2vbk: Difference between revisions

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New page: left|200px {{Structure |PDB= 2vbk |SIZE=350|CAPTION= <scene name='initialview01'>2vbk</scene>, resolution 1.25Å |SITE= <scene name='pdbsite=AC1:Mg+Binding+Site+F...
 
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[[Image:2vbk.jpg|left|200px]]


{{Structure
==NATIVE TAILSPIKE PROTEIN OF BACTERIOPHAGE SF6==
|PDB= 2vbk |SIZE=350|CAPTION= <scene name='initialview01'>2vbk</scene>, resolution 1.25&Aring;
<StructureSection load='2vbk' size='340' side='right'caption='[[2vbk]], [[Resolution|resolution]] 1.25&Aring;' scene=''>
|SITE= <scene name='pdbsite=AC1:Mg+Binding+Site+For+Chain+A'>AC1</scene>, <scene name='pdbsite=AC2:Mg+Binding+Site+For+Chain+A'>AC2</scene>, <scene name='pdbsite=AC3:Edo+Binding+Site+For+Chain+A'>AC3</scene>, <scene name='pdbsite=AC4:Edo+Binding+Site+For+Chain+A'>AC4</scene>, <scene name='pdbsite=AC5:Edo+Binding+Site+For+Chain+A'>AC5</scene>, <scene name='pdbsite=AC6:Edo+Binding+Site+For+Chain+A'>AC6</scene>, <scene name='pdbsite=AC7:Edo+Binding+Site+For+Chain+A'>AC7</scene>, <scene name='pdbsite=AC8:Edo+Binding+Site+For+Chain+A'>AC8</scene>, <scene name='pdbsite=AC9:Edo+Binding+Site+For+Chain+A'>AC9</scene>, <scene name='pdbsite=BC1:Edo+Binding+Site+For+Chain+A'>BC1</scene>, <scene name='pdbsite=BC2:Edo+Binding+Site+For+Chain+A'>BC2</scene>, <scene name='pdbsite=BC3:Pgr+Binding+Site+For+Chain+A'>BC3</scene>, <scene name='pdbsite=BC4:Pgr+Binding+Site+For+Chain+A'>BC4</scene>, <scene name='pdbsite=BC5:Gol+Binding+Site+For+Chain+A'>BC5</scene>, <scene name='pdbsite=BC6:Gol+Binding+Site+For+Chain+A'>BC6</scene>, <scene name='pdbsite=BC7:Gol+Binding+Site+For+Chain+A'>BC7</scene>, <scene name='pdbsite=BC8:Gol+Binding+Site+For+Chain+A'>BC8</scene>, <scene name='pdbsite=BC9:Gol+Binding+Site+For+Chain+A'>BC9</scene>, <scene name='pdbsite=CC1:Gol+Binding+Site+For+Chain+A'>CC1</scene>, <scene name='pdbsite=CC2:Po4+Binding+Site+For+Chain+A'>CC2</scene>, <scene name='pdbsite=CC3:Po4+Binding+Site+For+Chain+A'>CC3</scene>, <scene name='pdbsite=CC4:Po4+Binding+Site+For+Chain+A'>CC4</scene>, <scene name='pdbsite=CC5:Co2+Binding+Site+For+Chain+A'>CC5</scene>, <scene name='pdbsite=CC6:Co2+Binding+Site+For+Chain+A'>CC6</scene>, <scene name='pdbsite=CC7:Edo+Binding+Site+For+Chain+A'>CC7</scene>, <scene name='pdbsite=CC8:Edo+Binding+Site+For+Chain+A'>CC8</scene> and <scene name='pdbsite=CC9:Edo+Binding+Site+For+Chain+A'>CC9</scene>
== Structural highlights ==
|LIGAND= <scene name='pdbligand=CO2:CARBON+DIOXIDE'>CO2</scene>, <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=PGR:R-1,2-PROPANEDIOL'>PGR</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene>
<table><tr><td colspan='2'>[[2vbk]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Shigella_virus_Sf6 Shigella virus Sf6]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2VBK OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2VBK FirstGlance]. <br>
|ACTIVITY=
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.25&#8491;</td></tr>
|GENE=
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CO2:CARBON+DIOXIDE'>CO2</scene>, <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=PGR:R-1,2-PROPANEDIOL'>PGR</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene></td></tr>
|DOMAIN=<span class='plainlinks'>[http://www.ncbi.nlm.nih.gov/Structure/cdd/cddsrv.cgi?uid=COG5434 PGU1]</span>
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=2vbk FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2vbk OCA], [https://pdbe.org/2vbk PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2vbk RCSB], [https://www.ebi.ac.uk/pdbsum/2vbk PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2vbk ProSAT]</span></td></tr>
|RELATEDENTRY=[[2vbe|2VBE]], [[2vbm|2VBM]]
</table>
|RESOURCES=<span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2vbk FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2vbk OCA], [http://www.ebi.ac.uk/pdbsum/2vbk PDBsum], [http://www.rcsb.org/pdb/explore.do?structureId=2vbk RCSB]</span>
== Function ==
}}
[https://www.uniprot.org/uniprot/FIBER_BPSFV FIBER_BPSFV] Non-covalently bound to the neck of the phage capsid and mediating attachment of the viral particle to host cell-surface polysaccharide. It displays endorhamnosidase enzymatic activity, hydrolyzing the alpha-1,3-O-glycosidic linkage between rhamnose and galactose of the O-antigen polysaccharide.<ref>PMID:18462681</ref> <ref>PMID:12424253</ref> <ref>PMID:6284</ref>
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
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.


