PDBsum entry 2vbk

Viral protein

PDB id: 2vbk

Contents

Protein chain

511 a.a.

Ligands

EDO ×12

PGR ×2

GOL ×6

PO4 ×3

CO2 ×2

Metals

_MG ×2

Waters ×664

PDB id:

2vbk

Name:

Viral protein

Title:

Native tailspike protein of bacteriophage sf6

Structure:

Tailspike-protein. Chain: a. Fragment: residues 110-623 lacking the n-terminal putative head- binding domain. Synonym: sf6 tailspike protein, tsp. Engineered: yes

Source:

Enterobacteria phage sf6. Organism_taxid: 10761. Expressed in: escherichia coli. Expression_system_taxid: 562.

Resolution:

1.25Å R-factor: 0.120 R-free: 0.142

Authors:

J.J.Mueller,S.Barbirz,K.Heinle,A.Freiberg,R.Seckler,U.Heinemann

Key ref:

J.J.Müller et al. (2008). An intersubunit active site between supercoiled parallel beta helices in the trimeric tailspike endorhamnosidase of Shigella flexneri Phage Sf6. Structure, 16, 766-775. PubMed id: 18462681 DOI: 10.1016/j.str.2008.01.019

Date:

14-Sep-07 Release date: 01-Apr-08

Protein chain

Q9XJP3  (FIBER_BPSFV) -  Tail spike protein from Shigella phage Sf6

Seq: 623 a.a.

Struc: 511 a.a.

Enzyme reactions

• Enzyme class: E.C.3.2.1.- - ?????

DOI no: 10.1016/j.str.2008.01.019

Structure 16:766-775 (2008)

PubMed id: 18462681

An intersubunit active site between supercoiled parallel beta helices in the trimeric tailspike endorhamnosidase of Shigella flexneri Phage Sf6.

J.J.Müller, S.Barbirz, K.Heinle, A.Freiberg, R.Seckler, U.Heinemann.

ABSTRACT

Sf6 belongs to the Podoviridae family of temperate bacteriophages that infect gram-negative bacteria by insertion of their double-stranded DNA. They attach to their hosts specifically via their tailspike proteins. The 1.25 A crystal structure of Shigella phage Sf6 tailspike protein (Sf6 TSP) reveals a conserved architecture with a central, right-handed beta helix. In the trimer of Sf6 TSP, the parallel beta helices form a left-handed, coiled-beta coil with a pitch of 340 A. The C-terminal domain consists of a beta sandwich reminiscent of viral capsid proteins. Further crystallographic and biochemical analyses show a Shigella cell wall O-antigen fragment to bind to an endorhamnosidase active site located between two beta-helix subunits each anchoring one catalytic carboxylate. The functionally and structurally related bacteriophage, P22 TSP, lacks sequence identity with Sf6 TSP and has its active sites on single subunits. Sf6 TSP may serve as an example for the evolution of different host specificities on a similar general architecture.

Selected figure(s)

Figure 2.
Figure 2. Structural Comparison of Sf6 TSP and P22 TSP
Crystal structures of the monomers and biologically active trimers of Sf6 TSPΔN (A and C), and of P22 TSPΔN (B and D) (PDB code: 1TSP [Steinbacher et al., 1994]). The view is perpendicular to the trimer axis onto the intersubunit cleft (rotated by vert, similar 45° relative to Figure 1).

Figure 6.
Figure 6. Localization of the Endorhamnosidase Active Site of Sf6 TSPΔN
(A) Difference electron density (contoured at 3σ) observed in a complex of the protein with one repeating unit (RU) of an O-antigen hydrolysis product (α-l-Rhap-(1-3)-β-l-GlcpNAc-(1-2)-α-l-Rhap-(1-2)-α-l-Rhap). The sugar points upwards to the N terminus of Sf6 TSP with its nonreducing end. Glu293 (chain C) and Asp247 (chain A) belong to the binding site.
(B) Kinetics of hydrolysis of a fluorescence-labeled dodecasaccharide (3 RU, 2 μM) with 0.36 μM Sf6 TSPΔN wild-type (closed triangles) and mutants D247N (closed diamonds), E293Q (closed squares), E366Q (closed circles) and D399N (open circles) at 15°C, as determined by HPLC (Freiberg et al., 2003). See Table 1 for k[cat]/K[M] values calculated from these data.
(C) An octasaccharide (2 RU) modeled into the binding site with its reducing end reaching the catalytic residues Asp399 and Glu366, which lie on different chains, as indicated. Bridging water molecules are colored purple.

The above figures are reprinted by permission from Cell Press: Structure (2008, 16, 766-775) copyright 2008.

Figures were selected by the author.