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PDBsum entry 1d2i

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protein dna_rna metals Protein-protein interface(s) links
Hydrolase/DNA PDB id
1d2i
Jmol
Contents
Protein chains
223 a.a.
DNA/RNA
Metals
_MG ×2
Waters ×543
PDB id:
1d2i
Name: Hydrolase/DNA
Title: Crystal structure of restriction endonuclease bglii complexe 16-mer
Structure: DNA (5'-d( Tp Ap Tp Tp Ap Tp Ap Gp Ap Tp Cp Tp Ap 3'). Chain: c, d. Engineered: yes. Protein (restriction endonuclease bglii). Chain: a, b
Source: Synthetic: yes. Other_details: oligomers were produced commercially. Bacillus subtilis. Organism_taxid: 1423
Biol. unit: Tetramer (from PQS)
Resolution:
1.70Å     R-factor:   0.182     R-free:   0.200
Authors: C.M.Lukacs,R.Kucera,I.Schildkraut,A.K.Aggarwal
Key ref:
C.M.Lukacs et al. (2000). Understanding the immutability of restriction enzymes: crystal structure of BglII and its DNA substrate at 1.5 A resolution. Nat Struct Biol, 7, 134-140. PubMed id: 10655616 DOI: 10.1038/72405
Date:
23-Sep-99     Release date:   21-Feb-00    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chains
Pfam   ArchSchema ?
Q45488  (T2B2_BACIU) -  Type-2 restriction enzyme BglII
Seq:
Struc:
223 a.a.
223 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     7 terms  

 

 
DOI no: 10.1038/72405 Nat Struct Biol 7:134-140 (2000)
PubMed id: 10655616  
 
 
Understanding the immutability of restriction enzymes: crystal structure of BglII and its DNA substrate at 1.5 A resolution.
C.M.Lukacs, R.Kucera, I.Schildkraut, A.K.Aggarwal.
 
  ABSTRACT  
 
Restriction endonucleases are remarkably resilient to alterations in their DNA binding specificity. To understand the basis of this immutability, we have determined the crystal structure of endonuclease BglII bound to its recognition sequence (AGATCT), at 1. 5 A resolution. We compare the structure of BglII to endonuclease BamHI, which recognizes a closely related DNA site (GGATCC). We show that both enzymes share a similar alpha/beta core, but in BglII, the core is augmented by a beta-sandwich domain that encircles the DNA to provide extra specificity. Remarkably, the DNA is contorted differently in the two structures, leading to different protein-DNA contacts for even the common base pairs. Furthermore, the BglII active site contains a glutamine in place of the glutamate at the general base position in BamHI, and only a single metal is found coordinated to the putative nucleophilic water and the phosphate oxygens. This surprising diversity in structures shows that different strategies can be successful in achieving site-specific recognition and catalysis in restriction endonucleases.
 
  Selected figure(s)  
 
Figure 4.
Figure 4. DNA recognition. a, Stereo view of the protein - base contacts in one half-site of the recognition sequence. The two monomers of BglII are colored in different shades of yellow and are labeled A and B. b, Schematic representation of the phosphate and base contacts from (left) one monomer of BglII and (right) one monomer of BamHI. c, Superimposition of the outer base pair recognition residues Asn 140 and Ser 141 from Bgl II with Asn 154 and Arg 155 of BamHI. The superimposition reveals a 2.5 shift in the position of the outer bases.
Figure 5.
Figure 5. Active site. A stereo view closeup of the BglII active site around the scissile phosphodiester bond. Residues Asn 69, Asp 84, Glu 93 and Gln 95 correspond to the BamHI active site residues Glu 77, Asp 94, Glu 111 and Glu 113. The structure reveals numerous water molecules and an octahedrally coordinated cation (orange sphere) between the conserved residues and the DNA. Five of the six ligands have distances ranging from 2.2 to 2.5 ; the sixth ligand (to the proposed nucleophilic water molecule) is 2.7 . One water molecule in the coordination sphere of the cation (labeled NW) makes a 155 angle with the scissile P -O3 bond, and appears to be the attacking nucleophile.
 
