PDBsum entry 2wc9

Viral protein

PDB id

2wc9

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Contents

			Protein chain

					177 a.a. *

			Ligands

					SO4

			Metals

					_MN ×2

			Waters ×24

* Residue conservation analysis

PDB id:

2wc9

Links

Name:

Viral protein

Title:

Crystal structure of the g2p (large terminase) nuclease domain from the bacteriophage spp1 with bound mn

Structure:

Terminase large subunit. Chain: a. Fragment: nuclease domain, residues 232-422. Synonym: g2p. Engineered: yes

Source:

Bacillus phage spp1. Bacteriophage spp1. Organism_taxid: 10724. Expressed in: escherichia coli. Expression_system_taxid: 562.

Resolution:

2.50Å

R-factor:

0.198

R-free:

0.259

Authors:

C.Smits,M.Chechik,O.V.Kovalevskiy,M.B.Shevtsov,A.W.Foster,J.C.Alonso, A.A.Antson

Key ref:

C.Smits et al. (2009). Structural basis for the nuclease activity of a bacteriophage large terminase. Embo Rep, 10, 592-598. PubMed id: 19444313

Date:

10-Mar-09

Release date:

24-Mar-09

PROCHECK

	Headers

	References

Protein chain

P54308 (TERL_BPSPP) - Terminase, large subunit from Bacillus phage SPP1

Seq: Struc:					422 a.a. 177 a.a.

Key:

PfamA domain

Secondary structure

CATH domain



		Enzyme reactions

Enzyme class 1:

E.C.3.1.-.-

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

Enzyme class 2:

E.C.3.6.4.- - ?????

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

Note, where more than one E.C. class is given (as above), each may correspond to a different protein domain or, in the case of polyprotein precursors, to a different mature protein.

	Embo Rep 10:592-598 (2009)
PubMed id: 19444313

Structural basis for the nuclease activity of a bacteriophage large terminase.
C.Smits, M.Chechik, O.V.Kovalevskiy, M.B.Shevtsov, A.W.Foster, J.C.Alonso, A.A.Antson.

ABSTRACT

The DNA-packaging motor in tailed bacteriophages requires nuclease activity to ensure that the genome is packaged correctly. This nuclease activity is tightly regulated as the enzyme is inactive for the duration of DNA translocation. Here, we report the X-ray structure of the large terminase nuclease domain from bacteriophage SPP1. Similarity with the RNase H family endonucleases allowed interactions with the DNA to be predicted. A structure-based alignment with the distantly related T4 gp17 terminase shows the conservation of an extended beta-sheet and an auxiliary beta-hairpin that are not found in other RNase H family proteins. The model with DNA suggests that the beta-hairpin partly blocks the active site, and in vivo activity assays show that the nuclease domain is not functional in the absence of the ATPase domain. Here, we propose that the nuclease activity is regulated by movement of the beta-hairpin, altering active site access and the orientation of catalytically essential residues.

Literature references that cite this PDB file's key reference

PubMed id

Reference

21109524

M.Ghosh-Kumar, T.I.Alam, B.Draper, J.D.Stack, and V.B.Rao (2011).
Regulation by interdomain communication of a headful packaging nuclease from bacteriophage T4.

Nucleic Acids Res, 39, 2742-2755.

20056615

L.Oliveira, A.Cuervo, and P.Tavares (2010).
Direct interaction of the bacteriophage SPP1 packaging ATPase with the portal protein.

J Biol Chem, 285, 7366-7373.

20805464

M.Nadal, P.J.Mas, P.J.Mas, A.G.Blanco, C.Arnan, M.Solà, D.J.Hart, and M.Coll (2010).
Structure and inhibition of herpesvirus DNA packaging terminase nuclease domain.

Proc Natl Acad Sci U S A, 107, 16078-16083.

PDB codes:

3n4p 3n4q

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 codes are shown on the right.