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1dyo

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[[Image:1dyo.gif|left|200px]]
 
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{{Structure
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==Xylan-Binding Domain from CBM 22, formally x6b domain==
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|PDB= 1dyo |SIZE=350|CAPTION= <scene name='initialview01'>1dyo</scene>, resolution 2.1&Aring;
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<StructureSection load='1dyo' size='340' side='right'caption='[[1dyo]], [[Resolution|resolution]] 2.10&Aring;' scene=''>
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|SITE=
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== Structural highlights ==
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|LIGAND= <scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene>
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<table><tr><td colspan='2'>[[1dyo]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Acetivibrio_thermocellus Acetivibrio thermocellus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1DYO OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1DYO FirstGlance]. <br>
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|ACTIVITY=
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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]] 2.1&#8491;</td></tr>
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|GENE=
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<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene></td></tr>
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|DOMAIN=
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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=1dyo FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1dyo OCA], [https://pdbe.org/1dyo PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1dyo RCSB], [https://www.ebi.ac.uk/pdbsum/1dyo PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1dyo ProSAT]</span></td></tr>
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|RELATEDENTRY=
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</table>
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|RESOURCES=<span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1dyo FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1dyo OCA], [http://www.ebi.ac.uk/pdbsum/1dyo PDBsum], [http://www.rcsb.org/pdb/explore.do?structureId=1dyo RCSB]</span>
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== Function ==
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}}
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[https://www.uniprot.org/uniprot/XYNY_ACETH XYNY_ACETH]
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== Evolutionary Conservation ==
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'''XYLAN-BINDING DOMAIN FROM CBM 22, FORMALLY X6B DOMAIN'''
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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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==Overview==
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<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/dy/1dyo_consurf.spt"</scriptWhenChecked>
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Organophosphorus acid anhydride (OP) nerve agents are potent inhibitors which rapidly phosphonylate acetylcholinesterase (AChE) and then may undergo an internal dealkylation reaction (called "aging") to produce an OP-enzyme conjugate that cannot be reactivated. To understand the basis for irreversible inhibition, we solved the structures of aged conjugates obtained by reaction of Torpedo californica AChE (TcAChE) with diisopropylphosphorofluoridate (DFP), O-isopropylmethylphosponofluoridate (sarin), or O-pinacolylmethylphosphonofluoridate (soman) by X-ray crystallography to 2.3, 2.6, or 2.2 A resolution, respectively. The highest positive difference density peak corresponded to the OP phosphorus and was located within covalent bonding distance of the active-site serine (S200) in each structure. The OP-oxygen atoms were within hydrogen-bonding distance of four potential donors from catalytic subsites of the enzyme, suggesting that electrostatic forces significantly stabilize the aged enzyme. The active sites of aged sarin- and soman-TcAChE were essentially identical and provided structural models for the negatively charged, tetrahedral intermediate that occurs during deacylation with the natural substrate, acetylcholine. Phosphorylation with DFP caused an unexpected movement in the main chain of a loop that includes residues F288 and F290 of the TcAChE acyl pocket. This is the first major conformational change reported in the active site of any AChE-ligand complex, and it offers a structural explanation for the substrate selectivity of AChE.
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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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==About this Structure==
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</jmolCheckbox>
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1DYO is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Clostridium_thermocellum Clostridium thermocellum]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1DYO OCA].
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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=1dyo ConSurf].
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<div style="clear:both"></div>
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==Reference==
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__TOC__
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Crystal structures of aged phosphonylated acetylcholinesterase: nerve agent reaction products at the atomic level., Millard CB, Kryger G, Ordentlich A, Greenblatt HM, Harel M, Raves ML, Segall Y, Barak D, Shafferman A, Silman I, Sussman JL, Biochemistry. 1999 Jun 1;38(22):7032-9. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/10353814 10353814]
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</StructureSection>
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[[Category: Clostridium thermocellum]]
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[[Category: Acetivibrio thermocellus]]
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[[Category: Single protein]]
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[[Category: Large Structures]]
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[[Category: Charnock, S J.]]
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[[Category: Charnock SJ]]
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[[Category: Davies, G J.]]
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[[Category: Davies GJ]]
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[[Category: Fontes, C M.G A.]]
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[[Category: Fontes CMGA]]
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[[Category: Gilbert, H J.]]
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[[Category: Gilbert HJ]]
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[[Category: carbohydrate-binding module]]
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[[Category: xylan-binding]]
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[[Category: xylanase]]
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''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sun Mar 30 19:51:32 2008''
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Current revision

Xylan-Binding Domain from CBM 22, formally x6b domain

PDB ID 1dyo

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