3LGB

Crystal Structure of the Fe-S Domain of the yeast DNA primase

PDB DOI: https://doi.org/10.2210/pdb3LGB/pdb

Classification: TRANSFERASE
Organism(s): Saccharomyces cerevisiae
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2010-01-20 Released: 2010-04-21
Deposition Author(s): Sauguet, L., Pellegrini, L.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.54 Å
R-Value Free: 0.164
R-Value Work: 0.154
R-Value Observed: 0.155

wwPDB Validation 3D Report Full Report

This is version 1.2 of the entry. See complete history.

Literature

Shared Active Site Architecture between the Large Subunit of Eukaryotic Primase and DNA Photolyase

Sauguet, L., Klinge, S., Perera, R.L., Maman, J.D., Pellegrini, L.

(2010) PLoS One 5: 10083-10083

PubMed: 20404922 Search on PubMedSearch on PubMed Central
DOI: https://doi.org/10.1371/journal.pone.0010083
Primary Citation of Related Structures:
3LGB

PubMed Abstract:
DNA synthesis during replication relies on RNA primers synthesised by the primase, a specialised DNA-dependent RNA polymerase that can initiate nucleic acid synthesis de novo. In archaeal and eukaryotic organisms, the primase is a heterodimeric enzyme resulting from the constitutive association of a small (PriS) and large (PriL) subunit. The ability of the primase to initiate synthesis of an RNA primer depends on a conserved Fe-S domain at the C-terminus of PriL (PriL-CTD). However, the critical role of the PriL-CTD in the catalytic mechanism of initiation is not understood.

Organizational Affiliation

Department of Biochemistry, University of Cambridge, Cambridge, United Kingdom.

Macromolecule Content

Total Structure Weight: 47.29 kDa
Atom Count: 3,704
Modelled Residue Count: 374
Deposited Residue Count: 388
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA primase large subunit	A, B	194	Saccharomyces cerevisiae	Mutation(s): 0 Gene Names: PRI2, YKL045W, YKL258 EC: 2.7.7
UniProt
Find proteins for P20457 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P20457 Go to UniProtKB: P20457
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P20457
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
SF4 Query on SF4 Download Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain F [auth B] MOL2 format, chain C [auth A] MOL2 format, chain F [auth B]	C [auth A], F [auth B]	IRON/SULFUR CLUSTER Fe₄ S₄ LJBDFODJNLIPKO-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain F [auth B] Interactions & Density Focus chain C [auth A] Focus chain F [auth B]
EPE Query on EPE Download Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain E [auth A] MOL2 format, chain D [auth A] MOL2 format, chain E [auth A]	D [auth A], E [auth A]	4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID C₈ H₁₈ N₂ O₄ S JKMHFZQWWAIEOD-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Focus chain E [auth A] Interactions & Density Focus chain D [auth A] Focus chain E [auth A]
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain I [auth B] MOL2 format, chain I [auth B]	I [auth B]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain I [auth B] Interactions & Density Focus chain I [auth B]
ZN Query on ZN Download Ideal Coordinates CCD File SDF format, chain G [auth B] SDF format, chain H [auth B] MOL2 format, chain G [auth B] MOL2 format, chain H [auth B]	G [auth B], H [auth B]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain G [auth B] Focus chain H [auth B] Interactions & Density Focus chain G [auth B] Focus chain H [auth B]