.Halford, L.E.Catto, C.Pernstich, D.A.Rusling, and K.L.Sanders (2011).
The reaction mechanism of FokI excludes the possibility of targeting zinc finger nucleases to unique DNA sites.
  Biochem Soc Trans, 39, 584-588.  
20854710 W.Yang (2011).
Nucleases: diversity of structure, function and mechanism.
  Q Rev Biophys, 44, 1.  
19380375 M.Sokolowska, H.Czapinska, and M.Bochtler (2009).
Crystal structure of the beta beta alpha-Me type II restriction endonuclease Hpy99I with target DNA.
  Nucleic Acids Res, 37, 3799-3810.
PDB codes: 3fc3 3gox
19567736 R.D.Morgan, and Y.A.Luyten (2009).
Rational engineering of type II restriction endonuclease DNA binding and cleavage specificity.
  Nucleic Acids Res, 37, 5222-5233.  
19596810 S.R.Bellamy, Y.S.Kovacheva, I.H.Zulkipli, and S.E.Halford (2009).
Differences between Ca2+ and Mg2+ in DNA binding and release by the SfiI restriction endonuclease: implications for DNA looping.
  Nucleic Acids Res, 37, 5443-5453.  
19787108 W.H.Ang, and S.J.Lippard (2009).
Functional consequence of plasmid DNA modified site-specifically with 7-deaza-deoxyadenosine at a single, programmable site.
  Chem Commun (Camb), (), 5820-5822.  
18456708 J.Orlowski, and J.M.Bujnicki (2008).
Structural and evolutionary classification of Type II restriction enzymes based on theoretical and experimental analyses.
  Nucleic Acids Res, 36, 3552-3569.  
17375191 J.I.Daksis, and G.H.Erikson (2007).
Heteropolymeric triplex-based genomic assay to detect pathogens or single-nucleotide polymorphisms in human genomic samples.
  PLoS ONE, 2, e305.  
17873858 J.M.Hadden, A.C.Déclais, S.B.Carr, D.M.Lilley, and S.E.Phillips (2007).
The structural basis of Holliday junction resolution by T7 endonuclease I.
  Nature, 449, 621-624.
PDB code: 2pfj
17242028 J.Orlowski, M.Boniecki, and J.M.Bujnicki (2007).
I-Ssp6803I: the first homing endonuclease from the PD-(D/E)XK superfamily exhibits an unusual mode of DNA recognition.
  Bioinformatics, 23, 527-530.  
17214552 L.Mones, I.Simon, and M.Fuxreiter (2007).
Metal-binding sites at the active site of restriction endonuclease BamHI can conform to a one-ion mechanism.
  Biol Chem, 388, 73-78.  
17344322 M.Kaus-Drobek, H.Czapinska, M.Sokołowska, G.Tamulaitis, R.H.Szczepanowski, C.Urbanke, V.Siksnys, and M.Bochtler (2007).
Restriction endonuclease MvaI is a monomer that recognizes its target sequence asymmetrically.
  Nucleic Acids Res, 35, 2035-2046.
PDB codes: 2oa9 2oaa
17870087 S.R.Bellamy, S.E.Milsom, Y.S.Kovacheva, R.B.Sessions, and S.E.Halford (2007).
A switch in the mechanism of communication between the two DNA-binding sites in the SfiI restriction endonuclease.
  J Mol Biol, 373, 1169-1183.  
16962970 G.Tamulaitiene, A.Jakubauskas, C.Urbanke, R.Huber, S.Grazulis, and V.Siksnys (2006).
The crystal structure of the rare-cutting restriction enzyme SdaI reveals unexpected domain architecture.
  Structure, 14, 1389-1400.
PDB code: 2ixs
16710870 K.D.Roberts, J.N.Lambert, N.J.Ede, and A.M.Bray (2006).
Efficient methodology for the cyclization of linear peptide libraries via intramolecular S-alkylation using Multipin solid phase peptide synthesis.
  J Pept Sci, 12, 525-532.  
16628220 M.Bochtler, R.H.Szczepanowski, G.Tamulaitis, S.Grazulis, H.Czapinska, E.Manakova, and V.Siksnys (2006).
Nucleotide flips determine the specificity of the Ecl18kI restriction endonuclease.
  EMBO J, 25, 2219-2229.
PDB codes: 2fqz 2gb7
15667656 A.A.Chmiel, J.M.Bujnicki, and K.J.Skowronek (2005).
A homology model of restriction endonuclease SfiI in complex with DNA.
  BMC Struct Biol, 5, 2.  
16223716 E.Armalyte, J.M.Bujnicki, J.Giedriene, G.Gasiunas, J.Kosiński, and A.Lubys (2005).
Mva1269I: a monomeric type IIS restriction endonuclease from Micrococcus varians with two EcoRI- and FokI-like catalytic domains.
  J Biol Chem, 280, 41584-41594.  
16308566 E.S.Vanamee, H.Viadiu, R.Kucera, L.Dorner, S.Picone, I.Schildkraut, and A.K.Aggarwal (2005).
A view of consecutive binding events from structures of tetrameric endonuclease SfiI bound to DNA.
