PDBsum entry: 2cw8

Hydrolase

PDB id: 2cw8

Contents

Protein chain

537 a.a. *

Ligands

SO4 ×8

GOL ×4

Waters ×279

* Residue conservation analysis

PDB id:

2cw8

Name:

Hydrolase

Title:

Crystal structure of intein homing endonuclease ii

Structure:

Endonuclease pi-pkoii. Chain: a. Engineered: yes

Source:

Thermococcus kodakarensis. Organism_taxid: 69014. Strain: kod1. Expressed in: escherichia coli bl21(de3). Expression_system_taxid: 469008.

Resolution:

2.50Å R-factor: 0.217 R-free: 0.252

Authors:

H.Matsumura,H.Takahashi,T.Inoue,H.Hashimoto,M.Nishioka,S.Fuj M.Takagi,T.Imanaka,Y.Kai

Key ref:

H.Matsumura et al. (2006). Crystal structure of intein homing endonuclease II encoded in DNA polymerase gene from hyperthermophilic archaeon Thermococcus kodakaraensis strain KOD1. Proteins, 63, 711-715. PubMed id: 16493661 DOI: 10.1002/prot.20858

Date:

17-Jun-05 Release date: 18-Apr-06

Protein chain

P77933  (DPOL_PYRKO) -  DNA polymerase

Seq: 1671 a.a.

Struc: 537 a.a.*

* PDB and UniProt seqs differ at 3 residue positions (black crosses)

Enzyme reactions

• Enzyme class: E.C.2.7.7.7 - DNA-directed Dna polymerase.
• Reaction: Deoxynucleoside triphosphate + DNA(n) = diphosphate + DNA(n+1)

Molecule diagrams generated from .mol files obtained from the KEGG ftp site

 Gene Ontology (GO) functional annotation 

• Biological process: intein-mediated protein splicing (1 term)
• Biochemical function: endonuclease activity (1 term)

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.