PDBsum entry 1iaw

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protein dna_rna Protein-protein interface(s) links
Hydrolase/DNA PDB id
Protein chains
304 a.a.
Waters ×44
PDB id:
Name: Hydrolase/DNA
Title: Crystal structure of naei complexed with 17mer DNA
Structure: 5'-d( Tp Gp Cp Cp Ap Cp Gp Cp Cp Gp Gp Cp Gp Tp G 3'. Chain: c, d, e, f. Engineered: yes. Type ii restriction enzyme naei. Chain: a, b. Engineered: yes
Source: Synthetic: yes. Lechevalieria aerocolonigenes. Organism_taxid: 68170. Gene: nae i. Expressed in: escherichia coli. Expression_system_taxid: 562.
Biol. unit: Hexamer (from PQS)
2.40Å     R-factor:   0.243     R-free:   0.293
Authors: Q.Huai,J.D.Colandene,M.D.Topal,H.Ke
Key ref:
Q.Huai et al. (2001). Structure of NaeI-DNA complex reveals dual-mode DNA recognition and complete dimer rearrangement. Nat Struct Biol, 8, 665-669. PubMed id: 11473254 DOI: 10.1038/90366
23-Mar-01     Release date:   03-Aug-01    
Go to PROCHECK summary

Protein chains
Pfam   ArchSchema ?
P50187  (T2N1_NOCAE) -  Type-2 restriction enzyme NaeI
317 a.a.
304 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Enzyme reactions 
   Enzyme class: E.C.  - 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: 10.1038/90366 Nat Struct Biol 8:665-669 (2001)
PubMed id: 11473254  
Structure of NaeI-DNA complex reveals dual-mode DNA recognition and complete dimer rearrangement.
Q.Huai, J.D.Colandene, M.D.Topal, H.Ke.
NaeI, a novel DNA endonuclease, shows topoisomerase and recombinase activities when a Lys residue is substituted for Leu 43. The NaeI-DNA structure demonstrates that each of the two domains of NaeI recognizes one molecule of DNA duplex. DNA recognition induces dramatic rearrangements: narrowing the binding site of the Topo domain 16 A to grip DNA, widening that of the Endo domain 8 A to encircle and bend DNA 45 degrees for cleavage, and completely rebuilding the homodimer interface. The NaeI-DNA structure presents the first example of novel recognition of two copies of one DNA sequence by two different amino acid sequences and two different structural motifs in one polypeptide.
  Selected figure(s)  
Figure 1.
Figure 1. Dimeric structure of NaeI -DNA complex. a,b, Ribbon presentation of dimeric NaeI (orange and gold) bound to DNA (ball-and-stick). R-loop indicates recognition loop (Asn 144 -Lys 148). (a) and (b) are related by a 90 rotation about the vertical molecular two-fold axis. c, Example of electron density for the central base pairs of the 17mer DNA bound to the CAP motifs. The (2F[o] - F[c]) map was calculated using the structure without DNAs and contoured at 1.5 .
Figure 2.
Figure 2. DNA binding. a, Stereo view of DNA binding to the Endo domain. The central 10 base pairs of the 17mer DNA are shown (gold sticks are ACGCC GGCGT and scissile bonds are ball-and-stick). H4 helices are shown as green and cyan ribbons. Asn 144, Asp 146 and Lys 148 (ball-and-stick, shown in one monomer) bind in the major groove. Lys 59 and Thr 63 bind in the minor groove. b, Schematic diagram of DNA binding to the Endo domain. Pink and green represent amino acids from different monomers. The scissile bond (C9 -G10) is shown with a dashed cyan line. Dotted lines represent hydrogen bonds: Asn 144 -G7 (OD1 -O6, ND2 -O6, ND2 -N7), Asn 144 -G11 (ND2 -O6), Asp 146 -C8 (OD1 -N4), Lys 148 -G10 (NZ -N7, NZ -O6), Lys 148 -G11 (NZ -O6, NZ -N7), Arg 150 -C6 (NH1 -N4) and Arg 150 -G13 (NH1 -O6, NH2 -O6) in the major groove; and Lys 59 -C8 (NZ -O2), Lys 59 -C12 (NZ -O2) and Thr 63 -G10 (OG1 -N2) in the minor groove. c, Stereo view of DNA binding to the helix-turn-helix/CAP motifs of the Topo domains. H9a is a 3[10]-helix. The central 10 base pairs of the DNA substrate are shown (gold sticks). The recognition residues Asp 226, Lys 229, Arg 230, Arg 232 and Ser 234 are represented by ball-and-stick models. d, Schematic diagram of DNA binding to the Topo domain. Hydrogen bonding in major groove: Arg 192 -G16 (NH2 -N3), Asp 226 -C8 (OD2 -N4), Lys 229 -G11 (NZ -N7), Arg 230 -G7 (NH2 -N7, NH2 -O6), Arg 232 -G10 (NE -N7, NH2 -O6), Lys 269 -G13 (NZ -N2) and Lys 269 -G7 (NZ -N3). The spatial alignment of Ser 234 (OG) with C12 (C5) suggests an interaction.
