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41  structures 1734  species 0  interactions 2365  sequences 53  architectures

Family: DNA_primase_lrg (PF04104)

Summary: Eukaryotic and archaeal DNA primase, large subunit

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Eukaryotic and archaeal DNA primase, large subunit Provide feedback

DNA primase is the polymerase that synthesises small RNA primers for the Okazaki fragments made during discontinuous DNA replication. DNA primase is a heterodimer of two subunits, the small subunit Pri1 (48 kDa in yeast), and the large subunit Pri2 (58 kDa in the yeast S. cerevisiae) [1]. The large subunit of DNA primase forms interactions with the small subunit and the structure implicates that it is not directly involved in catalysis, but plays roles in correctly positioning the primase/DNA complex, and in the transfer of RNA to DNA polymerase [4].

Literature references

  1. Foiani M, Santocanale C, Plevani P, Lucchini G; , Mol Cell Biol 1989;9:3081-3087.: A single essential gene, PRI2, encodes the large subunit of DNA primase in Saccharomyces cerevisiae. PUBMED:2528682 EPMC:2528682

  2. Francesconi S, Longhese MP, Piseri A, Santocanale C, Lucchini G, Plevani P; , Proc Natl Acad Sci U S A 1991;88:3877-3881.: Mutations in conserved yeast DNA primase domains impair DNA replication in vivo. PUBMED:2023935 EPMC:2023935

  3. Stadlbauer F, Brueckner A, Rehfuess C, Eckerskorn C, Lottspeich F, Forster V, Tseng BY, Nasheuer HP; , Eur J Biochem 1994;222:781-793.: DNA replication in vitro by recombinant DNA-polymerase-alpha-primase. PUBMED:8026492 EPMC:8026492

  4. Lao-Sirieix SH, Nookala RK, Roversi P, Bell SD, Pellegrini L; , Nat Struct Mol Biol. 2005;12:1137-1144.: Structure of the heterodimeric core primase. PUBMED:16273105 EPMC:16273105

  5. Iyer LM, Koonin EV, Leipe DD, Aravind L; , Nucleic Acids Res. 2005;33:3875-3896.: Origin and evolution of the archaeo-eukaryotic primase superfamily and related palm-domain proteins: structural insights and new members. PUBMED:16027112 EPMC:16027112

This tab holds annotation information from the InterPro database.

InterPro entry IPR007238

DNA primase is the polymerase that synthesises small RNA primers for the Okazaki fragments made during discontinuous DNA replication. Primases are grouped into two classes, bacteria/bacteriophage and archaeal/eukaryotic. The proteins in the two classes differ in structure and the replication apparatus components. Archaeal/eukaryotic core primase is a heterodimeric enzyme consisting of a small catalytic subunit (PriS or Pri1) and a large subunit (PriL or Pri2). In the yeast Saccharomyces cerevisiae the small subunit is 48kDa and the large subunit 58kDa [ PUBMED:2528682 ]. In eukaryotic organisms, a heterotetrameric enzyme formed by DNA polymerase alpha, the B subunit and two primase subunits has primase activity. Although the catalytic activity and the the ATP binding site reside within PriS [ PUBMED:2023935 ], the PriL subunit is essential for primase function as disruption of the PriL gene in yeast is lethal. PriL is composed of two structural domains. Several functions have been proposed for PriL such as stabilization of the PriS, involvement in synthesis initiation, improvement of primase processivity, determination of product size and transfer of the products to DNA polymerase alpha [ PUBMED:16273105 ]. Primase function has also been demonstrated for human and mouse primase subunits [ PUBMED:8026492 ].

Gene Ontology

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Domain organisation

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Pfam Clan

This family is a member of clan DNA_primase_lrg (CL0242), which has the following description:

This clan contains the large subunit of archaeal and eukaryotic DNA primase, an enzyme which synthesises the oligoribonucleotide primers essential to DNA replication. The large subunit of DNA primase forms interactions with the small subunit and the structure implicates that it is not directly involved in catalysis, but plays a roles in correctly positioning the primase/DNA complex, and in the transfer of RNA to DNA polymerase [1]. The clan also contains the Lef-2 family, which is required for the expression of late genes. There is some evidence to suggest that LEF2 binds to both DNA and the DNA primase small subunit LEF-1 [3].

The clan contains the following 2 members:

Baculo_LEF-2 DNA_primase_lrg


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Curation and family details

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Seed source: COG2219
Previous IDs: none
Type: Family
Sequence Ontology: SO:0100021
Author: Kerrison ND , Finn RD
Number in seed: 42
Number in full: 2365
Average length of the domain: 242.00 aa
Average identity of full alignment: 34 %
Average coverage of the sequence by the domain: 53.48 %

HMM information View help on HMM parameters

HMM build commands:
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 61295632 -E 1000 --cpu 4 HMM pfamseq
Model details:
Parameter Sequence Domain
Gathering cut-off 22.4 22.4
Trusted cut-off 23.0 22.4
Noise cut-off 22.2 22.2
Model length: 266
Family (HMM) version: 17
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Species distribution

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Colour assignments

Archea Archea Eukaryota Eukaryota
Bacteria Bacteria Other sequences Other sequences
Viruses Viruses Unclassified Unclassified
Viroids Viroids Unclassified sequence Unclassified sequence


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For those sequences which have a structure in the Protein DataBank, we use the mapping between UniProt, PDB and Pfam coordinate systems from the PDBe group, to allow us to map Pfam domains onto UniProt sequences and three-dimensional protein structures. The table below shows the structures on which the DNA_primase_lrg domain has been found. There are 41 instances of this domain found in the PDB. Note that there may be multiple copies of the domain in a single PDB structure, since many structures contain multiple copies of the same protein sequence.

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