PDBsum entry 4ppx

Transferase, lyase/DNA

PDB id: 4ppx

Contents

Protein chain

314 a.a.

DNA/RNA

Metals

_NA ×2

Waters ×348

PDB id:

4ppx

Name:

Transferase, lyase/DNA

Title:

DNA polymerase beta e295k with spiroiminodihydantoin in templating position

Structure:

DNA polymerase beta. Chain: a. Engineered: yes. Mutation: yes. 5'-d( Cp Cp Gp Ap Cp (Sdh)p Gp Cp Gp Cp Ap Tp Cp Ap Gp C)- 3'. Chain: t. Engineered: yes. Other_details: DNA template strand.

Source:

Homo sapiens. Human. Organism_taxid: 9606. Gene: polb. Expressed in: escherichia coli. Expression_system_taxid: 469008. Synthetic: yes. Synthetic: yes

Resolution:

2.08Å R-factor: 0.181 R-free: 0.217

Authors:

B.E.Eckenroth,S.Doublie

Key ref:

B.E.Eckenroth et al. (2014). Crystal structure of DNA polymerase β with DNA containing the base lesion spiroiminodihydantoin in a templating position. Biochemistry, 53, 2075-2077. PubMed id: 24649945 DOI: 10.1021/bi500270e

Date:

27-Feb-14 Release date: 02-Apr-14

Protein chain

P06746  (DPOLB_HUMAN) -  DNA polymerase beta from Homo sapiens

Seq: 335 a.a.

Struc: 314 a.a.*

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

DNA/RNA chains

C-C-G-A-C-SDH-G-C-G-C-A-T-C-A-G-C 16 bases

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

G-T-C-G-G 5 bases

Enzyme reactions

• Enzyme class 1: E.C.2.7.7.7 - DNA-directed Dna polymerase.
• Reaction: DNA(n) + a 2'-deoxyribonucleoside 5'-triphosphate = DNA(n+1) + diphosphate
• Enzyme class 2: E.C.4.2.99.- - ?????
• Enzyme class 3: E.C.4.2.99.18 - DNA-(apurinic or apyrimidinic site) lyase.
• Reaction: 2'-deoxyribonucleotide-(2'-deoxyribose 5'-phosphate)- 2'-deoxyribonucleotide-DNA = a 3'-end 2'-deoxyribonucleotide-(2,3- dehydro-2,3-deoxyribose 5'-phosphate)-DNA + a 5'-end 5'-phospho- 2'-deoxyribonucleoside-DNA + H⁺

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: 10.1021/bi500270e

Biochemistry 53:2075-2077 (2014)

PubMed id: 24649945

Crystal structure of DNA polymerase β with DNA containing the base lesion spiroiminodihydantoin in a templating position.

B.E.Eckenroth, A.M.Fleming, J.B.Sweasy, C.J.Burrows, S.Doublié.

ABSTRACT

The first high-resolution crystal structure of spiroiminodihydantoin (dSp1) was obtained in the context of the DNA polymerase β active site and reveals two areas of significance. First, the structure verifies the recently determined S configuration at the spirocyclic carbon. Second, the distortion of the DNA duplex is similar to that of the single-oxidation product 8-oxoguanine. For both oxidized lesions, adaptation of the syn conformation results in similar backbone distortions in the DNA duplex. The resulting conformation positions the dSp1 A-ring as the base-pairing face whereas the B-ring of dSp1 protrudes into the major groove.