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New page: left|200px<br /><applet load="1qaz" size="450" color="white" frame="true" align="right" spinBox="true" caption="1qaz, resolution 1.78Å" /> '''CRYSTAL STRUCTURE OF...
 
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[[Image:1qaz.gif|left|200px]]<br /><applet load="1qaz" size="450" color="white" frame="true" align="right" spinBox="true"
caption="1qaz, resolution 1.78&Aring;" />
'''CRYSTAL STRUCTURE OF ALGINATE LYASE A1-III FROM SPHINGOMONAS SPECIES A1 AT 1.78A RESOLUTION'''<br />


==Overview==
==CRYSTAL STRUCTURE OF ALGINATE LYASE A1-III FROM SPHINGOMONAS SPECIES A1 AT 1.78A RESOLUTION==
The three-dimensional structure of alginate lyase A1-III (ALYIII) from a, Sphingomonas species A1 was determined by X-ray crystallography. The, enzyme was crystallized by the hanging-drop vapour-diffusion method in the, presence of 49% ammonium sulfate at 20 degrees C. The crystals are, monoclinic and belong to the space group C2 with unit cell dimensions of, a=49.18 A, b=93.08 A, c=82.10 A and beta=104.12 degrees. There was one, molecule of alginate lyase in the asymmetric unit of the crystal. The, diffraction data up to 1. 71 A were collected with Rsymof 5.0%. The, crystal structure of ALYIII was solved by the multiple isomorphous, replacement method and refined at 1.78 A resolution using X-PLOR with a, final R -factor of 18.0% for 10.0 to 1.78 A resolution data. The refined, model of ALYIII contained 351 amino acid residues, 299 water molecules and, two sulfate ions. The three-dimensional structure of ALYIII was abundant, in helices and had a deep tunnel-like cleft in a novel, (alpha6/alpha5)-barrel structure, which was similar to the, (alpha6/alpha6)-barrel found in glucoamylase and cellulase. This structure, presented the possibility that alginate molecules might penetrate into the, cleft to interact with the catalytic site of ALYIII.
<StructureSection load='1qaz' size='340' side='right'caption='[[1qaz]], [[Resolution|resolution]] 1.78&Aring;' scene=''>
== Structural highlights ==
<table><tr><td colspan='2'>[[1qaz]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Sphingomonas_sp. Sphingomonas sp.]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1QAZ OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1QAZ 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]] 1.78&#8491;</td></tr>
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=SO4:SULFATE+ION'>SO4</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=1qaz FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1qaz OCA], [https://pdbe.org/1qaz PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1qaz RCSB], [https://www.ebi.ac.uk/pdbsum/1qaz PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1qaz ProSAT]</span></td></tr>
</table>
== Function ==
[https://www.uniprot.org/uniprot/Q9KWU1_SPHSX Q9KWU1_SPHSX]
== 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/qa/1qaz_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=1qaz ConSurf].
<div style="clear:both"></div>
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
The three-dimensional structure of alginate lyase A1-III (ALYIII) from a Sphingomonas species A1 was determined by X-ray crystallography. The enzyme was crystallized by the hanging-drop vapour-diffusion method in the presence of 49% ammonium sulfate at 20 degrees C. The crystals are monoclinic and belong to the space group C2 with unit cell dimensions of a=49.18 A, b=93.08 A, c=82.10 A and beta=104.12 degrees. There was one molecule of alginate lyase in the asymmetric unit of the crystal. The diffraction data up to 1. 71 A were collected with Rsymof 5.0%. The crystal structure of ALYIII was solved by the multiple isomorphous replacement method and refined at 1.78 A resolution using X-PLOR with a final R -factor of 18.0% for 10.0 to 1.78 A resolution data. The refined model of ALYIII contained 351 amino acid residues, 299 water molecules and two sulfate ions. The three-dimensional structure of ALYIII was abundant in helices and had a deep tunnel-like cleft in a novel (alpha6/alpha5)-barrel structure, which was similar to the (alpha6/alpha6)-barrel found in glucoamylase and cellulase. This structure presented the possibility that alginate molecules might penetrate into the cleft to interact with the catalytic site of ALYIII.


==About this Structure==
Crystal structure of alginate lyase A1-III from Sphingomonas species A1 at 1.78 A resolution.,Yoon HJ, Mikami B, Hashimoto W, Murata K J Mol Biol. 1999 Jul 9;290(2):505-14. PMID:10390348<ref>PMID:10390348</ref>
1QAZ is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Sphingomonas_sp. Sphingomonas sp.] with SO4 as [http://en.wikipedia.org/wiki/ligand ligand]. Active as [http://en.wikipedia.org/wiki/Urea_carboxylase Urea carboxylase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=6.3.4.6 6.3.4.6] Full crystallographic information is available from [http://ispc.weizmann.ac.il/oca-bin/ocashort?id=1QAZ OCA].


==Reference==
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
Crystal structure of alginate lyase A1-III from Sphingomonas species A1 at 1.78 A resolution., Yoon HJ, Mikami B, Hashimoto W, Murata K, J Mol Biol. 1999 Jul 9;290(2):505-14. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=10390348 10390348]
</div>
[[Category: Single protein]]
<div class="pdbe-citations 1qaz" style="background-color:#fffaf0;"></div>
[[Category: Sphingomonas sp.]]
== References ==
[[Category: Urea carboxylase]]
<references/>
[[Category: Yoon, H.J.]]
__TOC__
[[Category: SO4]]
</StructureSection>
[[Category: alginate lyase]]
[[Category: Large Structures]]
[[Category: crystals]]
[[Category: Sphingomonas sp]]
[[Category: x-ray structure]]
[[Category: Yoon H-J]]
 
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Latest revision as of 08:45, 6 November 2024

CRYSTAL STRUCTURE OF ALGINATE LYASE A1-III FROM SPHINGOMONAS SPECIES A1 AT 1.78A RESOLUTION

1qaz, resolution 1.78Å

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