5a3h: Difference between revisions

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{{Seed}}
[[Image:5a3h.png|left|200px]]


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==2-DEOXY-2-FLURO-B-D-CELLOBIOSYL/ENZYME INTERMEDIATE COMPLEX OF THE ENDOGLUCANASE CEL5A FROM BACILLUS AGARADHEARANS AT 1.8 ANGSTROMS RESOLUTION==
The line below this paragraph, containing "STRUCTURE_5a3h", creates the "Structure Box" on the page.
<StructureSection load='5a3h' size='340' side='right'caption='[[5a3h]], [[Resolution|resolution]] 1.82&Aring;' scene=''>
You may change the PDB parameter (which sets the PDB file loaded into the applet)
== Structural highlights ==
or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
<table><tr><td colspan='2'>[[5a3h]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Salipaludibacillus_agaradhaerens Salipaludibacillus agaradhaerens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5A3H OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5A3H FirstGlance]. <br>
or leave the SCENE parameter empty for the default display.
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.82&#8491;</td></tr>
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<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=BGC:BETA-D-GLUCOSE'>BGC</scene>, <scene name='pdbligand=G2F:2-DEOXY-2-FLUORO-ALPHA-D-GLUCOPYRANOSE'>G2F</scene>, <scene name='pdbligand=PRD_900050:2-deoxy-2-fluoro-beta-cellobiose'>PRD_900050</scene></td></tr>
{{STRUCTURE_5a3h|  PDB=5a3h  |  SCENE=  }}
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=5a3h FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5a3h OCA], [https://pdbe.org/5a3h PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5a3h RCSB], [https://www.ebi.ac.uk/pdbsum/5a3h PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5a3h ProSAT]</span></td></tr>
</table>
== Function ==
[https://www.uniprot.org/uniprot/GUN5_SALAG GUN5_SALAG]
== 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/a3/5a3h_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=5a3h ConSurf].
<div style="clear:both"></div>
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
The enzymatic hydrolysis of O-glycosidic linkages is one of the most diverse and widespread reactions in nature and involves a classic "textbook" enzyme mechanism. A multidisciplinary analysis of a beta-glycoside hydrolase, the Cel5A from Bacillus agaradhaerens, is presented in which the structures of each of the native, substrate, covalent-intermediate, and product complexes have been determined and their interconversions analyzed kinetically, providing unprecedented insights into the mechanism of this enzyme class. Substrate is bound in a distorted 1S3 skew-boat conformation, thereby presenting the anomeric carbon appropriately for nucleophilic attack as well as satisfying the stereoelectronic requirements for an incipient oxocarbenium ion. Leaving group departure results in the trapping of a covalent alpha-glycosyl-enzyme intermediate in which the sugar adopts an undistorted 4C1 conformation. Finally, hydrolysis of this intermediate yields a product complex in which the sugar is bound in a partially disordered mode, consistent with unfavorable interactions and low product affinity.


===2-DEOXY-2-FLURO-B-D-CELLOBIOSYL/ENZYME INTERMEDIATE COMPLEX OF THE ENDOGLUCANASE CEL5A FROM BACILLUS AGARADHEARANS AT 1.8 ANGSTROMS RESOLUTION===
Snapshots along an enzymatic reaction coordinate: analysis of a retaining beta-glycoside hydrolase.,Davies GJ, Mackenzie L, Varrot A, Dauter M, Brzozowski AM, Schulein M, Withers SG Biochemistry. 1998 Aug 25;37(34):11707-13. PMID:9718293<ref>PMID:9718293</ref>


From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
</div>
<div class="pdbe-citations 5a3h" style="background-color:#fffaf0;"></div>


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==See Also==
The line below this paragraph, {{ABSTRACT_PUBMED_9718293}}, adds the Publication Abstract to the page
*[[Glucanase 3D structures|Glucanase 3D structures]]
(as it appears on PubMed at http://www.pubmed.gov), where 9718293 is the PubMed ID number.
== References ==
-->
<references/>
{{ABSTRACT_PUBMED_9718293}}
__TOC__
 
