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537 a.a.
 N deoxynucleoside triphosphate |
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 N diphosphate |
+ |
{DNA}(N) |
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Key reference
DOI no: 10.1002/prot.20858 Proteins 63:711-715 (2006) PubMed id: 16493661
Crystal structure of intein homing endonuclease II encoded in DNA polymerase gene from hyperthermophilic archaeon Thermococcus kodakaraensis strain KOD1. H.Matsumura, H.Takahashi, T.Inoue, T.Yamamoto, H.Hashimoto, M.Nishioka, S.Fujiwara, M.Takagi, T.Imanaka, Y.Kai. ABSTRACT
No abstract given.
Selected figure(s)
Figure 1.
Figure 1. Structures of PI-TkoII, PI-PfuI, and PI-SceI. A: Stereo ribbon diagram of PI-TkoII. PI-TkkoII contains the endonuclease, Hint, III, and IV domains colored in green, blue, light blue, and pink, respectively. Active site residues are shown. B: Ribbon diagram of PI-PfuI. C: Ribbon diagram of PI-SceI. D: Domain organization and multiple sequence alignment of PI-TkoII, PI-PfuI, and PI-SceI. The aligned sequences were displayed in ESPript.[24] Secondary structures were calculated by DSSP.[25] Secondary structure annotations and numberings on top correspond to PI-TkoII.-Helices are represented by spirals and
-strand by arrows. White lettering boxed with a red background indicates residues that are conserved in all three sequences, and red lettering indicates similar residues. The conserved sequence blocks of inteins are indicated.
Figure 2.
Figure 2. A: Electrostatic charge distribution on the surface of PI-TkoII; the view is projected in the same orientation as Figure 1(A). B: View is rotated by 180° with respect to a vertical axis. C: Docking model for the protein-DNA complex. The minimal 16-bp DNA recognition sequence is shown as a ribbon.The above figures are reprinted by permission from John Wiley & Sons, Inc.: Proteins (2006, 63, 711-715) copyright 2006.
Literature references that cite this PDB file's key reference
PubMed id Reference
17586768 M.A.Johnson, M.W.Southworth, T.Herrmann, L.Brace, F.B.Perler, and K.Wüthrich (2007).
NMR structure of a KlbA intein precursor from Methanococcus jannaschii.Protein Sci, 16, 1316-1328.
PDB codes: 2jmz 2jnq 17254599 P.Van Roey, B.Pereira, Z.Li, K.Hiraga, M.Belfort, and V.Derbyshire (2007).
Crystallographic and mutational studies of Mycobacterium tuberculosis recA mini-inteins suggest a pivotal role for a highly conserved aspartate residue.J Mol Biol, 367, 162-173.
PDB codes: 2imz 2in0 2in8 2in9 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.
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