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PDBsum entry 2bam

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protein dna_rna metals Protein-protein interface(s) links
Hydrolase/DNA PDB id
2bam
Jmol
Contents
Protein chains
207 a.a.
DNA/RNA
Metals
_CA ×2
Waters ×317
PDB id:
2bam
Name: Hydrolase/DNA
Title: Restriction endonuclease bamhi complex with DNA and calcium reactive complex).
Structure: DNA (5'-d( Tp Ap Tp Gp Gp Ap Tp Cp Cp Ap Tp A)-3' chain: c, d. Fragment: palindromic specific site. Engineered: yes. Protein (endonuclease bamhi). Chain: a, b. Synonym: r. Bamhi. Engineered: yes
Source: Synthetic: yes. Bacillus amyloliquefaciens. Organism_taxid: 1390. Expressed in: escherichia coli. Expression_system_taxid: 562
Biol. unit: Tetramer (from PQS)
Resolution:
2.00Å     R-factor:   0.233     R-free:   0.251
Authors: H.Viadiu,A.K.Aggarwal
Key ref:
H.Viadiu and A.K.Aggarwal (1998). The role of metals in catalysis by the restriction endonuclease BamHI. Nat Struct Biol, 5, 910-916. PubMed id: 9783752 DOI: 10.1038/2352
Date:
19-Aug-98     Release date:   31-Oct-99    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chains
Pfam   ArchSchema ?
P23940  (T2BA_BACAM) -  Type-2 restriction enzyme BamHI
Seq:
Struc:
213 a.a.
207 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: 10.1038/2352 Nat Struct Biol 5:910-916 (1998)
PubMed id: 9783752  
 
 
The role of metals in catalysis by the restriction endonuclease BamHI.
H.Viadiu, A.K.Aggarwal.
 
  ABSTRACT  
 
Type II restriction enzymes are characterized by their remarkable specificity and simplicity. They require only divalent metals (such as Mg2+ or Mn2+) as cofactors to catalyze the hydrolysis of DNA. However, most of the structural work on endonucleases has been performed in the absence of metals, leaving unanswered questions about their mechanisms of DNA cleavage. Here we report structures of the endonuclease BamHI-DNA complex, determined in the presence of Mn2+ and Ca2+, that describe the enzyme at different stages of catalysis. Overall, the results support a two-metal mechanism of DNA cleavage for BamHI which is distinct from that of EcoRV.
 
  Selected figure(s)  
 
Figure 3.
Figure 3. A stereo view of the refined 2F[o] - F[c] map around the R active site of the manganese bound post-reactive BamHI−DNA complex. Note that the scissile phosphodiester bond is cleaved in the cocrystal. The two manganese ions (Mn^2+A and Mn^2+B) are shown as yellow spheres. The water molecules are shown as small red spheres. A sketch summarizing the coordination geometries of Mn^2+A and Mn^2+B is shown at the bottom.
Figure 4.
Figure 4. a, A comparison of the pre-reactive (blue) and the post-reactive (red) BamHI−DNA complexes. The calcium ions (A and B) bound to the pre-reactive complex are shown as blue spheres, while the manganese ions (A and B) bound to the post-reactive complex are shown as red spheres. The phosphate group moves towards Glu 113 after cleavage. b, The BamHI reaction mechanism based on the structures of the pre- and post-reactive complexes. Me^2+A and Me^2+B denote the metal sites; Wat1 and Wat4 refer to water molecules.
 
