3f9l

From Proteopedia

(Difference between revisions)

Current revision

Evaulaution at Atomic Resolution of the Role of Strain in Destabilizing the Temperature Sensitive T4 Lysozyme Mutant Arg96-->His

Structural highlights

3f9l is a 1 chain structure with sequence from Escherichia virus T4. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	X-ray diffraction, Resolution 1.19Å
Ligands:	, , ,
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

ENLYS_BPT4 Endolysin with lysozyme 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.^[1]

Evolutionary Conservation

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

Publication Abstract from PubMed

Mutant R96H is a classic temperature-sensitive mutant of bacteriophage T4 lysozyme. It was in fact the first variant of the protein to be characterized structurally. Subsequently, it has been studied extensively by a variety of experimental and computational techniques, but the reasons for the loss of stability of the mutant protein remain controversial. In the crystallographic refinement of the mutant structure at 1.9 A resolution one of the bond angles at the site of substitution appeared to be distorted by about 11( degrees ), and it was suggested that this steric strain was one of the major factors in destabilizing the mutant. Different computationally-derived models of the mutant structure, however, did not show such distortion. To determine the geometry at the site of mutation more reliably, we have extended the resolution of the data and refined the wildtype (WT) and mutant structures to be better than 1.1 A resolution. The high-resolution refinement of the structure of R96H does not support the bond angle distortion seen in the 1.9 A structure determination. At the same time, it does confirm other manifestations of strain seen previously including an unusual rotameric state for His96 with distorted hydrogen bonding. The rotamer strain has been estimated as about 0.8 kcal/mol, which is about 25% of the overall reduction in stability of the mutant. Because of concern that contacts from a neighboring molecule in the crystal might influence the geometry at the site of mutation we also constructed and analyzed supplemental mutant structures in which this crystal contact was eliminated. High-resolution refinement shows that the crystal contacts have essentially no effect on the conformation of Arg96 in WT or on His96 in the R96H mutant.

Evaluation at atomic resolution of the role of strain in destabilizing the temperature-sensitive T4 lysozyme mutant Arg 96 --> His.,Mooers BH, Tronrud DE, Matthews BW Protein Sci. 2009 May;18(5):863-70. PMID:19384984^[2]

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

References

↑ Moussa SH, Kuznetsov V, Tran TA, Sacchettini JC, Young R. Protein determinants of phage T4 lysis inhibition. Protein Sci. 2012 Apr;21(4):571-82. doi: 10.1002/pro.2042. Epub 2012 Mar 2. PMID:22389108 doi:http://dx.doi.org/10.1002/pro.2042
↑ Mooers BH, Tronrud DE, Matthews BW. Evaluation at atomic resolution of the role of strain in destabilizing the temperature-sensitive T4 lysozyme mutant Arg 96 --> His. Protein Sci. 2009 May;18(5):863-70. PMID:19384984 doi:10.1002/pro.93

1 Structural highlights
2 Function
3 Evolutionary Conservation
4 Publication Abstract from PubMed
5 See Also
6 References

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/3f9l"

Categories: Escherichia virus T4 | Large Structures | Matthews BW | Mooers BHM

@@ Line 3: / Line 3: @@
 <StructureSection load='3f9l' size='340' side='right'caption='[[3f9l]], [[Resolution|resolution]] 1.19&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[3f9l]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Bpt4 Bpt4]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3F9L OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3F9L FirstGlance]. <br>
+<table><tr><td colspan='2'>[[3f9l]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_virus_T4 Escherichia virus T4]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3F9L OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3F9L FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=K:POTASSIUM+ION'>K</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene></td></tr>
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.19&#8491;</td></tr>
-<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[1l34|1l34]], [[1l63|1l63]], [[3c7w|3c7w]], [[3c7y|3c7y]], [[3c7z|3c7z]], [[3c80|3c80]], [[3c81|3c81]], [[3c82|3c82]], [[3c83|3c83]], [[3c8q|3c8q]], [[3c8r|3c8r]], [[3c8s|3c8s]], [[3cdo|3cdo]], [[3cdq|3cdq]], [[3cdr|3cdr]], [[3cdt|3cdt]], [[3cdv|3cdv]], [[3f8v|3f8v]], [[3fa0|3fa0]], [[3fad|3fad]], [[3fi5|3fi5]]</div></td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=K:POTASSIUM+ION'>K</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene></td></tr>
-<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">gene e ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=10665 BPT4])</td></tr>
-<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/Lysozyme Lysozyme], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.2.1.17 3.2.1.17] </span></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=3f9l FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3f9l OCA], [https://pdbe.org/3f9l PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3f9l RCSB], [https://www.ebi.ac.uk/pdbsum/3f9l PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3f9l ProSAT]</span></td></tr>
 </table>
 == Function ==
-[[https://www.uniprot.org/uniprot/LYS_BPT4 LYS_BPT4]] Helps to release the mature phage particles from the cell wall by breaking down the peptidoglycan.
+[https://www.uniprot.org/uniprot/ENLYS_BPT4 ENLYS_BPT4] Endolysin with lysozyme 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.<ref>PMID:22389108</ref>
 == Evolutionary Conservation ==
 [[Image:Consurf_key_small.gif|200px|right]]
@@ Line 38: / Line 36: @@
 __TOC__
 </StructureSection>
-[[Category: Bpt4]]
+[[Category: Escherichia virus T4]]
 [[Category: Large Structures]]
-[[Category: Lysozyme]]
+[[Category: Matthews BW]]
-[[Category: Matthews, B W]]
+[[Category: Mooers BHM]]
-[[Category: Mooers, B H.M]]
-[[Category: Antimicrobial]]
-[[Category: Bacteriolytic enzyme]]
-[[Category: Bond angle strain]]
-[[Category: Glycosidase]]
-[[Category: Hydrolase]]
-[[Category: Rotamer strain]]
-[[Category: T4 lysozyme]]
-[[Category: Temperature sensitive mutant]]

3f9l

From Proteopedia

Current revision

Evaulaution at Atomic Resolution of the Role of Strain in Destabilizing the Temperature Sensitive T4 Lysozyme Mutant Arg96-->His

Structural highlights

Function

Evolutionary Conservation

Publication Abstract from PubMed

See Also

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

Views

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