Sandbox Reserved 717
From Proteopedia
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'''The 33kDa Fragment''' <ref name=r3>PMID: 12888344</ref> <ref>PMID:11530935</ref> | '''The 33kDa Fragment''' <ref name=r3>PMID: 12888344</ref> <ref>PMID:11530935</ref> | ||
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The <scene name='Sandbox_Reserved_717/Myscene/11'>33kDa fragment</scene> (PDB:1H6W) was generated in the presence of EDTA <ref name=r3>PMID: 12888344</ref>. This fragment contains the residues <scene name='Sandbox_Reserved_717/Myfirstscene/1'>85-395</scene> and <scene name='Sandbox_Reserved_717/Mysecondscene/1'>518-527</scene> . The residues 397-517 are lacking because of internal deletion. | The <scene name='Sandbox_Reserved_717/Myscene/11'>33kDa fragment</scene> (PDB:1H6W) was generated in the presence of EDTA <ref name=r3>PMID: 12888344</ref>. This fragment contains the residues <scene name='Sandbox_Reserved_717/Myfirstscene/1'>85-395</scene> and <scene name='Sandbox_Reserved_717/Mysecondscene/1'>518-527</scene> . The residues 397-517 are lacking because of internal deletion. | ||
The 33kDa fragment can be further sub-divided into two subunits <ref name=r3>PMID: 12888344</ref>. The <scene name='Sandbox_Reserved_717/Mythirdscene/1'>neck</scene> (residue 333-341) and the <scene name='Sandbox_Reserved_717/Myscene/12'>collar</scene> (residues <scene name='Sandbox_Reserved_717/Mythirdscene/2'>342-396 </scene> plus <scene name='Sandbox_Reserved_717/Mythirdscene/3'> 518-527</scene>). The neck connects the body of the fibre to its C-terminal collar and receptor-binding site. It consists of a triple alpha-helix which is built by the residues 333-341. | The 33kDa fragment can be further sub-divided into two subunits <ref name=r3>PMID: 12888344</ref>. The <scene name='Sandbox_Reserved_717/Mythirdscene/1'>neck</scene> (residue 333-341) and the <scene name='Sandbox_Reserved_717/Myscene/12'>collar</scene> (residues <scene name='Sandbox_Reserved_717/Mythirdscene/2'>342-396 </scene> plus <scene name='Sandbox_Reserved_717/Mythirdscene/3'> 518-527</scene>). The neck connects the body of the fibre to its C-terminal collar and receptor-binding site. It consists of a triple alpha-helix which is built by the residues 333-341. | ||
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'''The 45kDa Fragment <ref name=r3>PMID: 12888344</ref> | '''The 45kDa Fragment <ref name=r3>PMID: 12888344</ref> | ||
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For generating the 45kDa fragment the full length gp12 was co-expressed with its chaperone gp57 and purified <ref name=r3>PMID: 12888344</ref>. Like the 33kDa fragment it also starts with the amino acid Leu85. The 45kDa fragment contains the residues <scene name='Sandbox_Reserved_717/Mythirdscene/4'>397-517</scene> , which are in the 33kDa fragment internal deleted <ref name=r3>PMID: 12888344</ref> . | For generating the 45kDa fragment the full length gp12 was co-expressed with its chaperone gp57 and purified <ref name=r3>PMID: 12888344</ref>. Like the 33kDa fragment it also starts with the amino acid Leu85. The 45kDa fragment contains the residues <scene name='Sandbox_Reserved_717/Mythirdscene/4'>397-517</scene> , which are in the 33kDa fragment internal deleted <ref name=r3>PMID: 12888344</ref> . | ||
Like the 33kDa fragment the 45kDa fragment can also be divided into two subunits. These two subunits are called <scene name='Sandbox_Reserved_717/Myscene/13'>head </scene> (residues <scene name='Sandbox_Reserved_717/Mythirdscene/5'>397-446 </scene> and residues <scene name='Sandbox_Reserved_717/Mythirdscene/6'>487-517</scene> ) and <scene name='Sandbox_Reserved_717/Mythirdscene/7'>bonnet</scene> (residues 447-487). On the border between the head and the bonnet subunit there is a metal-binding site <ref name=r3>PMID: 12888344</ref>. | Like the 33kDa fragment the 45kDa fragment can also be divided into two subunits. These two subunits are called <scene name='Sandbox_Reserved_717/Myscene/13'>head </scene> (residues <scene name='Sandbox_Reserved_717/Mythirdscene/5'>397-446 </scene> and residues <scene name='Sandbox_Reserved_717/Mythirdscene/6'>487-517</scene> ) and <scene name='Sandbox_Reserved_717/Mythirdscene/7'>bonnet</scene> (residues 447-487). On the border between the head and the bonnet subunit there is a metal-binding site <ref name=r3>PMID: 12888344</ref>. | ||
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'''Receptor-Binding Domain '''<ref name=r3>PMID: 12888344</ref> | '''Receptor-Binding Domain '''<ref name=r3>PMID: 12888344</ref> | ||
