4EDV

The structure of the S. aureus DnaG RNA Polymerase Domain bound to pppGpp and Manganese

Summary for 4EDV

• Entry DOI: 10.2210/pdb4edv/pdb
• Related: 4E2K 4EDR 4EDT 4EDY 4EDZ 4EE1
• Descriptor: DNA primase, BENZAMIDINE, guanosine 5'-(tetrahydrogen triphosphate) 3'-(trihydrogen diphosphate), ... (5 entities in total)
• Functional Keywords: catalytic domain, bacterial, nucleotide, nucleoside triphosphate, nucleoside polyphosphate, protein-ligand complex, transferase, transferase-transferase inhibitor complex, transferase/transferase inhibitor
• Biological source: Staphylococcus aureus
• Total number of polymer chains: 1
• Total formula weight: 38645.61

Authors

Rymer, R.U.,Solorio, F.A.,Chu, C.,Corn, J.E.,Wang, J.D.,Berger, J.M. (deposition date: 2012-03-27, release date: 2012-07-25, Last modification date: 2024-02-28)

Primary citation

Rymer, R.U.,Solorio, F.A.,Tehranchi, A.K.,Chu, C.,Corn, J.E.,Keck, J.L.,Wang, J.D.,Berger, J.M.
Binding Mechanism of Metal-NTP Substrates and Stringent-Response Alarmones to Bacterial DnaG-Type Primases.
Structure, 20:1478-1489, 2012

PubMed Abstract: Primases are DNA-dependent RNA polymerases found in all cellular organisms. In bacteria, primer synthesis is carried out by DnaG, an essential enzyme that serves as a key component of DNA replication initiation, progression, and restart. How DnaG associates with nucleotide substrates and how certain naturally prevalent nucleotide analogs impair DnaG function are unknown. We have examined one of the earliest stages in primer synthesis and its control by solving crystal structures of the S. aureus DnaG catalytic core bound to metal ion cofactors and either individual nucleoside triphosphates or the nucleotidyl alarmones, pppGpp and ppGpp. These structures, together with both biochemical analyses and comparative studies of enzymes that use the same catalytic fold as DnaG, pinpoint the predominant nucleotide-binding site of DnaG and explain how the induction of the stringent response in bacteria interferes with primer synthesis.

PubMed: 22795082
DOI: 10.1016/j.str.2012.05.017

Experimental method

X-RAY DIFFRACTION (2.01 Å)