  The above figures are reprinted by permission from Macmillan Publishers Ltd: Nat Struct Biol (2000, 7, 134-140) copyright 2000.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
20833632 E.S.Vanamee, H.Viadiu, S.H.Chan, A.Ummat, A.M.Hartline, S.Y.Xu, and A.K.Aggarwal (2011).
Asymmetric DNA recognition by the OkrAI endonuclease, an isoschizomer of BamHI.
  Nucleic Acids Res, 39, 712-719.
PDB code: 3odh
20861000 M.Firczuk, M.Wojciechowski, H.Czapinska, and M.Bochtler (2011).
DNA intercalation without flipping in the specific ThaI-DNA complex.
  Nucleic Acids Res, 39, 744-754.
PDB code: 3ndh
20961958 M.Laganeckas, M.Margelevicius, and C.Venclovas (2011).
Identification of new homologs of PD-(D/E)XK nucleases by support vector machines trained on data derived from profile-profile alignments.
  Nucleic Acids Res, 39, 1187-1196.  
  20703329 J.E.Deweese, and N.Osheroff (2010).
The Use of Divalent Metal Ions by Type II Topoisomerases.
  Metallomics, 2, 450-459.  
19089001 C.Liu, and L.Wang (2009).
DNA hydrolytic cleavage catalyzed by synthetic multinuclear metallonucleases.
  Dalton Trans, (), 227-239.  
19233205 G.Nimrod, A.Szilágyi, C.Leslie, and N.Ben-Tal (2009).
Identification of DNA-binding proteins using structural, electrostatic and evolutionary features.
  J Mol Biol, 387, 1040-1053.  
19194458 P.Yuan, M.Bartlam, Z.Lou, S.Chen, J.Zhou, X.He, Z.Lv, R.Ge, X.Li, T.Deng, E.Fodor, Z.Rao, and Y.Liu (2009).
Crystal structure of an avian influenza polymerase PA(N) reveals an endonuclease active site.
  Nature, 458, 909-913.
PDB code: 3ebj
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.  
18400177 A.R.Lambert, D.Sussman, B.Shen, R.Maunus, J.Nix, J.Samuelson, S.Y.Xu, and B.L.Stoddard (2008).
Structures of the rare-cutting restriction endonuclease NotI reveal a unique metal binding fold involved in DNA binding.
  Structure, 16, 558-569.
PDB codes: 3bvq 3c25
18653531 J.E.Deweese, A.B.Burgin, and N.Osheroff (2008).
Human topoisomerase IIalpha uses a two-metal-ion mechanism for DNA cleavage.
  Nucleic Acids Res, 36, 4883-4893.  
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.  
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.  
16614449 A.Obarska, A.Blundell, M.Feder, S.Vejsadová, E.Sisáková, M.Weiserová, J.M.Bujnicki, and K.Firman (2006).
Structural model for the multisubunit Type IC restriction-modification DNA methyltransferase M.EcoR124I in complex with DNA.
  Nucleic Acids Res, 34, 1992-2005.  
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
16011798 J.Kosinski, M.Feder, and J.M.Bujnicki (2005).
The PD-(D/E)XK superfamily revisited: identification of new members among proteins involved in DNA metabolism and functional predictions for domains of (hitherto) unknown function.
  BMC Bioinformatics, 6, 172.  
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
15720711 M.Feder, and J.M.Bujnicki (2005).
Identification of a new family of putative PD-(D/E)XK nucleases with unusual phylogenomic distribution and a new type of the active site.
  BMC Genomics, 6, 21.  
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
15563460 V.Pingoud, A.Sudina, H.Geyer, J.M.Bujnicki, R.Lurz, G.Lüder, R.Morgan, E.Kubareva, and A.Pingoud (2005).
Specificity changes in the evolution of type II restriction endonucleases: a biochemical and bioinformatic analysis of restriction enzymes that recognize unrelated sequences.
  J Biol Chem, 280, 4289-4298.  
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
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.  
11780147 J.C.Stroud, C.Lopez-Rodriguez, A.Rao, and L.Chen (2002).
Structure of a TonEBP-DNA complex reveals DNA encircled by a transcription factor.
  Nat Struct Biol, 9, 90-94.
PDB code: 1imh
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.  
11842098 S.Grazulis, M.Deibert, R.Rimseliene, R.Skirgaila, G.Sasnauskas, A.Lagunavicius, V.Repin, C.Urbanke, R.Huber, and V.Siksnys (2002).
Crystal structure of the Bse634I restriction endonuclease: comparison of two enzymes recognizing the same DNA sequence.
  Nucleic Acids Res, 30, 876-885.
PDB code: 1knv
11557805 A.Pingoud, and A.Jeltsch (2001).
Structure and function of type II restriction endonucleases.
  Nucleic Acids Res, 29, 3705-3727.  
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.  
11179886 C.M.Lukacs, and A.K.Aggarwal (2001).
BglII and MunI: what a difference a base makes.
  Curr Opin Struct Biol, 11, 14-18.  
11557807 I.Kobayashi (2001).
Behavior of restriction-modification systems as selfish mobile elements and their impact on genome evolution.
  Nucleic Acids Res, 29, 3742-3756.  
11410656 L.S.Higgins, C.Besnier, and H.Kong (2001).
The nicking endonuclease N.BstNBI is closely related to type IIs restriction endonucleases MlyI and PleI.
  Nucleic Acids Res, 29, 2492-2501.  
11160929 P.Lucas, C.Otis, J.P.Mercier, M.Turmel, and C.Lemieux (2001).
Rapid evolution of the DNA-binding site in LAGLIDADG homing endonucleases.
  Nucleic Acids Res, 29, 960-969.  
11585830 R.S.Appa, C.G.Shin, P.Lee, and S.A.Chow (2001).
Role of the nonspecific DNA-binding region and alpha helices within the core domain of retroviral integrase in selecting target DNA sites for integration.
  J Biol Chem, 276, 45848-45855.  
11557809 S.E.Tsutakawa, and K.Morikawa (2001).
The structural basis of damaged DNA recognition and endonucleolytic cleavage for very short patch repair endonuclease.
  Nucleic Acids Res, 29, 3775-3783.  
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.  
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 code is shown on the right.