  The above figures are reprinted by permission from Macmillan Publishers Ltd: Nat Struct Biol (1998, 5, 910-916) copyright 1998.  
  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
20854710 W.Yang (2011).
Nucleases: diversity of structure, function and mechanism.
  Q Rev Biophys, 44, 1.  
  20703329 J.E.Deweese, and N.Osheroff (2010).
The use of divalent metal ions by type II topoisomerases.
  Metallomics, 2, 450-459.  
19915993 M.J.Marcaida, I.G.Muñoz, F.J.Blanco, J.Prieto, and G.Montoya (2010).
Homing endonucleases: from basics to therapeutic applications.
  Cell Mol Life Sci, 67, 727-748.  
20140205 S.H.Chan, L.Opitz, L.Higgins, D.O'loane, and S.Y.Xu (2010).
Cofactor requirement of HpyAV restriction endonuclease.
  PLoS One, 5, e9071.  
19194459 A.Dias, D.Bouvier, T.Crépin, A.A.McCarthy, D.J.Hart, F.Baudin, S.Cusack, and R.W.Ruigrok (2009).
The cap-snatching endonuclease of influenza virus polymerase resides in the PA subunit.
  Nature, 458, 914-918.
PDB code: 2w69
19089001 C.Liu, and L.Wang (2009).
DNA hydrolytic cleavage catalyzed by synthetic multinuclear metallonucleases.
  Dalton Trans, (), 227-239.  
19815502 J.M.Wojciak, N.Zhu, K.T.Schuerenberg, K.Moreno, W.S.Shestowsky, M.Hiraiwa, R.Sabbadini, and T.Huxford (2009).
The crystal structure of sphingosine-1-phosphate in complex with a Fab fragment reveals metal bridging of an antibody and its antigen.
  Proc Natl Acad Sci U S A, 106, 17717-17722.
PDB code: 3i9g
19966419 N.Watanabe, Y.Takasaki, C.Sato, S.Ando, and I.Tanaka (2009).
Structures of restriction endonuclease HindIII in complex with its cognate DNA and divalent cations.
  Acta Crystallogr D Biol Crystallogr, 65, 1326-1333.
PDB codes: 2e52 3a4k
18424798 C.M.Moure, F.S.Gimble, and F.A.Quiocho (2008).
Crystal structures of I-SceI complexed to nicked DNA substrates: snapshots of intermediates along the DNA cleavage reaction pathway.
  Nucleic Acids Res, 36, 3287-3296.
PDB codes: 3c0w 3c0x
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.  
17623842 C.R.Guzzo, R.A.Nagem, J.A.Barbosa, and C.S.Farah (2007).
Structure of Xanthomonas axonopodis pv. citri YaeQ reveals a new compact protein fold built around a variation of the PD-(D/E)XK nuclease motif.
  Proteins, 69, 644-651.
PDB code: 2g3w
17308914 G.A.Papadakos, H.Nastri, P.Riggs, and C.M.Dupureur (2007).
Uncoupling metallonuclease metal ion binding sites via nudge mutagenesis.
  J Biol Inorg Chem, 12, 557-569.  
17603475 J.C.Miller, M.C.Holmes, J.Wang, D.Y.Guschin, Y.L.Lee, I.Rupniewski, C.M.Beausejour, A.J.Waite, N.S.Wang, K.A.Kim, P.D.Gregory, C.O.Pabo, and E.J.Rebar (2007).
An improved zinc-finger nuclease architecture for highly specific genome editing.
  Nat Biotechnol, 25, 778-785.  
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.  
17039546 N.Nagano, T.Noguchi, and Y.Akiyama (2007).
Systematic comparison of catalytic mechanisms of hydrolysis and transfer reactions classified in the EzCatDB database.
  Proteins, 66, 147-159.  
16601679 M.Nowotny, and W.Yang (2006).
Stepwise analyses of metal ions in RNase H catalysis from substrate destabilization to product release.
  EMBO J, 25, 1924-1933.
PDB codes: 2g8f 2g8h 2g8i 2g8k 2g8u 2g8v 2g8w
16600865 W.Yang, J.Y.Lee, and M.Nowotny (2006).
Making and breaking nucleic acids: two-Mg2+-ion catalysis and substrate specificity.
  Mol Cell, 22, 5.  
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
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
15894630 M.Fuxreiter, M.Mezei, I.Simon, and R.Osman (2005).
Interfacial water as a "hydration fingerprint" in the noncognate complex of BamHI.
  Biophys J, 89, 903-911.  
15893669 S.A.Townson, J.C.Samuelson, S.Y.Xu, and A.K.Aggarwal (2005).
Implications for switching restriction enzyme specificities from the structure of BstYI bound to a BglII DNA sequence.
  Structure, 13, 791-801.
PDB codes: 1vrr 1yuv
14725771 G.Paillard, and R.Lavery (2004).
Analyzing protein-DNA recognition mechanisms.
  Structure, 12, 113-122.  
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.  
12719261 J.Sun, H.Viadiu, A.K.Aggarwal, and H.Weinstein (2003).
Energetic and structural considerations for the mechanism of protein sliding along DNA in the nonspecific BamHI-DNA complex.
  Biophys J, 84, 3317-3325.  
12917398 P.Bist, and D.N.Rao (2003).
Identification and mutational analysis of Mg2+ binding site in EcoP15I DNA methyltransferase: involvement in target base eversion.
  J Biol Chem, 278, 41837-41848.  
12496295 T.Mordasini, A.Curioni, and W.Andreoni (2003).
Why do divalent metal ions either promote or inhibit enzymatic reactions? The case of BamHI restriction endonuclease from combined quantum-classical simulations.
  J Biol Chem, 278, 4381-4384.  
12067333 A.S.Bhagwat, and M.Lieb (2002).
Cooperation and competition in mismatch repair: very short-patch repair and methyl-directed mismatch repair in Escherichia coli.
  Mol Microbiol, 44, 1421-1428.  
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
11751298 T.W.Lynch, D.Kosztin, M.A.McLean, K.Schulten, and S.G.Sligar (2002).
Dissecting the molecular origins of specific protein-nucleic acid recognition: hydrostatic pressure and molecular dynamics.
  Biophys J, 82, 93-98.  
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.  
11148032 C.M.Dupureur, and M.A.Dominguez (2001).
The PD...(D/E)XK motif in restriction enzymes: a link between function and conformation.
  Biochemistry, 40, 387-394.  
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.  
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.  
11433022 S.J.Garforth, D.Patel, M.Feng, and J.R.Sayers (2001).
Unusually wide co-factor tolerance in a metalloenzyme; divalent metal ions modulate endo-exonuclease activity in T5 exonuclease.
  Nucleic Acids Res, 29, 2772-2779.  
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.  
10911996 A.B.Hickman, Y.Li, S.V.Mathew, E.W.May, N.L.Craig, and F.Dyda (2000).
Unexpected structural diversity in DNA recombination: the restriction endonuclease connection.
  Mol Cell, 5, 1025-1034.
PDB code: 1f1z
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.  
10882125 H.Viadiu, and A.K.Aggarwal (2000).
Structure of BamHI bound to nonspecific DNA: a model for DNA sliding.
  Mol Cell, 5, 889-895.
PDB code: 1esg
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.  
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
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.  
10220350 L.Doan, B.Handa, N.A.Roberts, and K.Klumpp (1999).
Metal ion catalysis of RNA cleavage by the influenza virus endonuclease.
  Biochemistry, 38, 5612-5619.  
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.  
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 code is shown on the right.