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Gp12 is fixed with its N-terminal domain to the baseplate. So the C-terminal domain has to be involved in LPS-binding. To detect where the receptor-binding domain is, full-length gp12, 33kDa fragments and 45kDa fragments were immobilised in micro-plate wells and were allowed to bind to bacteria <ref name=r3>PMID: 12888344</ref>. The result was that the 33kDa fragment did never bind to a bacteria <ref name=r3>PMID: 12888344</ref>. The 45kDa fragment did bind. So the receptor-binding domain is absent in the 33kDa fragment but present in the 45kDa fragment. The residues which are present in the 45kDa fragment and lacking in the 33kDa fragment are the residues <scene name='Sandbox_Reserved_717/Mythirdscene/8'>397-517</scene>. They are referred to be part of the receptor-binding domain. | Gp12 is fixed with its N-terminal domain to the baseplate. So the C-terminal domain has to be involved in LPS-binding. To detect where the receptor-binding domain is, full-length gp12, 33kDa fragments and 45kDa fragments were immobilised in micro-plate wells and were allowed to bind to bacteria <ref name=r3>PMID: 12888344</ref>. The result was that the 33kDa fragment did never bind to a bacteria <ref name=r3>PMID: 12888344</ref>. The 45kDa fragment did bind. So the receptor-binding domain is absent in the 33kDa fragment but present in the 45kDa fragment. The residues which are present in the 45kDa fragment and lacking in the 33kDa fragment are the residues <scene name='Sandbox_Reserved_717/Mythirdscene/8'>397-517</scene>. They are referred to be part of the receptor-binding domain. | ||
The receptor-binding domain can be sub-divided into head and bonnet. On the border between these two subdomains there is a metal-binding site <ref name=r3>PMID: 12888344</ref>. This site binds presumably to zinc. <scene name='Sandbox_Reserved_717/Mynewscene/3'>Two His amino acids </scene> (<scene name='Sandbox_Reserved_717/Mynewscene/1'>His445</scene> and <scene name='Sandbox_Reserved_717/Mynewscene/2'>His447</scene>) from each monomere are octahedrally coordinated around the zinc. | The receptor-binding domain can be sub-divided into head and bonnet. On the border between these two subdomains there is a metal-binding site <ref name=r3>PMID: 12888344</ref>. This site binds presumably to zinc. <scene name='Sandbox_Reserved_717/Mynewscene/3'>Two His amino acids </scene> (<scene name='Sandbox_Reserved_717/Mynewscene/1'>His445</scene> and <scene name='Sandbox_Reserved_717/Mynewscene/2'>His447</scene>) from each monomere are octahedrally coordinated around the zinc. | ||
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'''The LPS-Bindind Site''' <ref name=r3>PMID: 12888344</ref> | '''The LPS-Bindind Site''' <ref name=r3>PMID: 12888344</ref> | ||
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The exact position of the lipo-polysaccharide(LPS)-binding site is not known. Proteolysis experiments showed, that it contains to the domain with the residues <scene name='Sandbox_Reserved_717/Mythirdscene/8'>397-517</scene>. Compared with the homologous bacteriophage T4-like strain AR1 sequence, which also binds to the same LPS core molecule like gp12, there can be some possible binding residues be assumed. | The exact position of the lipo-polysaccharide(LPS)-binding site is not known. Proteolysis experiments showed, that it contains to the domain with the residues <scene name='Sandbox_Reserved_717/Mythirdscene/8'>397-517</scene>. Compared with the homologous bacteriophage T4-like strain AR1 sequence, which also binds to the same LPS core molecule like gp12, there can be some possible binding residues be assumed. | ||
Current revision
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| 1ocy, resolution 1.50Å () | |||||||||
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| Ligands: | , , | ||||||||
| Related: | 1h6w | ||||||||
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| Resources: | FirstGlance, OCA, RCSB, PDBsum | ||||||||
| Coordinates: | save as pdb, mmCIF, xml | ||||||||
1OCY : ONE COMPONENT OF THE BACTERIOPHAGE T4 SHORT TAIL FIBRE
Contents |
Description of Bacteriophage T4
Bacteriophage T4 belongs to the Myoviridae family and the Caudovirales order. It belongs to this order and family because of its complex tail structure. Many proteins are involved in this complex tail structures. It infects Escherichia coli bacteria.
It consists of three parts : a DNA-containing head, a doubles-tubed tail with a contractile outer tail-sheath and a baseplate with long and short tail fibers.
