PDBsum entry 3mgi

Lyase,transferase/DNA

PDB id: 3mgi

Contents

Protein chain

319 a.a. *

DNA/RNA

Ligands

D3T

Metals

_NA

_MG

Waters ×156

* Residue conservation analysis

PDB id:

3mgi

Name:

Lyase,transferase/DNA

Title:

Ternary complex of a DNA polymerase lambda loop mutant

Structure:

DNA polymerase lambda. Chain: a. Fragment: loop mutant of DNA polymerase lambda. Synonym: pol lambda, DNA polymerase kappa, DNA polymerase beta-2, pol beta2. Engineered: yes. Mutation: yes. DNA. Chain: t.

Source:

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

Resolution:

2.60Å R-factor: 0.203 R-free: 0.270

Authors:

M.Garcia-Diaz,K.Bebenek,R.Z.Zhou,L.F.Povirk,T.Kunkel

Key ref:

K.Bebenek et al. (2010). Loop 1 modulates the fidelity of DNA polymerase lambda. Nucleic Acids Res, 38, 5419-5431. PubMed id: 20435673

Date:

06-Apr-10 Release date: 19-May-10

Protein chain

Q9UGP5  (DPOLL_HUMAN) -  DNA polymerase lambda from Homo sapiens

Seq: 575 a.a.

Struc: 319 a.a.*

* PDB and UniProt seqs differ at 3 residue positions (black crosses)

DNA/RNA chains

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

C-A-G-T-A-T 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

Nucleic Acids Res 38:5419-5431 (2010)

PubMed id: 20435673

Loop 1 modulates the fidelity of DNA polymerase lambda.

K.Bebenek, M.Garcia-Diaz, R.Z.Zhou, L.F.Povirk, T.A.Kunkel.

ABSTRACT

Differences in the substrate specificity of mammalian family X DNA polymerases are proposed to partly depend on a loop (loop 1) upstream of the polymerase active site. To examine if this is the case in DNA polymerase lambda (pol lambda), here we characterize a variant of the human polymerase in which nine residues of loop 1 are replaced with four residues from the equivalent position in pol beta. Crystal structures of the mutant enzyme bound to gapped DNA with and without a correct dNTP reveal that the change in loop 1 does not affect the overall structure of the protein. Consistent with these structural data, the mutant enzyme has relatively normal catalytic efficiency for correct incorporation, and it efficiently participates in non-homologous end joining of double-strand DNA breaks. However, DNA junctions recovered from end-joining reactions are more diverse than normal, and the mutant enzyme is substantially less accurate than wild-type pol lambda in three different biochemical assays. Comparisons of the binary and ternary complex crystal structures of mutant and wild-type pol lambda suggest that loop 1 modulates pol lambda's fidelity by controlling dNTP-induced movements of the template strand and the primer-terminal 3'-OH as the enzyme transitions from an inactive to an active conformation.