3b9d: Difference between revisions

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[[Image:3b9d.png|left|200px]]


{{STRUCTURE_3b9d| PDB=3b9d | SCENE= }}
==Crystal structure of Vibrio harveyi chitinase A complexed with pentasaccharide==
<StructureSection load='3b9d' size='340' side='right'caption='[[3b9d]], [[Resolution|resolution]] 1.72&Aring;' scene=''>
== Structural highlights ==
<table><tr><td colspan='2'>[[3b9d]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Vibrio_harveyi Vibrio harveyi]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3B9D OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3B9D 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]] 1.72&#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></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=3b9d FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3b9d OCA], [https://pdbe.org/3b9d PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3b9d RCSB], [https://www.ebi.ac.uk/pdbsum/3b9d PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3b9d ProSAT]</span></td></tr>
</table>
== Function ==
[https://www.uniprot.org/uniprot/Q9AMP1_VIBHA Q9AMP1_VIBHA]
== 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/b9/3b9d_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=3b9d ConSurf].
<div style="clear:both"></div>
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
This research describes four X-ray structures of Vibrio harveyi chitinase A and its catalytically inactive mutant (E315M) in the presence and absence of substrates. The overall structure of chitinase A is that of a typical family-18 glycosyl hydrolase comprising three distinct domains: (i) the amino-terminal chitin-binding domain; (ii) the main catalytic (alpha/beta)(8) TIM-barrel domain; and (iii) the small (alpha+beta) insertion domain. The catalytic cleft of chitinase A has a long, deep groove, which contains six chitooligosaccharide ring-binding subsites (-4)(-3)(-2)(-1)(+1)(+2). The binding cleft of the ligand-free E315M is partially blocked by the C-terminal (His)(6)-tag. Structures of E315M-chitooligosaccharide complexes display a linear conformation of pentaNAG, but a bent conformation of hexaNAG. Analysis of the final 2F(o)-F(c) omit map of E315M-NAG6 reveals the existence of the linear conformation of the hexaNAG at a lower occupancy with respect to the bent conformation. These crystallographic data provide evidence that the interacting sugars undergo conformational changes prior to hydrolysis by the wild-type enzyme.


===Crystal structure of Vibrio harveyi chitinase A complexed with pentasaccharide===
Crystal structures of Vibrio harveyi chitinase A complexed with chitooligosaccharides: implications for the catalytic mechanism.,Songsiriritthigul C, Pantoom S, Aguda AH, Robinson RC, Suginta W J Struct Biol. 2008 Jun;162(3):491-9. Epub 2008 Mar 26. PMID:18467126<ref>PMID:18467126</ref>


{{ABSTRACT_PUBMED_18467126}}
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
 
</div>
==About this Structure==
<div class="pdbe-citations 3b9d" style="background-color:#fffaf0;"></div>
[[3b9d]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Vibrio_harveyi Vibrio harveyi]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3B9D OCA].


==See Also==
==See Also==
*[[Chitinase|Chitinase]]
*[[Chitinase 3D structures|Chitinase 3D structures]]
 
== References ==
==Reference==
<references/>
<ref group="xtra">PMID:018467126</ref><references group="xtra"/>
__TOC__
[[Category: Chitinase]]
</StructureSection>
[[Category: Large Structures]]
[[Category: Vibrio harveyi]]
[[Category: Vibrio harveyi]]
[[Category: Aguda, A H.]]
[[Category: Aguda AH]]
[[Category: Robinson, R C.]]
[[Category: Robinson RC]]
[[Category: Songsiriritthigul, C.]]
[[Category: Songsiriritthigul C]]
[[Category: Suginta, W.]]
[[Category: Suginta W]]
[[Category: Glycosidase]]
[[Category: Hydrolase]]
[[Category: Pentasaccharide complex]]
[[Category: Tim-barrel]]
Retrieved from "https://proteopedia.org/3b9d"