</StructureSection>
==About this Structure==
[[Category: Large Structures]]
5A3H is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Bacillus_agaradhaerens Bacillus agaradhaerens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5A3H OCA].
[[Category: Salipaludibacillus agaradhaerens]]
 
[[Category: Brzozowski AM]]
==Reference==
[[Category: Dauter M]]
Snapshots along an enzymatic reaction coordinate: analysis of a retaining beta-glycoside hydrolase., Davies GJ, Mackenzie L, Varrot A, Dauter M, Brzozowski AM, Schulein M, Withers SG, Biochemistry. 1998 Aug 25;37(34):11707-13. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/9718293 9718293]
[[Category: Davies GJ]]
[[Category: Bacillus agaradhaerens]]
[[Category: Mackenzie L]]
[[Category: Cellulase]]
[[Category: Schulein M]]
[[Category: Single protein]]
[[Category: Varrot A]]
[[Category: Brzozowski, A M.]]
[[Category: Withers SG]]
[[Category: Dauter, M.]]
[[Category: Davies, G J.]]
[[Category: Mackenzie, L.]]
[[Category: Schulein, M.]]
[[Category: Varrot, A.]]
[[Category: Withers, S G.]]
[[Category: Cellulose degradation]]
[[Category: Distortion]]
[[Category: Endoglucanase]]
[[Category: Glycoside hydrolase family 5]]
[[Category: Hydrolase]]
[[Category: Michaelis complex]]
[[Category: Skew-boat]]
 
''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Jul  3 13:55:27 2008''

Latest revision as of 14:36, 6 November 2024

2-DEOXY-2-FLURO-B-D-CELLOBIOSYL/ENZYME INTERMEDIATE COMPLEX OF THE ENDOGLUCANASE CEL5A FROM BACILLUS AGARADHEARANS AT 1.8 ANGSTROMS RESOLUTION2-DEOXY-2-FLURO-B-D-CELLOBIOSYL/ENZYME INTERMEDIATE COMPLEX OF THE ENDOGLUCANASE CEL5A FROM BACILLUS AGARADHEARANS AT 1.8 ANGSTROMS RESOLUTION

Structural highlights

5a3h is a 1 chain structure with sequence from Salipaludibacillus agaradhaerens. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:X-ray diffraction, Resolution 1.82Å
Ligands:, ,
Resources:FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

GUN5_SALAG

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

The enzymatic hydrolysis of O-glycosidic linkages is one of the most diverse and widespread reactions in nature and involves a classic "textbook" enzyme mechanism. A multidisciplinary analysis of a beta-glycoside hydrolase, the Cel5A from Bacillus agaradhaerens, is presented in which the structures of each of the native, substrate, covalent-intermediate, and product complexes have been determined and their interconversions analyzed kinetically, providing unprecedented insights into the mechanism of this enzyme class. Substrate is bound in a distorted 1S3 skew-boat conformation, thereby presenting the anomeric carbon appropriately for nucleophilic attack as well as satisfying the stereoelectronic requirements for an incipient oxocarbenium ion. Leaving group departure results in the trapping of a covalent alpha-glycosyl-enzyme intermediate in which the sugar adopts an undistorted 4C1 conformation. Finally, hydrolysis of this intermediate yields a product complex in which the sugar is bound in a partially disordered mode, consistent with unfavorable interactions and low product affinity.

Snapshots along an enzymatic reaction coordinate: analysis of a retaining beta-glycoside hydrolase.,Davies GJ, Mackenzie L, Varrot A, Dauter M, Brzozowski AM, Schulein M, Withers SG Biochemistry. 1998 Aug 25;37(34):11707-13. PMID:9718293[1]

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

See Also

References

  1. ↑ Davies GJ, Mackenzie L, Varrot A, Dauter M, Brzozowski AM, Schulein M, Withers SG. Snapshots along an enzymatic reaction coordinate: analysis of a retaining beta-glycoside hydrolase. Biochemistry. 1998 Aug 25;37(34):11707-13. PMID:9718293 doi:http://dx.doi.org/10.1021/bi981315i

5a3h, resolution 1.82Å

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