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PDBsum entry 2pxi
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Lyase, transferase/DNA
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PDB id
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2pxi
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Contents |
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* Residue conservation analysis
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Enzyme class 1:
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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 2:
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E.C.4.2.99.-
- ?????
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Enzyme class 3:
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E.C.4.2.99.18
- DNA-(apurinic or apyrimidinic site) lyase.
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Reaction:
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2'-deoxyribonucleotide-(2'-deoxyribose 5'-phosphate)- 2'-deoxyribonucleotide-DNA = a 3'-end 2'-deoxyribonucleotide-(2,3- dehydro-2,3-deoxyribose 5'-phosphate)-DNA + a 5'-end 5'-phospho- 2'-deoxyribonucleoside-DNA + H+
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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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J Am Chem Soc
129:15412-15413
(2007)
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PubMed id:
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(R)-beta,gamma-fluoromethylene-dGTP-DNA ternary complex with DNA polymerase beta.
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C.E.McKenna,
B.A.Kashemirov,
T.G.Upton,
V.K.Batra,
M.F.Goodman,
L.C.Pedersen,
W.A.Beard,
S.H.Wilson.
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ABSTRACT
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Literature references that cite this PDB file's key reference
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PubMed id
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Reference
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C.Dalvit,
and
A.Vulpetti
(2011).
Fluorine-protein interactions and ¹⁹F NMR isotropic chemical shifts: An empirical correlation with implications for drug design.
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ChemMedChem,
6,
104-114.
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G.K.Surya Prakash,
M.Zibinsky,
T.G.Upton,
B.A.Kashemirov,
C.E.McKenna,
K.Oertell,
M.F.Goodman,
V.K.Batra,
L.C.Pedersen,
W.A.Beard,
D.D.Shock,
S.H.Wilson,
and
G.A.Olah
(2010).
Synthesis and biological evaluation of fluorinated deoxynucleotide analogs based on bis-(difluoromethylene)triphosphoric acid.
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Proc Natl Acad Sci U S A,
107,
15693-15698.
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PDB code:
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E.Gaidamauskas,
H.Parker,
B.A.Kashemirov,
A.A.Holder,
K.Saejueng,
C.E.McKenna,
and
D.C.Crans
(2009).
Complexation of bisphosphonates with ytterbium(III): application of phosphate and ATP detection assay based on Yb(3+)-pyrocatechol violet.
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J Inorg Biochem,
103,
1652-1657.
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S.C.Kamerlin,
C.E.McKenna,
M.F.Goodman,
M.F.Goondman,
and
A.Warshel
(2009).
A computational study of the hydrolysis of dGTP analogues with halomethylene-modified leaving groups in solution: implications for the mechanism of DNA polymerases.
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Biochemistry,
48,
5963-5971.
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F.Liang,
N.Jain,
T.Hutchens,
D.D.Shock,
W.A.Beard,
S.H.Wilson,
M.P.Chiarelli,
and
B.P.Cho
(2008).
Alpha,beta-methylene-2'-deoxynucleoside 5'-triphosphates as noncleavable substrates for DNA polymerases: isolation, characterization, and stability studies of novel 2'-deoxycyclonucleosides, 3,5'-cyclo-dG, and 2,5'-cyclo-dT.
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J Med Chem,
51,
6460-6470.
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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.
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Links
