1ktw: Difference between revisions
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==IOTA-CARRAGEENASE COMPLEXED TO IOTA-CARRAGEENAN FRAGMENTS== | |||
<StructureSection load='1ktw' size='340' side='right'caption='[[1ktw]], [[Resolution|resolution]] 2.00Å' scene=''> | |||
== Structural highlights == | |||
<table><tr><td colspan='2'>[[1ktw]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Alteromonas_macleodii Alteromonas macleodii]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1KTW OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1KTW 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]] 2Å</td></tr> | |||
- | <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=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=DGS:3,6-ANHYDRO-D-GALACTOSE-2-SULFATE'>DGS</scene>, <scene name='pdbligand=G4S:4-O-SULFO-BETA-D-GALACTOPYRANOSE'>G4S</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</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=1ktw FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1ktw OCA], [https://pdbe.org/1ktw PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1ktw RCSB], [https://www.ebi.ac.uk/pdbsum/1ktw PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1ktw ProSAT]</span></td></tr> | |||
</table> | |||
''' | == Function == | ||
[https://www.uniprot.org/uniprot/CGIA_ALTMA CGIA_ALTMA] Hydrolyzes iota-carrageenans, sulfated 1,3-alpha-1,4-beta galactans from red algal cell walls, with an inversion of anomeric configuration. Also active against hybrid iota-/nu-carrageenan, not active against kappa- or lambda-carrageenans.[UniProtKB:Q9F284]<ref>PMID:10934194</ref> <ref>PMID:20227066</ref> | |||
== 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/kt/1ktw_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=1ktw ConSurf]. | |||
<div style="clear:both"></div> | |||
<div style="background-color:#fffaf0;"> | |||
== Publication Abstract from PubMed == | |||
iota-Carrageenans are sulfated 1,3-alpha-1,4-beta-galactans from the cell walls of red algae, which auto-associate into crystalline fibers made of aggregates of double-stranded helices. iota-Carrageenases, which constitute family 82 of glycoside hydrolases, fold into a right-handed beta-helix. Here, the structure of Alteromonas fortis iota-carrageenase bound to iota-carrageenan fragments was solved at 2.0A resolution (PDB 1KTW). The enzyme holds a iota-carrageenan tetrasaccharide (subsites +1 to +4) and a disaccharide (subsites -3, -4), thus providing the first direct determination of a 3D structure of iota-carrageenan. Electrostatic interactions between basic protein residues and the sulfate substituents of the polysaccharide chain dominate iota-carrageenan recognition. Glu245 and Asp247 are the proton donor and the base catalyst, respectively. C-terminal domain A, which was highly flexible in the native enzyme structure, adopts a alpha/beta-fold, also found in DNA/RNA-binding domains. In the substrate-enzyme complex, this polyanion-binding module shifts toward the beta-helix groove, forming a tunnel. Thus, from an open conformation which allows for the initial endo-attack of iota-carrageenan chains, the enzyme switches to a closed-tunnel form, consistent with its highly processive character, as seen from the electron-microscopy analysis of the degradation of iota-carrageenan fibers. | iota-Carrageenans are sulfated 1,3-alpha-1,4-beta-galactans from the cell walls of red algae, which auto-associate into crystalline fibers made of aggregates of double-stranded helices. iota-Carrageenases, which constitute family 82 of glycoside hydrolases, fold into a right-handed beta-helix. Here, the structure of Alteromonas fortis iota-carrageenase bound to iota-carrageenan fragments was solved at 2.0A resolution (PDB 1KTW). The enzyme holds a iota-carrageenan tetrasaccharide (subsites +1 to +4) and a disaccharide (subsites -3, -4), thus providing the first direct determination of a 3D structure of iota-carrageenan. Electrostatic interactions between basic protein residues and the sulfate substituents of the polysaccharide chain dominate iota-carrageenan recognition. Glu245 and Asp247 are the proton donor and the base catalyst, respectively. C-terminal domain A, which was highly flexible in the native enzyme structure, adopts a alpha/beta-fold, also found in DNA/RNA-binding domains. In the substrate-enzyme complex, this polyanion-binding module shifts toward the beta-helix groove, forming a tunnel. Thus, from an open conformation which allows for the initial endo-attack of iota-carrageenan chains, the enzyme switches to a closed-tunnel form, consistent with its highly processive character, as seen from the electron-microscopy analysis of the degradation of iota-carrageenan fibers. | ||
The structural bases of the processive degradation of iota-carrageenan, a main cell wall polysaccharide of red algae.,Michel G, Helbert W, Kahn R, Dideberg O, Kloareg B J Mol Biol. 2003 Nov 28;334(3):421-33. PMID:14623184<ref>PMID:14623184</ref> | |||
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | |||
</div> | |||
[[Category: Alteromonas | <div class="pdbe-citations 1ktw" style="background-color:#fffaf0;"></div> | ||
== References == | |||
[[Category: | <references/> | ||
[[Category: Dideberg | __TOC__ | ||
[[Category: Kahn | </StructureSection> | ||
[[Category: Michel | [[Category: Alteromonas macleodii]] | ||
[[Category: Large Structures]] | |||
[[Category: Dideberg O]] | |||
[[Category: Kahn R]] | |||
[[Category: Michel G]] | |||
Latest revision as of 00:11, 21 November 2024
IOTA-CARRAGEENASE COMPLEXED TO IOTA-CARRAGEENAN FRAGMENTS
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