1h6m: Difference between revisions

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<StructureSection load='1h6m' size='340' side='right'caption='[[1h6m]], [[Resolution|resolution]] 1.64&Aring;' scene=''>
<StructureSection load='1h6m' size='340' side='right'caption='[[1h6m]], [[Resolution|resolution]] 1.64&Aring;' scene=''>
== Structural highlights ==
== Structural highlights ==
<table><tr><td colspan='2'>[[1h6m]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Chick Chick]. 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 [http://proteopedia.org/fgij/fg.htm?mol=1H6M FirstGlance]. <br>
<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='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=G2F:2-DEOXY-2-FLUORO-ALPHA-D-GLUCOPYRANOSE'>G2F</scene>, <scene name='pdbligand=NAG:N-ACETYL-D-GLUCOSAMINE'>NAG</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]] 1.64&#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;'>[[1w6z|1w6z]], [[1kxx|1kxx]], [[4lyo|4lyo]], [[3lyo|3lyo]], [[1kip|1kip]], [[1t6v|1t6v]], [[1ic7|1ic7]], [[1vds|1vds]], [[1lzt|1lzt]], [[1kir|1kir]], [[2xbr|2xbr]], [[1lys|1lys]], [[1bwj|1bwj]], [[132l|132l]], [[1e8l|1e8l]], [[1yil|1yil]], [[1heo|1heo]], [[1sfg|1sfg]], [[1kxw|1kxw]], [[2x0a|2x0a]], [[2c8o|2c8o]], [[1yl1|1yl1]], [[1sf4|1sf4]], [[1g7l|1g7l]], [[1ior|1ior]], [[1h87|1h87]], [[1ljg|1ljg]], [[3lyt|3lyt]], [[1dpx|1dpx]], [[1iot|1iot]], [[1v7s|1v7s]], [[1ja6|1ja6]], [[1jis|1jis]], [[1ir8|1ir8]], [[2w1m|2w1m]], [[1uic|1uic]], [[1xgq|1xgq]], [[1ykz|1ykz]], [[1uie|1uie]], [[2war|2war]], [[1lji|1lji]], [[8lyz|8lyz]], [[1lj3|1lj3]], [[1dpw|1dpw]], [[2lyo|2lyo]], [[2iff|2iff]], [[1bwi|1bwi]], [[1g7h|1g7h]], [[1jj0|1jj0]], [[1lks|1lks]], [[1rfp|1rfp]], [[5lyt|5lyt]], [[1jiy|1jiy]], [[1sfb|1sfb]], [[1iee|1iee]], [[1xei|1xei]], [[1ir7|1ir7]], [[1xek|1xek]], [[1hel|1hel]], [[1at6|1at6]], [[1ljf|1ljf]], [[1mlc|1mlc]], [[1f10|1f10]], [[2b5z|2b5z]], [[193l|193l]], [[1lsz|1lsz]], [[1ljk|1ljk]], [[6lyt|6lyt]], [[1sq2|1sq2]], [[1vdq|1vdq]], [[1zmy|1zmy]], [[2d91|2d91]], [[1lje|1lje]], [[2xth|2xth]], [[1b2k|1b2k]], [[1lze|1lze]], [[1aki|1aki]], [[1hen|1hen]], [[1uia|1uia]], [[1yik|1yik]], [[1xfp|1xfp]], [[2d6b|2d6b]], [[1lpi|1lpi]], [[1ndg|1ndg]], [[1flw|1flw]], [[1lsd|1lsd]], [[2blx|2blx]], [[6lyz|6lyz]], [[1nbz|1nbz]], [[1lsg|1lsg]], [[4lyt|4lyt]], [[1ved|1ved]], [[3hfm|3hfm]], [[1jit|1jit]], [[1lzn|1lzn]], [[1lyz|1lyz]], [[1wtn|1wtn]], [[1ja2|1ja2]], [[1uuz|1uuz]], [[2xbs|2xbs]], [[2d4i|2d4i]], [[2fbb|2fbb]], [[2lym|2lym]], [[1fdl|1fdl]], [[1gxx|1gxx]], [[1lz9|1lz9]], [[1lse|1lse]], [[1lzh|1lzh]], [[1lsm|1lsm]], [[3lym|3lym]], [[7lyz|7lyz]], [[1jj3|1jj3]], [[1yky|1yky]], [[1t3p|1t3p]], [[1heq|1heq]], [[1kiq|1kiq]], [[2lzh|2lzh]], [[1uih|1uih]], [[1kxy|1kxy]], [[2w1l|2w1l]], [[2bly|2bly]], [[1b0d|1b0d]], [[1g7j|1g7j]], [[1bhz|1bhz]], [[1her|1her]], [[1wtm|1wtm]], [[1hep|1hep]], [[1ioq|1ioq]], [[1nby|1nby]], [[1jtt|1jtt]], [[1qio|1qio]], [[1lza|1lza]], [[1xgp|1xgp]], [[1ps5|1ps5]], [[1gwd|1gwd]], [[1v7t|1v7t]], [[1jpo|1jpo]], [[1dqj|1dqj]], [[2a7d|2a7d]], [[1j1p|1j1p]], [[2c8p|2c8p]], [[1z55|1z55]], [[1ljj|1ljj]], [[1lsb|1lsb]], [[1f0w|1f0w]], [[2w1x|2w1x]], [[1lzg|1lzg]], [[1flq|1flq]], [[1lzc|1lzc]], [[1jj1|1jj1]], [[1rcm|1rcm]], [[1uid|1uid]], [[1yqv|1yqv]], [[1hsx|1hsx]], [[1bgi|1bgi]], [[1lcn|1lcn]], [[1lzd|1lzd]], [[1hew|1hew]], [[2cds|2cds]], [[2vb1|2vb1]], [[2aub|2aub]], [[1hf4|1hf4]], [[1uib|1uib]], [[1ir9|1ir9]], [[2cgi|2cgi]], [[1j1x|1j1x]], [[1rjc|1rjc]], [[1ios|1ios]], [[1uc0|1uc0]], [[1azf|1azf]], [[1ljh|1ljh]], [[1ic4|1ic4]], [[4lyz|4lyz]], [[1gpq|1gpq]], [[2a6u|2a6u]], [[2d4k|2d4k]], [[1xej|1xej]], [[1ja7|1ja7]], [[1mel|1mel]], [[1ri8|1ri8]], [[1uig|1uig]], [[1bvx|1bvx]], [[1qtk|1qtk]], [[1c10|1c10]], [[1lkr|1lkr]], [[1lyo|1lyo]], [[2xjw|2xjw]], [[1hsw|1hsw]], [[1n4f|1n4f]], [[2w1y|2w1y]], [[1jto|1jto]], [[1g7m|1g7m]], [[1sf7|1sf7]], [[1lsf|1lsf]], [[1fn5|1fn5]], [[5lyz|5lyz]], [[2d4j|2d4j]], [[1c08|1c08]], [[3lzt|3lzt]], [[1ndm|1ndm]], [[1sf6|1sf6]], [[3lyz|3lyz]], [[1bvk|1bvk]], [[1uif|1uif]], [[2lyz|2lyz]], [[1vau|1vau]], [[1fly|1fly]], [[1lma|1lma]], [[1yl0|1yl0]], [[1j1o|1j1o]], [[1hc0|1hc0]], [[2lzt|2lzt]], [[4lzt|4lzt]], [[1a2y|1a2y]], [[1uco|1uco]], [[1lsy|1lsy]], [[1lsa|1lsa]], [[1ic5|1ic5]], [[1p2c|1p2c]], [[5lym|5lym]], [[1gxv|1gxv]], [[1ua6|1ua6]], [[1at5|1at5]], [[1f3j|1f3j]], [[1vat|1vat]], [[1lj4|1lj4]], [[1hem|1hem]], [[1vfb|1vfb]], [[1ja4|1ja4]], [[4lym|4lym]], [[2a7f|2a7f]], [[194l|194l]], [[1flu|1flu]], [[1lz8|1lz8]], [[1ykx|1ykx]], [[1bwh|1bwh]], [[2hfm|2hfm]], [[1vdt|1vdt]], [[1io5|1io5]], [[1lsn|1lsn]], [[1lzb|1lzb]], [[2bpu|2bpu]], [[1g7i|1g7i]], [[1lsc|1lsc]], [[1vdp|1vdp]]</div></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='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[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] </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=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>
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://proteopedia.org/fgij/fg.htm?mol=1h6m FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1h6m OCA], [http://pdbe.org/1h6m PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1h6m RCSB], [http://www.ebi.ac.uk/pdbsum/1h6m PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1h6m ProSAT]</span></td></tr>
</table>
</table>
== Function ==
== Function ==
[[http://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>
[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 ==
== Evolutionary Conservation ==
[[Image:Consurf_key_small.gif|200px|right]]
[[Image:Consurf_key_small.gif|200px|right]]
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</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].
</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="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.
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>
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
</div>
<div class="pdbe-citations 1h6m" style="background-color:#fffaf0;"></div>


