PDBsum entry 5u8h

Transferase,lyase/DNA

PDB id: 5u8h

Contents

Protein chain

316 a.a.

DNA/RNA

Metals

_NA ×2

Waters ×249

PDB id:

5u8h

Name:

Transferase,lyase/DNA

Title:

DNA polymerase beta g231d crystallized in peg 400

Structure:

DNA polymerase beta. Chain: a. Engineered: yes. Mutation: yes. DNA (5'-d( Cp Cp Gp Ap Cp Ap 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: 562. Synthetic: yes. Synthetic construct. Organism_taxid: 32630.

Resolution:

2.16Å R-factor: 0.187 R-free: 0.234

Authors:

B.E.Eckenroth,S.Doublie

Key ref:

B.E.Eckenroth et al. (2017). Remote Mutations Induce Functional Changes in Active Site Residues of Human DNA Polymerase β. Biochemistry, 56, 2363-2371. PubMed id: 28402631

Date:

14-Dec-16 Release date: 26-Apr-17

Protein chain

P06746  (DPOLB_HUMAN) -  DNA polymerase beta from Homo sapiens

Seq: 335 a.a.

Struc: 316 a.a.*

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

DNA/RNA chains

C-C-G-A-C-A-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

Biochemistry 56:2363-2371 (2017)

PubMed id: 28402631

Remote Mutations Induce Functional Changes in Active Site Residues of Human DNA Polymerase β.

B.E.Eckenroth, J.B.Towle-Weicksel, A.A.Nemec, D.L.Murphy, J.B.Sweasy, S.Doublié.

ABSTRACT

With the formidable growth in the volume of genetic information, it has become essential to identify and characterize mutations in macromolecules not only to predict contributions to disease processes but also to guide the design of therapeutic strategies. While mutations of certain residues have a predictable phenotype based on their chemical nature and known structural position, many types of mutations evade prediction based on current information. Described in this work are the crystal structures of two cancer variants located in the palm domain of DNA polymerase β (pol β), S229L and G231D, whose biological phenotype was not readily linked to a predictable structural implication. Structural results demonstrate that the mutations elicit their effect through subtle influences on secondary interactions with a residue neighboring the active site. Residues 229 and 231 are 7.5 and 12.5 Å, respectively, from the nearest active site residue, with a β-strand between them. A residue on this intervening strand, M236, appears to transmit fine structural perturbations to the catalytic metal-coordinating residue D256, affecting its conformational stability.