2dpe

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(New page: 200px<br /><applet load="2dpe" size="450" color="white" frame="true" align="right" spinBox="true" caption="2dpe, resolution 2.07&Aring;" /> '''Crystal structure of...)
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[[Image:2dpe.gif|left|200px]]<br /><applet load="2dpe" size="450" color="white" frame="true" align="right" spinBox="true"
 
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caption="2dpe, resolution 2.07&Aring;" />
 
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'''Crystal structure of a secretory 40KDA glycoprotein from sheep at 2.0A resolution'''<br />
 
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==Overview==
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==Crystal structure of a secretory 40KDA glycoprotein from sheep at 2.0A resolution==
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A 40kDa glycoprotein from dry secretion of sheep is implicated as a, signaling factor and is named as SPS-40. This protein is secreted only, during the early phase of involution when the drastic tissue remodeling, occurs in the mammary gland. SPS-40 was purified from sheep dry secretions, and crystallized using hanging drop vapour diffusion method. The crystals, belong to orthorhombic space group P2(1)2(1)2(1) with cell dimensions, a=62.7A, b=66.4A, c=107.5A. The protein was also cloned for the, determination of its complete amino acid sequence. The three-dimensional, structure of SPS-40 was determined by X-ray crystallographic method at, 2.0A resolution. The structure revealed the presence of an N-linked glycan, chain at Asn39. The protein adopts a conformation with a classical, (beta/alpha)(8)-barrel fold of triosephosphate isomerase (TIM) (residues, 1-237 and 310-360) with an insertion of a small (alpha+beta) domain, (residues 240-307) similar to that observed in chitinases. However, the, Leu substitution for Glu in the consensus catalytic sequence in SPS-40, causes a loss of chitinase activity. Furthermore, the sugar-binding groove, in SPS-40 is distorted considerably from the standard chitin-binding site, in chitinase enzymes and hence the binding of chitin-like oligosaccharides, is considerably hampered. Three surface loops, His188-His197, Phe202-Arg212 and Phe244-Pro260 have exceptionally high values of, B-factors (average=70.5A(2)), indicating the presence of a less defined, region.
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<StructureSection load='2dpe' size='340' side='right'caption='[[2dpe]], [[Resolution|resolution]] 2.07&Aring;' scene=''>
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== Structural highlights ==
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<table><tr><td colspan='2'>[[2dpe]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Ovis_aries Ovis aries]. This structure supersedes the now removed PDB entry [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=1r2v 1r2v]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2DPE OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2DPE FirstGlance]. <br>
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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]] 2.07&#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=BMA:BETA-D-MANNOSE'>BMA</scene>, <scene name='pdbligand=MAN:ALPHA-D-MANNOSE'>MAN</scene>, <scene name='pdbligand=NAG:N-ACETYL-D-GLUCOSAMINE'>NAG</scene></td></tr>
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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=2dpe FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2dpe OCA], [https://pdbe.org/2dpe PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2dpe RCSB], [https://www.ebi.ac.uk/pdbsum/2dpe PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2dpe ProSAT]</span></td></tr>
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</table>
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== Function ==
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[https://www.uniprot.org/uniprot/CH3L1_SHEEP CH3L1_SHEEP] Carbohydrate-binding lectin with a preference for chitin. May play a role in defense against pathogens, or in tissue remodeling. May play an important role in the capacity of cells to respond to and cope with changes in their environment (By similarity).
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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/dp/2dpe_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=2dpe 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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A 40kDa glycoprotein from dry secretion of sheep is implicated as a signaling factor and is named as SPS-40. This protein is secreted only during the early phase of involution when the drastic tissue remodeling occurs in the mammary gland. SPS-40 was purified from sheep dry secretions and crystallized using hanging drop vapour diffusion method. The crystals belong to orthorhombic space group P2(1)2(1)2(1) with cell dimensions, a=62.7A, b=66.4A, c=107.5A. The protein was also cloned for the determination of its complete amino acid sequence. The three-dimensional structure of SPS-40 was determined by X-ray crystallographic method at 2.0A resolution. The structure revealed the presence of an N-linked glycan chain at Asn39. The protein adopts a conformation with a classical (beta/alpha)(8)-barrel fold of triosephosphate isomerase (TIM) (residues 1-237 and 310-360) with an insertion of a small (alpha+beta) domain (residues 240-307) similar to that observed in chitinases. However, the Leu substitution for Glu in the consensus catalytic sequence in SPS-40 causes a loss of chitinase activity. Furthermore, the sugar-binding groove in SPS-40 is distorted considerably from the standard chitin-binding site in chitinase enzymes and hence the binding of chitin-like oligosaccharides is considerably hampered. Three surface loops, His188-His197, Phe202-Arg212 and Phe244-Pro260 have exceptionally high values of B-factors (average=70.5A(2)), indicating the presence of a less defined region.
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==About this Structure==
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Crystal structure of a secretory signalling glycoprotein from sheep at 2.0A resolution.,Srivastava DB, Ethayathulla AS, Kumar J, Singh N, Sharma S, Das U, Srinivasan A, Singh TP J Struct Biol. 2006 Dec;156(3):505-16. Epub 2006 Jun 8. PMID:16859926<ref>PMID:16859926</ref>
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2DPE is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Ovis_aries Ovis aries]. This structure superseeds the now removed PDB entry 1R2V. Full crystallographic information is available from [http://ispc.weizmann.ac.il/oca-bin/ocashort?id=2DPE OCA].
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==Reference==
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From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
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Crystal structure of a secretory signalling glycoprotein from sheep at 2.0A resolution., Srivastava DB, Ethayathulla AS, Kumar J, Singh N, Sharma S, Das U, Srinivasan A, Singh TP, J Struct Biol. 2006 Dec;156(3):505-16. Epub 2006 Jun 8. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=16859926 16859926]
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</div>
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[[Category: Ovis aries]]
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<div class="pdbe-citations 2dpe" style="background-color:#fffaf0;"></div>
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[[Category: Single protein]]
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[[Category: Das, U.]]
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[[Category: Ethayathulla, A.S.]]
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[[Category: Kumar, J.]]
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[[Category: Sharma, S.]]
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[[Category: Singh, N.]]
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[[Category: Singh, T.P.]]
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[[Category: Srinivasan, A.]]
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[[Category: Srivastava, D.B.]]
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[[Category: involution]]
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[[Category: mammary gland secretion]]
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[[Category: signaling protein]]
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''Page seeded by [http://ispc.weizmann.ac.il/oca OCA ] on Wed Nov 21 09:42:18 2007''
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==See Also==
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*[[Chitinase-3-like protein 3D structures|Chitinase-3-like protein 3D structures]]
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== References ==
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<references/>
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__TOC__
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</StructureSection>
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[[Category: Large Structures]]
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[[Category: Ovis aries]]
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[[Category: Das U]]
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[[Category: Ethayathulla AS]]
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[[Category: Kumar J]]
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[[Category: Sharma S]]
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[[Category: Singh N]]
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[[Category: Singh TP]]
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[[Category: Srinivasan A]]
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[[Category: Srivastava DB]]

Current revision

Crystal structure of a secretory 40KDA glycoprotein from sheep at 2.0A resolution

PDB ID 2dpe

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