'''NATIVE TAILSPIKE PROTEIN OF BACTERIOPHAGE SF6'''
An intersubunit active site between supercoiled parallel beta helices in the trimeric tailspike endorhamnosidase of Shigella flexneri Phage Sf6.,Muller JJ, Barbirz S, Heinle K, Freiberg A, Seckler R, Heinemann U Structure. 2008 May;16(5):766-75. PMID:18462681<ref>PMID:18462681</ref>


From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
</div>
<div class="pdbe-citations 2vbk" style="background-color:#fffaf0;"></div>


==About this Structure==
==See Also==
2VBK is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Enterobacteria_phage_sf6 Enterobacteria phage sf6]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2VBK OCA].
*[[Tailspike protein 3D structures|Tailspike protein 3D structures]]
[[Category: Enterobacteria phage sf6]]
== References ==
[[Category: Single protein]]
<references/>
[[Category: Barbirz, S.]]
__TOC__
[[Category: Freiberg, A.]]
</StructureSection>
[[Category: Heinemann, U.]]
[[Category: Large Structures]]
[[Category: Heinle, K.]]
[[Category: Shigella virus Sf6]]
[[Category: Mueller, J J.]]
[[Category: Barbirz S]]
[[Category: Seckler, R.]]
[[Category: Freiberg A]]
[[Category: endorhamnosidase]]
[[Category: Heinemann U]]
[[Category: hydrolase]]
[[Category: Heinle K]]
[[Category: right-handed parallel beta-helix]]
[[Category: Mueller JJ]]
[[Category: tailspike]]
[[Category: Seckler R]]
[[Category: viral adhesion protein]]
[[Category: viral protein]]
 
''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Apr  2 11:58:36 2008''

Latest revision as of 18:13, 13 December 2023

NATIVE TAILSPIKE PROTEIN OF BACTERIOPHAGE SF6NATIVE TAILSPIKE PROTEIN OF BACTERIOPHAGE SF6

Structural highlights

2vbk is a 1 chain structure with sequence from Shigella virus Sf6. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:X-ray diffraction, Resolution 1.25Å
Ligands:, , , , ,
Resources:FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

FIBER_BPSFV Non-covalently bound to the neck of the phage capsid and mediating attachment of the viral particle to host cell-surface polysaccharide. It displays endorhamnosidase enzymatic activity, hydrolyzing the alpha-1,3-O-glycosidic linkage between rhamnose and galactose of the O-antigen polysaccharide.[1] [2] [3]

Publication Abstract from PubMed

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.

An intersubunit active site between supercoiled parallel beta helices in the trimeric tailspike endorhamnosidase of Shigella flexneri Phage Sf6.,Muller JJ, Barbirz S, Heinle K, Freiberg A, Seckler R, Heinemann U Structure. 2008 May;16(5):766-75. PMID:18462681[4]

From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.

See Also

References

  1. ↑ Muller JJ, Barbirz S, Heinle K, Freiberg A, Seckler R, Heinemann U. An intersubunit active site between supercoiled parallel beta helices in the trimeric tailspike endorhamnosidase of Shigella flexneri Phage Sf6. Structure. 2008 May;16(5):766-75. PMID:18462681 doi:10.1016/j.str.2008.01.019
  2. ↑ Freiberg A, Morona R, Van den Bosch L, Jung C, Behlke J, Carlin N, Seckler R, Baxa U. The tailspike protein of Shigella phage Sf6. A structural homolog of Salmonella phage P22 tailspike protein without sequence similarity in the beta-helix domain. J Biol Chem. 2003 Jan 17;278(3):1542-8. PMID:12424253 doi:10.1074/jbc.M205294200
  3. ↑ Iwashita S, Kanegasaki S. Enzymic and molecular properties of base-plate parts of bacteriophage P22. Eur J Biochem. 1976 May 17;65(1):87-94. PMID:6284 doi:10.1111/j.1432-1033.1976.tb10392.x
  4. ↑ Muller JJ, Barbirz S, Heinle K, Freiberg A, Seckler R, Heinemann U. An intersubunit active site between supercoiled parallel beta helices in the trimeric tailspike endorhamnosidase of Shigella flexneri Phage Sf6. Structure. 2008 May;16(5):766-75. PMID:18462681 doi:10.1016/j.str.2008.01.019

2vbk, resolution 1.25Å

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