  EMBO J, 24, 4198-4208.
PDB codes: 2ezv 2f03
15590682 H.Hashimoto, T.Shimizu, T.Imasaki, M.Kato, N.Shichijo, K.Kita, and M.Sato (2005).
Crystal structures of type II restriction endonuclease EcoO109I and its complex with cognate DNA.
  J Biol Chem, 280, 5605-5610.
PDB codes: 1wtd 1wte
16209953 J.Y.Lee, J.Chang, N.Joseph, R.Ghirlando, D.N.Rao, and W.Yang (2005).
MutH complexed with hemi- and unmethylated DNAs: coupling base recognition and DNA cleavage.
  Mol Cell, 20, 155-166.
PDB codes: 2aoq 2aor
16195548 Q.S.Xu, R.J.Roberts, and H.C.Guo (2005).
Two crystal forms of the restriction enzyme MspI-DNA complex show the same novel structure.
  Protein Sci, 14, 2590-2600.
PDB code: 1yfi
15684412 S.D.Pawlak, M.Radlinska, A.A.Chmiel, J.M.Bujnicki, and K.J.Skowronek (2005).
Inference of relationships in the 'twilight zone' of homology using a combination of bioinformatics and site-directed mutagenesis: a case study of restriction endonucleases Bsp6I and PvuII.
  Nucleic Acids Res, 33, 661-671.  
15942026 T.J.Su, M.R.Tock, S.U.Egelhaaf, W.C.Poon, and D.T.Dryden (2005).
DNA bending by M.EcoKI methyltransferase is coupled to nucleotide flipping.
  Nucleic Acids Res, 33, 3235-3244.  
15805123 Z.Yang, J.R.Horton, R.Maunus, G.G.Wilson, R.J.Roberts, and X.Cheng (2005).
Structure of HinP1I endonuclease reveals a striking similarity to the monomeric restriction enzyme MspI.
  Nucleic Acids Res, 33, 1892-1901.
PDB code: 1ynm
15195996 A.Dong, L.Zhou, X.Zhang, S.Stickel, R.J.Roberts, and X.Cheng (2004).
Structure of the Q237W mutant of HhaI DNA methyltransferase: an insight into protein-protein interactions.
  Biol Chem, 385, 373-379.
PDB code: 1svu
15226412 D.M.Gowers, S.R.Bellamy, and S.E.Halford (2004).
One recognition sequence, seven restriction enzymes, five reaction mechanisms.
  Nucleic Acids Res, 32, 3469-3479.  
15341737 Q.S.Xu, R.B.Kucera, R.J.Roberts, and H.C.Guo (2004).
An asymmetric complex of restriction endonuclease MspI on its palindromic DNA recognition site.
  Structure, 12, 1741-1747.
PDB code: 1sa3
15375161 S.Chandrashekaran, M.Saravanan, D.R.Radha, and V.Nagaraja (2004).
Ca(2+)-mediated site-specific DNA cleavage and suppression of promiscuous activity of KpnI restriction endonuclease.
  J Biol Chem, 279, 49736-49740.  
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.  
12606565 M.R.Tock, E.Frary, J.R.Sayers, and J.A.Grasby (2003).
Dynamic evidence for metal ion catalysis in the reaction mediated by a flap endonuclease.
  EMBO J, 22, 995.  
11729187 A.J.Bath, S.E.Milsom, N.A.Gormley, and S.E.Halford (2002).
Many type IIs restriction endonucleases interact with two recognition sites before cleaving DNA.
  J Biol Chem, 277, 4024-4033.  
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
12142452 M.Fuxreiter, and I.Simon (2002).
Protein stability indicates divergent evolution of PD-(D/E)XK type II restriction endonucleases.
  Protein Sci, 11, 1978-1983.  
11557805 A.Pingoud, and A.Jeltsch (2001).
Structure and function of type II restriction endonucleases.
  Nucleic Acids Res, 29, 3705-3727.  
11344334 J.M.Bujnicki, and L.Rychlewski (2001).
Unusual evolutionary history of the tRNA splicing endonuclease EndA: relationship to the LAGLIDADG and PD-(D/E)XK deoxyribonucleases.
  Protein Sci, 10, 656-660.  
11250198 M.J.van der Woerd, J.J.Pelletier, S.Xu, and A.M.Friedman (2001).
Restriction enzyme BsoBI-DNA complex: a tunnel for recognition of degenerate DNA sequences and potential histidine catalysis.
  Structure, 9, 133-144.
PDB code: 1dc1
11266549 S.A.Williams, and S.E.Halford (2001).
SfiI endonuclease activity is strongly influenced by the non-specific sequence in the middle of its recognition site.
  Nucleic Acids Res, 29, 1476-1483.  
11327870 S.L.Reid, D.Parry, H.H.Liu, and B.A.Connolly (2001).
Binding and recognition of GATATC target sequences by the EcoRV restriction endonuclease: a study using fluorescent oligonucleotides and fluorescence polarization.
  Biochemistry, 40, 2484-2494.  
