1d9u: Difference between revisions

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New page: left|200px<br /><applet load="1d9u" size="450" color="white" frame="true" align="right" spinBox="true" caption="1d9u, resolution 2.60Å" /> '''BACTERIOPHAGE LAMBDA...
 
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[[Image:1d9u.gif|left|200px]]<br /><applet load="1d9u" size="450" color="white" frame="true" align="right" spinBox="true"
caption="1d9u, resolution 2.60&Aring;" />
'''BACTERIOPHAGE LAMBDA LYSOZYME COMPLEXED WITH A CHITOHEXASACHARIDE'''<br />


==Overview==
==BACTERIOPHAGE LAMBDA LYSOZYME COMPLEXED WITH A CHITOHEXASACHARIDE==
The three-dimensional structure of the lytic transglycosylase from, bacteriophage lambda, also known as bacteriophage lambda lysozyme, complexed to the hexasaccharide inhibitor, hexa-N-acetylchitohexaose, has, been determined by X-ray crystallography at 2.6 A resolution. The unit, cell contains two molecules of the lytic transglycosylase with two, hexasaccharides bound. Each enzyme molecule is found to interact with four, N-acetylglucosamine units from one hexasaccharide (subsites A-D) and two, N-acetylglucosamine units from the second hexasaccharide (subsites E and, F), resulting in all six subsites of the active site of this enzyme being, filled. This crystallographic structure, therefore, represents the first, example of a lysozyme in which all subsites are occupied, and detailed, protein-oligosaccharide interactions are now available for this, bacteriophage lytic transglycosylase. Examination of the active site, furthermore reveals that of the two residues that have been implicated in, the reaction mechanism of most other c-type lysozymes (Glu35 and Asp52 in, hen egg white lysozyme), only a homologous Glu residue is present. The, lambda lytic transglycosylase is therefore functionally closely related to, the Escherichia coli Slt70 and Slt35 lytic transglycosylases and goose egg, white lysozyme which also lack the catalytic aspartic acid.
<StructureSection load='1d9u' size='340' side='right'caption='[[1d9u]], [[Resolution|resolution]] 2.60&Aring;' scene=''>
== Structural highlights ==
<table><tr><td colspan='2'>[[1d9u]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_virus_Lambda Escherichia virus Lambda]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1D9U OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1D9U FirstGlance]. <br>
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.6&#8491;</td></tr>
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=NAG:N-ACETYL-D-GLUCOSAMINE'>NAG</scene>, <scene name='pdbligand=NDG:2-(ACETYLAMINO)-2-DEOXY-A-D-GLUCOPYRANOSE'>NDG</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1d9u FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1d9u OCA], [https://pdbe.org/1d9u PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1d9u RCSB], [https://www.ebi.ac.uk/pdbsum/1d9u PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1d9u ProSAT]</span></td></tr>
</table>
== Function ==
[https://www.uniprot.org/uniprot/ENLYS_LAMBD ENLYS_LAMBD] Endolysin with transglycosylase activity that degrades host peptidoglycans and participates with the holin and spanin proteins in the sequential events which lead to the programmed host cell lysis releasing the mature viral particles. Once the holin has permeabilized the host cell membrane, the endolysin can reach the periplasm and break down the peptidoglycan layer.[HAMAP-Rule:MF_04109]<ref>PMID:10556513</ref> <ref>PMID:24113139</ref>
== Evolutionary Conservation ==
[[Image:Consurf_key_small.gif|200px|right]]
Check<jmol>
  <jmolCheckbox>
    <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/d9/1d9u_consurf.spt"</scriptWhenChecked>
    <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
    <text>to colour the structure by Evolutionary Conservation</text>
  </jmolCheckbox>
</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=1d9u ConSurf].
<div style="clear:both"></div>


==About this Structure==
==See Also==
1D9U is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Enterobacteria_phage_lambda Enterobacteria phage lambda] with SO4 as [http://en.wikipedia.org/wiki/ligand ligand]. Active as [http://en.wikipedia.org/wiki/Lysozyme Lysozyme], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.2.1.17 3.2.1.17] Full crystallographic information is available from [http://ispc.weizmann.ac.il/oca-bin/ocashort?id=1D9U OCA].
*[[Lysozyme 3D structures|Lysozyme 3D structures]]
 
== References ==
==Reference==
<references/>
Crystal structure of the lytic transglycosylase from bacteriophage lambda in complex with hexa-N-acetylchitohexaose., Leung AK, Duewel HS, Honek JF, Berghuis AM, Biochemistry. 2001 May 15;40(19):5665-73. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=11341831 11341831]
__TOC__
[[Category: Enterobacteria phage lambda]]
</StructureSection>
[[Category: Lysozyme]]
[[Category: Escherichia virus Lambda]]
[[Category: Single protein]]
[[Category: Large Structures]]
[[Category: Berghuis, A.M.]]
[[Category: Berghuis AM]]
[[Category: Duewel, H.S.]]
[[Category: Duewel HS]]
[[Category: Honek, J.F.]]
[[Category: Honek JF]]
[[Category: Leung, A.K.W.]]
[[Category: Leung AKW]]
[[Category: SO4]]
[[Category: glycosidase]]
[[Category: lysozyme]]
[[Category: six-sugar complex]]
[[Category: transglycosylase]]
 
''Page seeded by [http://ispc.weizmann.ac.il/oca OCA ] on Tue Nov 20 13:06:41 2007''

Latest revision as of 09:51, 7 February 2024

BACTERIOPHAGE LAMBDA LYSOZYME COMPLEXED WITH A CHITOHEXASACHARIDEBACTERIOPHAGE LAMBDA LYSOZYME COMPLEXED WITH A CHITOHEXASACHARIDE

Structural highlights

1d9u is a 2 chain structure with sequence from Escherichia virus Lambda. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:X-ray diffraction, Resolution 2.6Å
Ligands:, ,
Resources:FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

ENLYS_LAMBD Endolysin with transglycosylase activity that degrades host peptidoglycans and participates with the holin and spanin proteins in the sequential events which lead to the programmed host cell lysis releasing the mature viral particles. Once the holin has permeabilized the host cell membrane, the endolysin can reach the periplasm and break down the peptidoglycan layer.[HAMAP-Rule:MF_04109][1] [2]

Evolutionary Conservation

Check, as determined by ConSurfDB. You may read the explanation of the method and the full data available from ConSurf.

See Also

References

  1. ↑ Evrard C, Fastrez J, Soumillion P. Histidine modification and mutagenesis point to the involvement of a large conformational change in the mechanism of action of phage lambda lysozyme. FEBS Lett. 1999 Nov 5;460(3):442-6. PMID:10556513 doi:10.1016/s0014-5793(99)01395-2
  2. ↑ Young R. Phage lysis: do we have the hole story yet? Curr Opin Microbiol. 2013 Dec;16(6):790-7. PMID:24113139 doi:10.1016/j.mib.2013.08.008

1d9u, resolution 2.60Å

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