  The above figures are reprinted by permission from Macmillan Publishers Ltd: Nat Struct Biol (2001, 8, 665-669) copyright 2001.  
  Figures were selected by the author.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
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
19729506 D.Golovenko, E.Manakova, G.Tamulaitiene, S.Grazulis, and V.Siksnys (2009).
Structural mechanisms for the 5'-CCWGG sequence recognition by the N- and C-terminal domains of EcoRII.
  Nucleic Acids Res, 37, 6613-6624.
PDB codes: 3hqf 3hqg
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.  
17266985 J.J.Marshall, D.M.Gowers, and S.E.Halford (2007).
Restriction endonucleases that bridge and excise two recognition sites from DNA.
  J Mol Biol, 367, 419-431.  
16407332 B.van den Broek, F.Vanzi, D.Normanno, F.S.Pavone, and G.J.Wuite (2006).
Real-time observation of DNA looping dynamics of Type IIE restriction enzymes NaeI and NarI.
  Nucleic Acids Res, 34, 167-174.  
16723432 G.J.Gemmen, R.Millin, and D.E.Smith (2006).
DNA looping by two-site restriction endonucleases: heterogeneous probability distributions for loop size and unbinding force.
  Nucleic Acids Res, 34, 2864-2877.  
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
16556912 L.E.Catto, S.Ganguly, S.E.Milsom, A.J.Welsh, and S.E.Halford (2006).
Protein assembly and DNA looping by the FokI restriction endonuclease.
  Nucleic Acids Res, 34, 1711-1720.  
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.  
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
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
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
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.  
15139802 S.E.Halford, A.J.Welsh, and M.D.Szczelkun (2004).
Enzyme-mediated DNA looping.
  Annu Rev Biophys Biomol Struct, 33, 1.  
12851384 K.Hingorani-Varma, and J.Bitinaite (2003).
Kinetic analysis of the coordinated interaction of SgrAI restriction endonuclease with different DNA targets.
  J Biol Chem, 278, 40392-40399.  
12519752 K.L.Carrick, and M.D.Topal (2003).
Amino acid substitutions at position 43 of NaeI endonuclease. Evidence for changes in NaeI structure.
  J Biol Chem, 278, 9733-9739.  
14576294 M.Mucke, D.H.Kruger, and M.Reuter (2003).
Diversity of type II restriction endonucleases that require two DNA recognition sites.
  Nucleic Acids Res, 31, 6079-6084.  
12654995 R.J.Roberts, M.Belfort, T.Bestor, A.S.Bhagwat, T.A.Bickle, J.Bitinaite, R.M.Blumenthal, S.K.h.Degtyarev, D.T.Dryden, K.Dybvig, K.Firman, E.S.Gromova, R.I.Gumport, S.E.Halford, S.Hattman, J.Heitman, D.P.Hornby, A.Janulaitis, A.Jeltsch, J.Josephsen, A.Kiss, T.R.Klaenhammer, I.Kobayashi, H.Kong, D.H.Krüger, S.Lacks, M.G.Marinus, M.Miyahara, R.D.Morgan, N.E.Murray, V.Nagaraja, A.Piekarowicz, A.Pingoud, E.Raleigh, D.N.Rao, N.Reich, V.E.Repin, E.U.Selker, P.C.Shaw, D.C.Stein, B.L.Stoddard, W.Szybalski, T.A.Trautner, J.L.Van Etten, J.M.Vitor, G.G.Wilson, and S.Y.Xu (2003).
A nomenclature for restriction enzymes, DNA methyltransferases, homing endonucleases and their genes.
  Nucleic Acids Res, 31, 1805-1812.  
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.  
12356742 M.Mücke, G.Grelle, J.Behlke, R.Kraft, D.H.Krüger, and M.Reuter (2002).
EcoRII: a restriction enzyme evolving recombination functions?
  EMBO J, 21, 5262-5268.  
11832480 M.Mücke, V.Pingoud, G.Grelle, R.Kraft, D.H.Krüger, and M.Reuter (2002).
Asymmetric photocross-linking pattern of restriction endonuclease EcoRII to the DNA recognition sequence.
  J Biol Chem, 277, 14288-14293.  
11827971 V.Pingoud, E.Kubareva, G.Stengel, P.Friedhoff, J.M.Bujnicki, C.Urbanke, A.Sudina, and A.Pingoud (2002).
Evolutionary relationship between different subgroups of restriction endonucleases.
  J Biol Chem, 277, 14306-14314.  
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