Each bacteriophage T4 baseplate is composed of at least 16 different gene products, also called gp which are oligomeric proteins. These gene products can be divided in two groups: the six long and the six short tail fibers (on the schematic representation, on the left, not all shown tail fibres are shown). They form a multiprotein machine which plays an important role in the first stage of a phage infection. It is essential for the host cell recognition, the attachment of the bacteriophage and the sheath contraction which allows the viral DNA ejection. [2]
Adsorption and penetration phases
First, the viral particles recognize and bind reversibly to the outer membrane protein C (OmpC) or the cell-surface lipopolysaccharide receptors thanks to six long tail fibers which are connected to the baseplate. After at least three long tail fibers have bound, the baseplate changes conformation: from a hexagon shape, it becomes a six-pointed star. This change can be the result of changing the interactions between proteins. It has two consequences.
The first one is the unfolding of the short tail fibers, which are under the baseplate. Thus, they are able to attach irreversibly to the host cell surface.
The second one is the induction of the tail sheath’s contraction. Afterwards the tail tube is driving through the cell membrane. The activated lysozyme domain of gp5 degraded the peptidoglycan layer.
To finish, the phage DNA single-stranded is injected into the bacterial cytoplasm through the tail tube.
Presentation of gp12
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Ligands and their Binding-Sites
So4
In the gp12 there are two molecules of SO4 ligands. One of them interacts with the citric acid. The blue molecule is the SO4. The other . It builds two hydrogen bounds to Ser287 with the distances 2.66 Å and 3.20 Å.
Citric Acid
The is drawn in green. It interacts with following amino acids: Arg465 (distance 3.01 Å), Asp455(distance 2.42 Å) and Tyr454 (distance 2.94 Å). . These interactions are caused by hydrogen bounds.
Zinc
The zinc is located in the centre of the receptor-binding domain. The zinc-binding site lies on the border between the head and the bonnet of the 45kDa domain. It interacts with the amino acids of each monomer. The distances of the zinc ion to the NE2 of and are 2.22 Å and 2.25 Å. The normally found distances between His and zinc are shorter. The explaination that these distances are longer than normally found is the octahedral coordination of the zinc in this structure [3]. The role of the zinc ion is probably absolute of structural nature. It increases the stability of the C-terminus of gp12 against proteases, but it also raises the stability of the C-terminus in general [3].
Applications
The most important role of gp12 is its ability to recognize and adhere to the host cell. Three other gene products (gp36, gp37 and gp38) are also targeting proteins and have a similar function. Nowadays some patents actually use random changes to create a bank of genetically modified bacteriophages. Recombinant bacteriophages are becoming a hope for treatment against multiresistant bacterial strains. [5]
External Ressources
References
- ↑ 1.0 1.1 1.2 Leiman PG, Arisaka F, van Raaij MJ, Kostyuchenko VA, Aksyuk AA, Kanamaru S, Rossmann MG. Morphogenesis of the T4 tail and tail fibers. Virol J. 2010 Dec 3;7:355. doi: 10.1186/1743-422X-7-355. PMID:21129200 doi:10.1186/1743-422X-7-355
- ↑ Kostyuchenko VA, Leiman PG, Chipman PR, Kanamaru S, van Raaij MJ, Arisaka F, Mesyanzhinov VV, Rossmann MG. Three-dimensional structure of bacteriophage T4 baseplate. Nat Struct Biol. 2003 Sep;10(9):688-93. Epub 2003 Aug 17. PMID:12923574 doi:http://dx.doi.org/10.1038/nsb970
- ↑ 3.00 3.01 3.02 3.03 3.04 3.05 3.06 3.07 3.08 3.09 3.10 3.11 3.12 3.13 3.14 3.15 3.16 3.17 3.18 3.19 Thomassen E, Gielen G, Schutz M, Schoehn G, Abrahams JP, Miller S, van Raaij MJ. The structure of the receptor-binding domain of the bacteriophage T4 short tail fibre reveals a knitted trimeric metal-binding fold. J Mol Biol. 2003 Aug 8;331(2):361-73. PMID:12888344
- ↑ van Raaij MJ, Schoehn G, Jaquinod M, Ashman K, Burda MR, Miller S. Identification and crystallisation of a heat- and protease-stable fragment of the bacteriophage T4 short tail fibre. Biol Chem. 2001 Jul;382(7):1049-55. PMID:11530935 doi:10.1515/BC.2001.131
- ↑ EP2097516 (B1) - Method for preparing bacteriophages modified by the insertion of random sequences in the screening proteins of said bacteriophages, IRIS FRANCOIS, PHERECYDES PHARMA
Proteopedia Page Contributors and Editors
Anne-Lise Terrier, Bianca Waßmer