11257528 W.Cao, and J.Lu (2001).
Exploring the catalytic center of TaqI endonuclease: rescuing catalytic activity by double mutations and Mn2+.
  Biochim Biophys Acta, 1546, 253-260.  
10978180 C.M.Dupureur, and L.H.Conlan (2000).
A catalytically deficient active site variant of PvuII endonuclease binds Mg(II) ions.
  Biochemistry, 39, 10921-10927.  
10666447 E.A.Kubareva, H.Thole, A.S.Karyagina, T.S.Oretskaya, A.Pingoud, and V.Pingoud (2000).
Identification of a base-specific contact between the restriction endonuclease SsoII and its recognition sequence by photocross-linking.
  Nucleic Acids Res, 28, 1085-1091.  
10715131 J.J.Hlavaty, J.S.Benner, L.J.Hornstra, and I.Schildkraut (2000).
Identification of the metal-binding sites of restriction endonucleases by Fe2+-mediated oxidative cleavage.
  Biochemistry, 39, 3097-3105.  
10617645 J.Wang, R.Chen, and D.A.Julin (2000).
A single nuclease active site of the Escherichia coli RecBCD enzyme catalyzes single-stranded DNA degradation in both directions.
  J Biol Chem, 275, 507-513.  
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.  
10931930 M.R.Rice, and R.M.Blumenthal (2000).
Recognition of native DNA methylation by the PvuII restriction endonuclease.
  Nucleic Acids Res, 28, 3143-3150.  
10702254 N.A.Gormley, A.J.Bath, and S.E.Halford (2000).
Reactions of BglI and other type II restriction endonucleases with discontinuous recognition sites.
  J Biol Chem, 275, 6928-6936.  
10648519 P.C.Hsieh, J.P.Xiao, D.O'loane, and S.Y.Xu (2000).
Cloning, expression, and purification of a thermostable nonhomodimeric restriction enzyme, BslI.
  J Bacteriol, 182, 949-955.  
10856254 Q.Huai, J.D.Colandene, Y.Chen, F.Luo, Y.Zhao, M.D.Topal, and H.Ke (2000).
Crystal structure of NaeI-an evolutionary bridge between DNA endonuclease and topoisomerase.
  EMBO J, 19, 3110-3118.
PDB code: 1ev7
12760025 S.D.Bruner, D.P.Norman, J.C.Fromme, and G.L.Verdine (2000).
Structural and mechanistic studies on repair of 8-oxoguanine in mammalian cells.
  Cold Spring Harb Symp Quant Biol, 65, 103-111.  
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.  
11092936 T.J.O'Loughlin, Q.Xu, R.B.Kucera, L.F.Dorner, S.Sweeney, I.Schildkraut, and H.C.Guo (2000).
Crystallization and preliminary X-ray diffraction analysis of MspI restriction endonuclease in complex with its cognate DNA.
  Acta Crystallogr D Biol Crystallogr, 56, 1652-1655.  
10387089 A.M.Martin, N.C.Horton, S.Lusetti, N.O.Reich, and J.J.Perona (1999).
Divalent metal dependence of site-specific DNA binding by EcoRV endonuclease.
  Biochemistry, 38, 8430-8439.  
10103058 C.M.Dupureur, and L.M.Hallman (1999).
Effects of divalent metal ions on the activity and conformation of native and 3-fluorotyrosine-PvuII endonucleases.
  Eur J Biochem, 261, 261-268.  
10350476 M.D.Sam, and J.J.Perona (1999).
Catalytic roles of divalent metal ions in phosphoryl transfer by EcoRV endonuclease.
  Biochemistry, 38, 6576-6586.  
9914504 M.Elde, P.Haugen, N.P.Willassen, and S.Johansen (1999).
I-NjaI, a nuclear intron-encoded homing endonuclease from Naegleria, generates a pentanucleotide 3' cleavage-overhang within a 19 base-pair partially symmetric DNA recognition site.
  Eur J Biochem, 259, 281-288.  
9988771 M.Reuter, J.Schneider-Mergener, D.Kupper, A.Meisel, P.Mackeldanz, D.H.Krüger, and C.Schroeder (1999).
Regions of endonuclease EcoRII involved in DNA target recognition identified by membrane-bound peptide repertoires.
  J Biol Chem, 274, 5213-5221.  
10531503 N.C.Horton, L.F.Dorner, I.Schildkraut, and J.J.Perona (1999).
Crystallization and preliminary diffraction analysis of the HincII restriction endonuclease-DNA complex.
  Acta Crystallogr D Biol Crystallogr, 55, 1943-1945.  
10508668 R.A.Kovall, and B.W.Matthews (1999).
Type II restriction endonucleases: structural, functional and evolutionary relationships.
  Curr Opin Chem Biol, 3, 578-583.  
10360178 S.E.Tsutakawa, T.Muto, T.Kawate, H.Jingami, N.Kunishima, M.Ariyoshi, D.Kohda, M.Nakagawa, and K.Morikawa (1999).
Crystallographic and functional studies of very short patch repair endonuclease.
  Mol Cell, 3, 621-628.
PDB code: 1vsr
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.