PDBsum entry 3c5f

Transferase, lyase/DNA

PDB id: 3c5f

Contents

Protein chains

326 a.a. *

DNA/RNA

Metals

_NA ×6

Waters ×639

* Residue conservation analysis

PDB id:

3c5f

Name:

Transferase, lyase/DNA

Title:

Structure of a binary complex of the r517a pol lambda mutant

Structure:

DNA (5'-d( Dcp Dgp Dgp Dcp Dcp Dgp Dtp Dap Dcp Dtp Dg)-3'). Chain: t, u. Engineered: yes. Other_details: template. DNA (5'-d( Dcp Dap Dgp Dtp Dap Dc)-3'). Chain: p, q. Engineered: yes. Other_details: primer. DNA (5'-d(p Dgp Dcp Dcp Dg)-3').

Source:

Synthetic: yes. Homo sapiens. Human. Gene: poll. Expressed in: escherichia coli.

Resolution:

2.25Å R-factor: 0.224 R-free: 0.263

Ensemble:

2 models

Authors:

M.Garcia-Diaz,K.Bebenek,M.C.Foley,L.C.Pedersen,T.Schlick,T.A.Kunkel

Key ref:

K.Bebenek et al. (2008). Substrate-induced DNA strand misalignment during catalytic cycling by DNA polymerase lambda. Embo Rep, 9, 459-464. PubMed id: 18369368

Date:

31-Jan-08 Release date: 02-Sep-08

Protein chains

Q9UGP5  (DPOLL_HUMAN) -  DNA polymerase lambda from Homo sapiens

Seq: 575 a.a.

Struc: 326 a.a.*

* PDB and UniProt seqs differ at 1 residue position (black cross)

DNA/RNA chains

C-G-G-C-C-G-T-A-C-T-G 11 bases

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

G-C-C-G 4 bases

C-G-G-C-C-G-T-A-C-T-G 11 bases

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

G-C-C-G 4 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

Embo Rep 9:459-464 (2008)

PubMed id: 18369368

Substrate-induced DNA strand misalignment during catalytic cycling by DNA polymerase lambda.

K.Bebenek, M.Garcia-Diaz, M.C.Foley, L.C.Pedersen, T.Schlick, T.A.Kunkel.

ABSTRACT

The simple deletion of nucleotides is common in many organisms. It can be advantageous when it activates genes beneficial to microbial survival in adverse environments, and deleterious when it mutates genes relevant to survival, cancer or degenerative diseases. The classical idea is that simple deletions arise by strand slippage. A prime opportunity for slippage occurs during DNA synthesis, but it remains unclear how slippage is controlled during a polymerization cycle. Here, we report crystal structures and molecular dynamics simulations of mutant derivatives of DNA polymerase lambda bound to a primer-template during strand slippage. Relative to the primer strand, the template strand is in multiple conformations, indicating intermediates on the pathway to deletion mutagenesis. Consistent with these intermediates, the mutant polymerases generate single-base deletions at high rates. The results indicate that dNTP-induced template strand repositioning during conformational rearrangements in the catalytic cycle is crucial to controlling the rate of strand slippage.