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PDBsum entry 5omf
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DNA binding protein
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PDB id
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5omf
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PDB id:
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DNA binding protein
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Title:
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Closed, ternary structure of kod DNA polymerase
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Structure:
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DNA polymerase,DNA polymerase,DNA polymerase. Chain: a. Ec: 2.7.7.7,3.1.-.-,2.7.7.7,3.1.-.-,2.7.7.7,3.1.-.-. Engineered: yes. DNA (5'-d(p Cp Tp Gp Tp Gp Gp Cp Cp Gp Tp Gp Gp Tp C)-3'). Chain: t. Engineered: yes. DNA (5'-d( Gp Ap Cp Cp Ap Cp Gp Gp Cp Cp Ap C)-3'). Chain: p.
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Source:
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Thermococcus kodakarensis (strain atcc baa-918 / jcm 12380 / kod1). Organism_taxid: 69014. Gene: pol, tk0001. Expressed in: escherichia coli. Expression_system_taxid: 562. Synthetic: yes. Synthetic construct. Organism_taxid: 32630.
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Resolution:
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2.09Å
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R-factor:
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0.197
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R-free:
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0.234
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Authors:
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H.M.Kropp,K.Betz,J.Wirth,K.Diederichs,A.Marx
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Key ref:
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H.M.Kropp
et al.
(2017).
Crystal structures of ternary complexes of archaeal B-family DNA polymerases.
PLoS One,
12,
e0188005.
PubMed id:
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Date:
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31-Jul-17
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Release date:
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20-Dec-17
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PROCHECK
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Headers
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References
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P77933
(DPOL_THEKO) -
DNA polymerase from Thermococcus kodakarensis (strain ATCC BAA-918 / JCM 12380 / KOD1)
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Seq:
Struc:
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1671 a.a.
756 a.a.*
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Key: |
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PfamA domain |
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Secondary structure |
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*
PDB and UniProt seqs differ
at 2 residue positions (black
crosses)
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C-T-G-T-G-G-C-C-G-T-G-G-T-C
14 bases
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G-A-C-C-A-C-G-G-C-C-A-C
12 bases
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Enzyme class 2:
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E.C.2.7.7.7
- DNA-directed Dna polymerase.
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Reaction:
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DNA(n) + a 2'-deoxyribonucleoside 5'-triphosphate = DNA(n+1) + diphosphate
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DNA(n)
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+
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2'-deoxyribonucleoside 5'-triphosphate
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=
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DNA(n+1)
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+
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diphosphate
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Enzyme class 3:
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E.C.3.1.-.-
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Note, where more than one E.C. class is given (as above), each may
correspond to a different protein domain or, in the case of polyprotein
precursors, to a different mature protein.
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Molecule diagrams generated from .mol files obtained from the
KEGG ftp site
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PLoS One
12:e0188005
(2017)
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PubMed id:
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Crystal structures of ternary complexes of archaeal B-family DNA polymerases.
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H.M.Kropp,
K.Betz,
J.Wirth,
K.Diederichs,
A.Marx.
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ABSTRACT
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Archaeal B-family polymerases drive biotechnology by accepting a wide substrate
range of chemically modified nucleotides. By now no structural data for archaeal
B-family DNA polymerases in a closed, ternary complex are available, which would
be the basis for developing next generation nucleotides. We present the ternary
crystal structures of KOD and 9°N DNA polymerases complexed with DNA and the
incoming dATP. The structures reveal a third metal ion in the active site, which
was so far only observed for the eukaryotic B-family DNA polymerase δ and no
other B-family DNA polymerase. The structures reveal a wide inner channel and
numerous interactions with the template strand that provide space for
modifications within the enzyme and may account for the high processivity,
respectively. The crystal structures provide insights into the superiority over
other DNA polymerases concerning the acceptance of modified nucleotides.
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Links