==See Also==
==See Also==
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__TOC__
__TOC__
</StructureSection>
</StructureSection>
[[Category: Chick]]
[[Category: Gallus gallus]]
[[Category: Large Structures]]
[[Category: Large Structures]]
[[Category: Lysozyme]]
[[Category: Davies GJ]]
[[Category: Davies, G J]]
[[Category: Laine R]]
[[Category: Laine, R]]
[[Category: Vocadlo DJ]]
[[Category: Vocadlo, D J]]
[[Category: Withers SG]]
[[Category: Withers, S G]]
[[Category: Covalent intermediate]]
[[Category: Glycoside hydrolase]]
[[Category: Hydrolase]]

Latest revision as of 14:28, 27 March 2024

Covalent glycosyl-enzyme intermediate of hen egg white lysozymeCovalent glycosyl-enzyme intermediate of hen egg white lysozyme

Structural highlights

1h6m is a 1 chain structure with sequence from Gallus gallus. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:X-ray diffraction, Resolution 1.64Å
Ligands:, ,
Resources:FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

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.[1]

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. ↑ Maehashi K, Matano M, Irisawa T, Uchino M, Kashiwagi Y, Watanabe T. Molecular characterization of goose- and chicken-type lysozymes in emu (Dromaius novaehollandiae): evidence for extremely low lysozyme levels in emu egg white. Gene. 2012 Jan 15;492(1):244-9. doi: 10.1016/j.gene.2011.10.021. Epub 2011 Oct, 25. PMID:22044478 doi:10.1016/j.gene.2011.10.021

1h6m, resolution 1.64Å

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