PDBsum entry 2bcv

Transferase, lyase/DNA

PDB id: 2bcv

Contents

Protein chain

323 a.a. *

DNA/RNA

Ligands

TTP

Metals

_MG

_NA ×3

Waters ×345

* Residue conservation analysis

PDB id:

2bcv

Name:

Transferase, lyase/DNA

Title:

DNA polymerase lambda in complex with dttp and a DNA duplex containing an unpaired dtmp

Structure:

5'-d(p Gp Cp Cp G)-3'. Chain: d. Engineered: yes. Other_details: template. 5'-d( Cp Ap Gp Tp Ap (O2c))-3'. Chain: p. Engineered: yes. Other_details: primer. 5'-d( Cp Gp Gp Cp Ap Gp Tp Tp Ap Cp Tp G)-3'.

Source:

Synthetic: yes. Homo sapiens. Human. Organism_taxid: 9606. Expressed in: escherichia coli. Expression_system_taxid: 562.

Resolution:

2.00Å R-factor: 0.204 R-free: 0.232

Authors:

M.Garcia-Diaz,K.Bebenek,J.M.Krahn,L.C.Pedersen,T.A.Kunkel

Key ref:

M.Garcia-Diaz et al. (2006). Structural analysis of strand misalignment during DNA synthesis by a human DNA polymerase. Cell, 124, 331-342. PubMed id: 16439207 DOI: 10.1016/j.cell.2005.10.039

Date:

19-Oct-05 Release date: 07-Mar-06

Protein chain

Q9UGP5  (DPOLL_HUMAN) -  DNA polymerase lambda from Homo sapiens

Seq: 575 a.a.

Struc: 323 a.a.

DNA/RNA chains

G-C-C-G 4 bases

C-A-G-T-A-O2C 6 bases

C-G-G-C-A-G-T-T-A-C-T-G 12 bases

Enzyme reactions

• Enzyme class 2: E.C.2.7.7.7 - DNA-directed Dna polymerase.
• Reaction: DNA(n) + a 2'-deoxyribonucleoside 5'-triphosphate = DNA(n+1) + diphosphate
• Enzyme class 3: E.C.4.2.99.- - ?????

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.

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

Added reference

DOI no: 10.1016/j.cell.2005.10.039

Cell 124:331-342 (2006)

PubMed id: 16439207

Structural analysis of strand misalignment during DNA synthesis by a human DNA polymerase.

M.Garcia-Diaz, K.Bebenek, J.M.Krahn, L.C.Pedersen, T.A.Kunkel.

ABSTRACT

Insertions and deletions in coding sequences can alter the reading frame of genes and have profound biological consequences. In 1966, Streisinger proposed that these mutations result from strand slippage, which in repetitive sequences generates misaligned intermediates stabilized by correct base pairing that support polymerization. We report here crystal structures of human DNA polymerase lambda, which frequently generates deletion mutations, bound to such intermediates. Each contains an extrahelical template nucleotide upstream of the active site. Surprisingly, the extra nucleotide, even when combined with an adjacent mismatch, does not perturb polymerase active site geometry, which is indistinguishable from that for correctly aligned strands. These structures reveal how pol lambda can polymerize on substrates with minimal homology during repair of double-strand breaks and represent strand-slippage intermediates consistent with Streisinger's classical hypothesis. They are thus relevant to the origin of single-base deletions, a class of mutations that can confer strong biological phenotypes.

Selected figure(s)

Figure 3.
Figure 3. The Extrahelical Adenine Is in Close Proximity to β strand 8

Figure 4.
Figure 4. Pol λ Can Tolerate Distortion upstream of the Primer Terminus

The above figures are reprinted by permission from Cell Press: Cell (2006, 124, 331-342) copyright 2006.

Figures were selected by an automated process.