PDBsum entry 4p4p

Transferase/DNA

PDB id: 4p4p

Contents

Protein chain

282 a.a.

DNA/RNA

Ligands

_DG-_DC

Metals

_NA

Waters ×250

PDB id:

4p4p

Name:

Transferase/DNA

Title:

Crystal structure of leishmania infantum polymerase beta: nick complex

Structure:

DNA polymerase beta. Chain: a. Engineered: yes. DNA (5'-d( Cp Ap Gp Tp Ap Cp T)-3'). Chain: c. Engineered: yes. DNA (5'-d(p Gp Cp Cp G)-3'). Chain: d. Engineered: yes.

Source:

Leishmania infantum. Organism_taxid: 5671. Expressed in: escherichia coli. Expression_system_taxid: 562. Synthetic: yes. Synthetic construct. Organism_taxid: 32630. Organism_taxid: 32630

Resolution:

2.30Å R-factor: 0.195 R-free: 0.234

Authors:

E.Mejia,M.Burak,A.Alonso,V.Larraga,T.Kunkel,K.Bebenek,M.Garcia-Diaz

Key ref:

E.Mejia et al. (2014). Structures of the Leishmania infantum polymerase beta. Dna Repair (amst), 18, 1-9. PubMed id: 24666693 DOI: 10.1016/j.dnarep.2014.03.001

Date:

12-Mar-14 Release date: 06-Aug-14

Protein chain

Q9U6N3  (Q9U6N3_LEIIN) -  DNA polymerase from Leishmania infantum

Seq: 376 a.a.

Struc: 282 a.a.*

* PDB and UniProt seqs differ at 4 residue positions (black crosses)

DNA/RNA chains

C-A-G-T-A-C-T 7 bases

G-G-C-A-G-T-A-C-T-G 10 bases

Enzyme reactions

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

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

Added reference

DOI no: 10.1016/j.dnarep.2014.03.001

Dna Repair (amst) 18:1-9 (2014)

PubMed id: 24666693

Structures of the Leishmania infantum polymerase beta.

E.Mejia, M.Burak, A.Alonso, V.Larraga, T.A.Kunkel, K.Bebenek, M.Garcia-Diaz.

ABSTRACT

Protozoans of the genus Leishmania, the pathogenic agent causing leishmaniasis, encode the family X DNA polymerase Li Pol β. Here, we report the first crystal structures of Li Pol β. Our pre- and post-catalytic structures show that the polymerase adopts the common family X DNA polymerase fold. However, in contrast to other family X DNA polymerases, the dNTP-induced conformational changes in Li Pol β are much more subtle. Moreover, pre- and post-catalytic structures reveal that Li Pol β interacts with the template strand through a nonconserved, variable region known as loop3. Li Pol β Δloop3 mutants display a higher catalytic rate, catalytic efficiency and overall error rates with respect to WT Li Pol β. These results further demonstrate the subtle structural variability that exists within this family of enzymes and provides insight into how this variability underlies the substantial functional differences among their members.