PDBsum entry 1v34

Transferase

PDB id

1v34

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Contents

			Protein chain

					346 a.a. *

			Ligands

					UTP

			Metals

					_ZN

			Waters ×21

* Residue conservation analysis

PDB id:

1v34

Links

Name:

Transferase

Title:

Crystal structure of pyrococcus horikoshii DNA primase-utp complex

Structure:

DNA primase small subunit. Chain: a. Synonym: DNA primase 41 kda subunit, p41. Engineered: yes

Source:

Pyrococcus horikoshii. Organism_taxid: 53953. Expressed in: escherichia coli. Expression_system_taxid: 562.

Resolution:

2.70Å

R-factor:

0.210

R-free:

0.262

Authors:

N.Ito,O.Nureki,M.Shirouzu,S.Yokoyama,F.Hanaoka,Riken Structural Genomics/proteomics Initiative (Rsgi)

Key ref:

N.Ito et al. (2003). Crystal structure of the Pyrococcus horikoshii DNA primase-UTP complex: implications for the mechanism of primer synthesis. Genes Cells, 8, 913-923. PubMed id: 14750947

Date:

25-Oct-03

Release date:

23-Mar-04

PROCHECK

	Headers

	References

Protein chain

O57934 (PRIS_PYRHO) - DNA primase small subunit PriS from Pyrococcus horikoshii (strain ATCC 700860 / DSM 12428 / JCM 9974 / NBRC 100139 / OT-3)

Seq: Struc:					346 a.a. 346 a.a.

Key:

PfamA domain

Secondary structure

CATH domain



		Enzyme reactions

Enzyme class:

E.C.2.7.7.- - ?????

[IntEnz] [ExPASy] [KEGG] [BRENDA]

	Genes Cells 8:913-923 (2003)
PubMed id: 14750947

Crystal structure of the Pyrococcus horikoshii DNA primase-UTP complex: implications for the mechanism of primer synthesis.
N.Ito, O.Nureki, M.Shirouzu, S.Yokoyama, F.Hanaoka.

ABSTRACT

BACKGROUND: In chromosomal DNA replication, DNA primase initiates the synthesis of a dinucleotide on a single-stranded template DNA, and elongates it to form a primer RNA for the replicative DNA polymerase. Although the apo-structure of an archaeal primase has been reported, the mechanism of primer synthesis by the eukaryotic-type primase still remains to be elucidated. RESULTS: In this study, we present the crystal structure of the eukaryotic-type DNA primase from the hyperthermophilic archaeon (Pyrococcus horikoshii) with the uridine 5'-triphosphate (UTP). In the present primase-UTP complex, the primase binds the triphosphate moiety of the UTP at the active site, which includes Asp95, Asp97, and Asp280, the essential residues for the nucleotidyl transfer reaction. CONCLUSION: The nucleotide binding geometry in this complex explains the previous biochemical analyses of the eukaryotic primase. Based on the complex structure, we constructed a model between the DNA primase and a primer/template DNA for the primer synthesis. This model facilitates the comprehension of the reported features of DNA primase.

Literature references that cite this PDB file's key reference

PubMed id

Reference

20385010

A.Swiatek, and S.A.Macneill (2010).
The archaeo-eukaryotic GINS proteins and the archaeal primase catalytic subunit PriS share a common domain.

Biol Direct, 5, 17.

20163964

E.Johansson, and S.A.Macneill (2010).
The eukaryotic replicative DNA polymerases take shape.

Trends Biochem Sci, 35, 339-347.

20511586

K.Beck, A.Vannini, P.Cramer, and G.Lipps (2010).
The archaeo-eukaryotic primase of plasmid pRN1 requires a helix bundle domain for faithful primer synthesis.

Nucleic Acids Res, 38, 6707-6718.

PDB code:

3m1m

19540940

R.D.Kuchta, and G.Stengel (2010).
Mechanism and evolution of DNA primases.

Biochim Biophys Acta, 1804, 1180-1189.

19788334

N.A.Cavanaugh, K.A.Ramirez-Aguilar, M.Urban, and R.D.Kuchta (2009).
Herpes simplex virus-1 helicase-primase: roles of each subunit in DNA binding and phosphodiester bond formation.

Biochemistry, 48, 10199-10207.

19416864

S.Geibel, S.Banchenko, M.Engel, E.Lanka, and W.Saenger (2009).
Structure and function of primase RepB' encoded by broad-host-range plasmid RSF1010 that replicates exclusively in leading-strand mode.

Proc Natl Acad Sci U S A, 106, 7810-7815.

PDB codes:

3h20 3h25

18452509

S.A.Koepsell, M.A.Larson, C.A.Frey, S.H.Hinrichs, and M.A.Griep (2008).
Staphylococcus aureus primase has higher initiation specificity, interacts with single-stranded DNA stronger, but is less stimulated by its helicase than Escherichia coli primase.

Mol Microbiol, 68, 1570-1582.

17709343

K.Beck, and G.Lipps (2007).
Properties of an unusual DNA primase from an archaeal plasmid.

Nucleic Acids Res, 35, 5635-5645.

17286576

N.Ito, I.Matsui, and E.Matsui (2007).
Molecular basis for the subunit assembly of the primase from an archaeon Pyrococcus horikoshii.

FEBS J, 274, 1340-1351.

PDB code:

2dla

17938628

S.Shuman, and M.S.Glickman (2007).
Bacterial DNA repair by non-homologous end joining.

Nat Rev Microbiol, 5, 852-861.

17158702

E.R.Barry, and S.D.Bell (2006).
DNA replication in the archaea.

Microbiol Mol Biol Rev, 70, 876-887.

16446439

H.Zhu, J.Nandakumar, J.Aniukwu, L.K.Wang, M.S.Glickman, C.D.Lima, and S.Shuman (2006).
Atomic structure and nonhomologous end-joining function of the polymerase component of bacterial DNA ligase D.

Proc Natl Acad Sci U S A, 103, 1711-1716.

PDB codes:

2fao 2faq 2far

15778718

C.Gong, P.Bongiorno, A.Martins, N.C.Stephanou, H.Zhu, S.Shuman, and M.S.Glickman (2005).
Mechanism of nonhomologous end-joining in mycobacteria: a low-fidelity repair system driven by Ku, ligase D and ligase C.

Nat Struct Mol Biol, 12, 304-312.

16273105

S.H.Lao-Sirieix, R.K.Nookala, P.Roversi, S.D.Bell, and L.Pellegrini (2005).
Structure of the heterodimeric core primase.

Nat Struct Mol Biol, 12, 1137-1144.

PDB code:

1zt2

The most recent references are shown first. Citation data come partly from CiteXplore and partly from an automated harvesting procedure. Note that this is likely to be only a partial list as not all journals are covered by either method. However, we are continually building up the citation data so more and more references will be included with time. Where a reference describes a PDB structure, the PDB code is shown on the right.