2pi6

From Proteopedia

(Difference between revisions)
Jump to: navigation, search
Current revision (05:25, 17 October 2024) (edit) (undo)
 
(8 intermediate revisions not shown.)
Line 1: Line 1:
-
[[Image:2pi6.png|left|200px]]
 
-
{{STRUCTURE_2pi6| PDB=2pi6 | SCENE= }}
+
==Crystal structure of the sheep signalling glycoprotein (SPS-40) complex with 2-methyl-2-4-pentanediol at 1.65A resolution reveals specific binding characteristics of SPS-40==
 +
<StructureSection load='2pi6' size='340' side='right'caption='[[2pi6]], [[Resolution|resolution]] 1.65&Aring;' scene=''>
 +
== Structural highlights ==
 +
<table><tr><td colspan='2'>[[2pi6]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Ovis_aries Ovis aries]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2PI6 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2PI6 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]] 1.65&#8491;</td></tr>
 +
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=EOH:ETHANOL'>EOH</scene>, <scene name='pdbligand=MAN:ALPHA-D-MANNOSE'>MAN</scene>, <scene name='pdbligand=MPD:(4S)-2-METHYL-2,4-PENTANEDIOL'>MPD</scene>, <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=2pi6 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2pi6 OCA], [https://pdbe.org/2pi6 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2pi6 RCSB], [https://www.ebi.ac.uk/pdbsum/2pi6 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2pi6 ProSAT]</span></td></tr>
 +
</table>
 +
== Function ==
 +
[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).
 +
== 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/pi/2pi6_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=2pi6 ConSurf].
 +
<div style="clear:both"></div>
 +
<div style="background-color:#fffaf0;">
 +
== Publication Abstract from PubMed ==
 +
The 40 kDa secretory signalling glycoprotein (SPS-40) is the first example with Trp78 in three functional orientations: (i) a resting state with a pinched conformation, (ii) a stacked conformation when bound to hexasaccharide and (iii) an obstructive conformation when inhibited by 2-methylpentane-2,4-diol (MPD). Trp78 is present in the core of the sugar-binding groove. The hexasaccharide N-acetylglucosamine (GlcNAc(6)) has been shown to bind to SPS-40. As a result of this, the conformation of Trp78 alters from the native pinched conformation (chi(1) = -65.5 degrees , chi(2,1) = -78.8 degrees , chi(2,2) = 97.5 degrees ) to the stacked conformation (chi(1) = -170.0 degrees , chi(2,1) = -114.3 degrees , chi(2,2) = 61.6 degrees ). Further binding experiments showed that saccharide binding does not occur in the presence of 20% MPD. The crystal structure determination of the complex of SPS-40 with MPD revealed the presence of two MPD molecules in the sugar-binding groove. The very tightly bound MPD molecules at subsites -2 and -1 induced an unexpected and a rarely observed conformation of Trp78 (chi(1) = 55.9 degrees , chi(2,1) = 90.2 degrees , chi(2,2) = -88.9 degrees ) which is termed an obstructive conformation. The binding of MPD molecules also twisted the side chains of Glu269 and Ile272 considerably. These residues are also part of the sugar-binding groove. The observed obstructive conformation of the side chain of Trp78 in the present structure is the exact opposite of the stacked conformation. This rarely observed conformation is stabilized by a number of hydrogen bonds between Trp78 and Asn79 through water molecules W49, W229, W269, W547 and W557.
-
===Crystal structure of the sheep signalling glycoprotein (SPS-40) complex with 2-methyl-2-4-pentanediol at 1.65A resolution reveals specific binding characteristics of SPS-40===
+
Tryptophan as a three-way switch in regulating the function of the secretory signalling glycoprotein (SPS-40) from mammary glands: structure of SPS-40 complexed with 2-methylpentane-2,4-diol at 1.6 A resolution.,Sharma P, Singh N, Sinha M, Sharma S, Perbandt M, Betzel C, Kaur P, Srinivasan A, Singh TP Acta Crystallogr D Biol Crystallogr. 2009 Apr;65(Pt 4):375-8. Epub 2009, Mar 19. PMID:19307719<ref>PMID:19307719</ref>
-
{{ABSTRACT_PUBMED_19307719}}
+
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-
 
+
</div>
-
==About this Structure==
+
<div class="pdbe-citations 2pi6" style="background-color:#fffaf0;"></div>
-
[[2pi6]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Ovis_aries Ovis aries]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2PI6 OCA].
+
==See Also==
==See Also==
-
*[[Chitinase-3-like protein 1|Chitinase-3-like protein 1]]
+
*[[Chitinase-3-like protein 3D structures|Chitinase-3-like protein 3D structures]]
-
 
+
== References ==
-
==Reference==
+
<references/>
-
<ref group="xtra">PMID:019307719</ref><references group="xtra"/>
+
__TOC__
 +
</StructureSection>
 +
[[Category: Large Structures]]
[[Category: Ovis aries]]
[[Category: Ovis aries]]
-
[[Category: Betzel, C.]]
+
[[Category: Betzel C]]
-
[[Category: Kaur, P.]]
+
[[Category: Kaur P]]
-
[[Category: Sharma, P.]]
+
[[Category: Sharma P]]
-
[[Category: Sharma, S.]]
+
[[Category: Sharma S]]
-
[[Category: Singh, N.]]
+
[[Category: Singh N]]
-
[[Category: Singh, T P.]]
+
[[Category: Singh TP]]
-
[[Category: Complex]]
+
-
[[Category: Signaling protein]]
+

Current revision

Crystal structure of the sheep signalling glycoprotein (SPS-40) complex with 2-methyl-2-4-pentanediol at 1.65A resolution reveals specific binding characteristics of SPS-40

PDB ID 2pi6

Drag the structure with the mouse to rotate

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/2pi6"
Personal tools