3Q36

Crystal structure of the 4Fe-4S cluster domain of human DNA primase large subunit

Summary for 3Q36

• Entry DOI: 10.2210/pdb3q36/pdb
• Related: 3L9Q 3LGB
• Descriptor: DNA primase large subunit, IRON/SULFUR CLUSTER, FE (III) ION, ... (4 entities in total)
• Functional Keywords: pol alpha, primase, dna replication, polymerase, iron-sulfur cluster, dna-binding, dna-directed rna polymerase, metal-binding, nucleotidyltransferase, phosphoprotein, primosome, transcription, transferase
• Biological source: Homo sapiens (human)
• Total number of polymer chains: 2
• Total formula weight: 44927.78

Authors

Agarkar, V.B.,Babayeva, N.D.,Tahirov, T.H. (deposition date: 2010-12-21, release date: 2011-04-13, Last modification date: 2023-09-13)

Primary citation

Agarkar, V.B.,Babayeva, N.D.,Pavlov, Y.I.,Tahirov, T.H.
Crystal structure of the C-terminal domain of human DNA primase large subunit: Implications for the mechanism of the primase - polymerase alpha switch.
Cell Cycle, 10:926-931, 2011

PubMed Abstract: DNA polymerases cannot synthesize DNA without a primer, and DNA primase is the only specialized enzyme capable of de novo synthesis of short RNA primers. In eukaryotes, primase functions within a heterotetrameric complex in concert with a tightly bound DNA polymerase α (Pol α). In humans, the Pol α part is comprised of a catalytic subunit (p180) and an accessory subunit B (p70), and the primase part consists of a small catalytic subunit (p49) and a large essential subunit (p58). The latter subunit participates in primer synthesis, counts the number of nucleotides in a primer, assists the release of the primer-template from primase and transfers it to the Pol α active site. Recently reported crystal structures of the C-terminal domains of the yeast and human enzymes' large subunits provided critical information related to their structure, possible sites for binding of nucleotides and template DNA, as well as the overall organization of eukaryotic primases. However, the structures also revealed a difference in the folding of their proposed DNA-binding fragments, raising the possibility that yeast and human proteins are functionally different. Here we report new structure of the C-terminal domain of the human primase p58 subunit. This structure exhibits a fold similar to a fold reported for the yeast protein but different than a fold reported for the human protein. Based on a comparative analysis of all three C-terminal domain structures, we propose a mechanism of RNA primer length counting and dissociation of the primer-template from primase by a switch in conformation of the ssDNA-binding region of p58.

PubMed: 21346410

Experimental method

X-RAY DIFFRACTION (2.5 Å)