1h6m

From Proteopedia

(Difference between revisions)
Jump to: navigation, search
Current revision (06:06, 1 October 2025) (edit) (undo)
 
(22 intermediate revisions not shown.)
Line 1: Line 1:
-
[[Image:1h6m.gif|left|200px]]<br /><applet load="1h6m" size="450" color="white" frame="true" align="right" spinBox="true"
 
-
caption="1h6m, resolution 1.64&Aring;" />
 
-
'''COVALENT GLYCOSYL-ENZYME INTERMEDIATE OF HEN EGG WHITE LYSOZYME'''<br />
 
-
==Overview==
+
==Covalent glycosyl-enzyme intermediate of hen egg white lysozyme==
-
Hen egg-white lysozyme (HEWL) was the first enzyme to have its, three-dimensional structure determined by X-ray diffraction techniques. A, catalytic mechanism, featuring a long-lived oxocarbenium-ion intermediate, was proposed on the basis of model-building studies. The 'Phillips', mechanism is widely held as the paradigm for the catalytic mechanism of, beta-glycosidases that cleave glycosidic linkages with net retention of, configuration of the anomeric centre. Studies with other retaining, beta-glycosidases, however, provide strong evidence pointing to a common, mechanism for these enzymes that involves a covalent glycosyl-enzyme, intermediate, as previously postulated. Here we show, in three different, cases using electrospray ionization mass spectrometry, a catalytically, competent covalent glycosyl-enzyme intermediate during the catalytic cycle, of HEWL. We also show the three-dimensional structure of this intermediate, as determined by X-ray diffraction. We formulate a general catalytic, mechanism for all retaining beta-glycosidases that includes substrate, distortion, formation of a covalent intermediate, and the electrophilic, migration of C1 along the reaction coordinate.
+
<StructureSection load='1h6m' size='340' side='right'caption='[[1h6m]], [[Resolution|resolution]] 1.64&Aring;' scene=''>
 +
== Structural highlights ==
 +
<table><tr><td colspan='2'>[[1h6m]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Gallus_gallus Gallus gallus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1H6M OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1H6M 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]] 1.64&#8491;</td></tr>
 +
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=G2F:2-DEOXY-2-FLUORO-ALPHA-D-GLUCOPYRANOSE'>G2F</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=NAG:N-ACETYL-D-GLUCOSAMINE'>NAG</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=1h6m FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1h6m OCA], [https://pdbe.org/1h6m PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1h6m RCSB], [https://www.ebi.ac.uk/pdbsum/1h6m PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1h6m ProSAT]</span></td></tr>
 +
</table>
 +
== Function ==
 +
[https://www.uniprot.org/uniprot/LYSC_CHICK LYSC_CHICK] Lysozymes have primarily a bacteriolytic function; those in tissues and body fluids are associated with the monocyte-macrophage system and enhance the activity of immunoagents. Has bacteriolytic activity against M.luteus.<ref>PMID:22044478</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/h6/1h6m_consurf.spt"</scriptWhenChecked>
 +
<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview03.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=1h6m ConSurf].
 +
<div style="clear:both"></div>
 +
<div style="background-color:#fffaf0;">
 +
== Publication Abstract from PubMed ==
 +
Hen egg-white lysozyme (HEWL) was the first enzyme to have its three-dimensional structure determined by X-ray diffraction techniques. A catalytic mechanism, featuring a long-lived oxocarbenium-ion intermediate, was proposed on the basis of model-building studies. The 'Phillips' mechanism is widely held as the paradigm for the catalytic mechanism of beta-glycosidases that cleave glycosidic linkages with net retention of configuration of the anomeric centre. Studies with other retaining beta-glycosidases, however, provide strong evidence pointing to a common mechanism for these enzymes that involves a covalent glycosyl-enzyme intermediate, as previously postulated. Here we show, in three different cases using electrospray ionization mass spectrometry, a catalytically competent covalent glycosyl-enzyme intermediate during the catalytic cycle of HEWL. We also show the three-dimensional structure of this intermediate as determined by X-ray diffraction. We formulate a general catalytic mechanism for all retaining beta-glycosidases that includes substrate distortion, formation of a covalent intermediate, and the electrophilic migration of C1 along the reaction coordinate.
-
==About this Structure==
+
Catalysis by hen egg-white lysozyme proceeds via a covalent intermediate.,Vocadlo DJ, Davies GJ, Laine R, Withers SG Nature. 2001 Aug 23;412(6849):835-8. PMID:11518970<ref>PMID:11518970</ref>
-
1H6M is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Gallus_gallus Gallus gallus] with NA 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] Known structural/functional Sites: <scene name='pdbsite=NA:Na Binding Site For Chain A'>NA</scene>, <scene name='pdbsite=NAG:Nag Binding Site For Chain A'>NAG</scene> and <scene name='pdbsite=NUC:The Covalent Intermediate Is Linked To The Enzynmatic Nu ...'>NUC</scene>. Full crystallographic information is available from [http://ispc.weizmann.ac.il/oca-bin/ocashort?id=1H6M OCA].
+
-
==Reference==
+
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-
Catalysis by hen egg-white lysozyme proceeds via a covalent intermediate., Vocadlo DJ, Davies GJ, Laine R, Withers SG, Nature. 2001 Aug 23;412(6849):835-8. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=11518970 11518970]
+
</div>
-
[[Category: Gallus gallus]]
+
<div class="pdbe-citations 1h6m" style="background-color:#fffaf0;"></div>
-
[[Category: Lysozyme]]
+
-
[[Category: Single protein]]
+
-
[[Category: Davies, G.J.]]
+
-
[[Category: Laine, R.]]
+
-
[[Category: Vocadlo, D.J.]]
+
-
[[Category: Withers, S.G.]]
+
-
[[Category: NA]]
+
-
[[Category: covalent intermediate]]
+
-
[[Category: glycoside hydrolase]]
+
-
[[Category: lysozyme]]
+
-
[[Category: mechanism]]
+
-
''Page seeded by [http://ispc.weizmann.ac.il/oca OCA ] on Tue Dec 18 16:04:03 2007''
+
==See Also==
 +
*[[Lysozyme 3D structures|Lysozyme 3D structures]]
 +
== References ==
 +
<references/>
 +
__TOC__
 +
</StructureSection>
 +
[[Category: Gallus gallus]]
 +
[[Category: Large Structures]]
 +
[[Category: Davies GJ]]
 +
[[Category: Laine R]]
 +
[[Category: Vocadlo DJ]]
 +
[[Category: Withers SG]]

Current revision

Covalent glycosyl-enzyme intermediate of hen egg white lysozyme

PDB ID 1h6m

Drag the structure with the mouse to rotate

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/1h6m"
Personal tools