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3b9d

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[[Image:3b9d.jpg|left|200px]]
 
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==Crystal structure of Vibrio harveyi chitinase A complexed with pentasaccharide==
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The line below this paragraph, containing "STRUCTURE_3b9d", creates the "Structure Box" on the page.
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<StructureSection load='3b9d' size='340' side='right'caption='[[3b9d]], [[Resolution|resolution]] 1.72&Aring;' scene=''>
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You may change the PDB parameter (which sets the PDB file loaded into the applet)
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== Structural highlights ==
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or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
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<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>
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or leave the SCENE parameter empty for the default display.
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</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>
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<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>
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{{STRUCTURE_3b9d| PDB=3b9d | SCENE= }}
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<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>
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</table>
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== Function ==
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[https://www.uniprot.org/uniprot/Q9AMP1_VIBHA Q9AMP1_VIBHA]
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== Evolutionary Conservation ==
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[[Image:Consurf_key_small.gif|200px|right]]
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Check<jmol>
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<jmolCheckbox>
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<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/b9/3b9d_consurf.spt"</scriptWhenChecked>
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<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
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<text>to colour the structure by Evolutionary Conservation</text>
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</jmolCheckbox>
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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=3b9d ConSurf].
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<div style="clear:both"></div>
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<div style="background-color:#fffaf0;">
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== Publication Abstract from PubMed ==
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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.
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'''Crystal structure of Vibrio harveyi chitinase A complexed with pentasaccharide'''
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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>
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==Overview==
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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.
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==About this Structure==
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From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
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3B9D is a [[Single protein]] structure of 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].
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</div>
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<div class="pdbe-citations 3b9d" style="background-color:#fffaf0;"></div>
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==Reference==
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==See Also==
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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:[http://www.ncbi.nlm.nih.gov/pubmed/18467126 18467126]
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*[[Chitinase 3D structures|Chitinase 3D structures]]
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[[Category: Chitinase]]
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== References ==
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[[Category: Single protein]]
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<references/>
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__TOC__
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</StructureSection>
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[[Category: Large Structures]]
[[Category: Vibrio harveyi]]
[[Category: Vibrio harveyi]]
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[[Category: Aguda, A H.]]
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[[Category: Aguda AH]]
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[[Category: Robinson, R C.]]
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[[Category: Robinson RC]]
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[[Category: Songsiriritthigul, C.]]
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[[Category: Songsiriritthigul C]]
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[[Category: Suginta, W.]]
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[[Category: Suginta W]]
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[[Category: Glycosidase]]
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[[Category: Hydrolase]]
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[[Category: Pentasaccharide complex]]
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[[Category: Tim-barrel]]
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''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Jun 18 12:20:19 2008''
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Current revision

Crystal structure of Vibrio harveyi chitinase A complexed with pentasaccharide

PDB ID 3b9d

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