PDBsum entry 5yv2

DNA binding protein

PDB id: 5yv2

Contents

Protein chains

342 a.a.

DNA/RNA

Ligands

PO4 ×3

Metals

_MG ×4

Waters ×724

PDB id:

5yv2

Name:

DNA binding protein

Title:

DNA polymerase iv - DNA ternary complex 14

Structure:

DNA polymerase iv. Chain: f, a. Synonym: pol iv,translesion synthesis polymerase iv,tsl polymerase iv. Engineered: yes. Dtn1. Chain: g, b. Engineered: yes. Dtn2.

Source:

Escherichia coli k-12. Organism_taxid: 83333. Strain: k12. Gene: dinb, dinp, b0231, jw0221. Expressed in: escherichia coli. Expression_system_taxid: 562. Synthetic: yes. Organism_taxid: 83333

Resolution:

1.90Å R-factor: 0.206 R-free: 0.245

Authors:

J.Kottur,D.T.Nair

Key ref:

J.Kottur and D.T.Nair (2018). Pyrophosphate hydrolysis is an intrinsic and critical step of the DNA synthesis reaction. Nucleic Acids Res, 46, 5875-5885. PubMed id: 29850882 DOI: 10.1093/nar/gky402

Date:

23-Nov-17 Release date: 05-Sep-18

Protein chains

Q47155  (DPO4_ECOLI) -  DNA polymerase IV from Escherichia coli (strain K12)

Seq: 351 a.a.

Struc: 342 a.a.*

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

DNA/RNA chains

T-C-T-A-G-G-G-T-C-C-T-A-G-G-A-C-C-C 18 bases

G-G-G-T-C-C-T-A-G-G-A-C-C-C-T 15 bases

T-C-T-A-G-G-G-T-C-C-T-A-G-G-A-C-C-C 18 bases

C-T-A-G-G-G-T-C-C-T-A-G-G-A-C-C-C-T 18 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

DNA(n) + 2'-deoxyribonucleoside 5'-triphosphate = DNA(n+1) + diphosphate (Bound ligand (Het Group name = PO4) matches with 55.56% similarity)

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

Added reference

DOI no: 10.1093/nar/gky402

Nucleic Acids Res 46:5875-5885 (2018)

PubMed id: 29850882

Pyrophosphate hydrolysis is an intrinsic and critical step of the DNA synthesis reaction.

J.Kottur, D.T.Nair.

ABSTRACT

DNA synthesis by DNA polymerases (dPols) is central to duplication and maintenance of the genome in all living organisms. dPols catalyze the formation of a phosphodiester bond between the incoming deoxynucleoside triphosphate and the terminal primer nucleotide with the release of a pyrophosphate (PPi) group. It is believed that formation of the phosphodiester bond is an endergonic reaction and PPi has to be hydrolyzed by accompanying pyrophosphatase enzymes to ensure that the free energy change of the DNA synthesis reaction is negative and it can proceed in the forward direction. The fact that DNA synthesis proceeds in vitro in the absence of pyrophosphatases represents a long-standing conundrum regarding the thermodynamics of the DNA synthesis reaction. Using time-resolved crystallography, we show that hydrolysis of PPi is an intrinsic and critical step of the DNA synthesis reaction catalyzed by dPols. The hydrolysis of PPi occurs after the formation of the phosphodiester bond and ensures that the DNA synthesis reaction is energetically favorable without the need for additional enzymes. Also, we observe that DNA synthesis is a two Mg2+ ion assisted stepwise associative SN2 reaction. Overall, this study provides deep temporal insight regarding the primary enzymatic reaction responsible for genome duplication.