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PDBsum entry 3si8
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Transferase/DNA
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PDB id
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3si8
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PDB id:
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| Name: |
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Transferase/DNA
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Title:
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Human DNA polymerase eta - DNA ternary complex with the 5't of a cpd in the active site (tt2)
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Structure:
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DNA polymerase eta. Chain: a. Fragment: unp residues 1-432. Synonym: rad30 homolog a, xeroderma pigmentosum variant type protein. Engineered: yes. DNA (5'-d( Tp A Ap Cp (Ttd)p Ap Tp Gp Ap Cp Gp C)-3'). Chain: t. Engineered: yes. Other_details: DNA template (chain t).
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Source:
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Homo sapiens. Human. Organism_taxid: 9606. Strain: chemically synthesized. Gene: polh, rad30, rad30a, xpv. Expressed in: escherichia coli. Expression_system_taxid: 562. Synthetic: yes. Other_details: DNA oligonucleotide with thymine dimer (cyclobutane
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Resolution:
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2.15Å
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R-factor:
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0.241
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R-free:
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0.258
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Authors:
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C.Biertumpfel,Y.Zhao,Y.Kondo,S.Ramon-Maiques,M.Gregory,J.Y.Lee, C.Masutani,A.R.Lehmann,F.Hanaoka,W.Yang
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Key ref:
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C.Biertümpfel
et al.
(2010).
Structure and mechanism of human DNA polymerase eta.
Nature,
465,
1044-1048.
PubMed id:
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Date:
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17-Jun-11
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Release date:
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03-Aug-11
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Supersedes:
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PROCHECK
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Headers
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References
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Q9Y253
(POLH_HUMAN) -
DNA polymerase eta from Homo sapiens
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Seq:
Struc:
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713 a.a.
422 a.a.
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Key: |
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PfamA domain |
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Secondary structure |
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CATH domain |
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A-C-TTD-A-T-G-A-C-G-C
10 bases
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T-G-C-G-T-C-A-T-A
9 bases
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Enzyme class:
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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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Molecule diagrams generated from .mol files obtained from the
KEGG ftp site
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Nature
465:1044-1048
(2010)
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PubMed id:
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Structure and mechanism of human DNA polymerase eta.
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C.Biertümpfel,
Y.Zhao,
Y.Kondo,
S.Ramón-Maiques,
M.Gregory,
J.Y.Lee,
C.Masutani,
A.R.Lehmann,
F.Hanaoka,
W.Yang.
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ABSTRACT
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The variant form of the human syndrome xeroderma pigmentosum (XPV) is caused by
a deficiency in DNA polymerase eta (Poleta), a DNA polymerase that enables
replication through ultraviolet-induced pyrimidine dimers. Here we report
high-resolution crystal structures of human Poleta at four consecutive steps
during DNA synthesis through cis-syn cyclobutane thymine dimers. Poleta acts
like a 'molecular splint' to stabilize damaged DNA in a normal B-form
conformation. An enlarged active site accommodates the thymine dimer with
excellent stereochemistry for two-metal ion catalysis. Two residues conserved
among Poleta orthologues form specific hydrogen bonds with the lesion and the
incoming nucleotide to assist translesion synthesis. On the basis of the
structures, eight Poleta missense mutations causing XPV can be rationalized as
undermining the molecular splint or perturbing the active-site alignment. The
structures also provide an insight into the role of Poleta in replicating
through D loop and DNA fragile sites.
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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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A.Ummat,
O.Rechkoblit,
R.Jain,
J.Roy Choudhury,
R.E.Johnson,
T.D.Silverstein,
A.Buku,
S.Lone,
L.Prakash,
S.Prakash,
and
A.K.Aggarwal
(2012).
Structural basis for cisplatin DNA damage tolerance by human polymerase η during cancer chemotherapy.
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Nat Struct Mol Biol,
19,
628-632.
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PDB code:
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J.E.Sale,
A.R.Lehmann,
and
R.Woodgate
(2012).
Y-family DNA polymerases and their role in tolerance of cellular DNA damage.
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Nat Rev Mol Cell Biol,
13,
141-152.
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T.Nakamura,
Y.Zhao,
Y.Yamagata,
Y.J.Hua,
and
W.Yang
(2012).
Watching DNA polymerase η make a phosphodiester bond.
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Nature,
487,
196-201.
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PDB codes:
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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
