PDBsum entry 3hef

Viral protein

PDB id

3hef

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Contents

			Protein chains

					123 a.a. *


					130 a.a. *

			Waters ×254

* Residue conservation analysis

PDB id:

3hef

Links

Name:

Viral protein

Title:

Crystal structure of the bacteriophage sf6 terminase small subunit

Structure:

Gene 1 protein. Chain: a, b. Engineered: yes

Source:

Enterobacteria phage sf6. Shigella flexneri bacteriophage vi. Organism_taxid: 10761. Gene: gp1. Expressed in: escherichia coli. Expression_system_taxid: 562.

Resolution:

1.65Å

R-factor:

0.224

R-free:

0.251

Authors:

H.Zhao,L.Tang

Key ref:

H.Zhao et al. (2010). Crystal structure of the DNA-recognition component of the bacterial virus Sf6 genome-packaging machine. Proc Natl Acad Sci U S A, 107, 1971-1976. PubMed id: 20133842

Date:

08-May-09

Release date:

09-Feb-10

PROCHECK

	Headers

	References

Protein chain

Q716H4 (Q716H4_BPSFV) - Gene 1 protein from Shigella phage Sf6

Seq: Struc:					140 a.a. 123 a.a.

Protein chain

Q716H4 (Q716H4_BPSFV) - Gene 1 protein from Shigella phage Sf6

Seq: Struc:					140 a.a. 130 a.a.

Key:

Secondary structure

CATH domain



		Enzyme reactions

Enzyme class:

Chains A, B: E.C.?

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

	Proc Natl Acad Sci U S A 107:1971-1976 (2010)
PubMed id: 20133842

Crystal structure of the DNA-recognition component of the bacterial virus Sf6 genome-packaging machine.
H.Zhao, C.J.Finch, R.D.Sequeira, B.A.Johnson, J.E.Johnson, S.R.Casjens, L.Tang.

ABSTRACT

In herpesviruses and many bacterial viruses, genome-packaging is a precisely mediated process fulfilled by a virally encoded molecular machine called terminase that consists of two protein components: A DNA-recognition component that defines the specificity for packaged DNA, and a catalytic component that provides energy for the packaging reaction by hydrolyzing ATP. The terminase docks onto the portal protein complex embedded in a single vertex of a preformed viral protein shell called procapsid, and pumps the viral DNA into the procapsid through a conduit formed by the portal. Here we report the 1.65 A resolution structure of the DNA-recognition component gp1 of the Shigella bacteriophage Sf6 genome-packaging machine. The structure reveals a ring-like octamer formed by interweaved protein monomers with a highly extended fold, embracing a tunnel through which DNA may be translocated. The N-terminal DNA-binding domains form the peripheral appendages surrounding the octamer. The central domain contributes to oligomerization through interactions of bundled helices. The C-terminal domain forms a barrel with parallel beta-strands. The structure reveals a common scheme for oligomerization of terminase DNA-recognition components, and provides insights into the role of gp1 in formation of the packaging-competent terminase complex and assembly of the terminase with the portal, in which ring-like protein oligomers stack together to form a continuous channel for viral DNA translocation.

Literature references that cite this PDB file's key reference

PubMed id

Reference

21499245

A.S.Olia, P.E.Prevelige, J.E.Johnson, and G.Cingolani (2011).
Three-dimensional structure of a viral genome-delivery portal vertex.

Nat Struct Mol Biol, 18, 597-603.

PDB codes:

1vt0 3lj4 3lj5

21836625

S.R.Casjens (2011).
The DNA-packaging nanomotor of tailed bacteriophages.

Nat Rev Microbiol, 9, 647-657.

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

20722407

P.Jing, F.Haque, D.Shu, C.Montemagno, and P.Guo (2010).
One-way traffic of a viral motor channel for double-stranded DNA translocation.

Nano Lett, 10, 3620-3627.

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.