This old version of Proteopedia is provided for student assignments while the new version is undergoing repairs. Content and edits done in this old version of Proteopedia after March 1, 2026 will eventually be lost when it is retired in about June of 2026.

Apply for new accounts at the new Proteopedia. Your logins will work in both the old and new versions.


1o4z

From Proteopedia

(Difference between revisions)
Jump to: navigation, search
Current revision (06:09, 3 April 2024) (edit) (undo)
 
(11 intermediate revisions not shown.)
Line 1: Line 1:
-
[[Image:1o4z.jpg|left|200px]]
 
-
<!--
+
==THE THREE-DIMENSIONAL STRUCTURE OF BETA-AGARASE B FROM ZOBELLIA GALACTANIVORANS==
-
The line below this paragraph, containing "STRUCTURE_1o4z", creates the "Structure Box" on the page.
+
<StructureSection load='1o4z' size='340' side='right'caption='[[1o4z]], [[Resolution|resolution]] 2.30&Aring;' scene=''>
-
You may change the PDB parameter (which sets the PDB file loaded into the applet)
+
== Structural highlights ==
-
or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
+
<table><tr><td colspan='2'>[[1o4z]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Zobellia_galactanivorans Zobellia galactanivorans]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1O4Z OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1O4Z FirstGlance]. <br>
-
or leave the SCENE parameter empty for the default display.
+
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.3&#8491;</td></tr>
-
-->
+
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=EPE:4-(2-HYDROXYETHYL)-1-PIPERAZINE+ETHANESULFONIC+ACID'>EPE</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene></td></tr>
-
{{STRUCTURE_1o4z| PDB=1o4z | SCENE= }}
+
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1o4z FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1o4z OCA], [https://pdbe.org/1o4z PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1o4z RCSB], [https://www.ebi.ac.uk/pdbsum/1o4z PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1o4z ProSAT]</span></td></tr>
-
 
+
</table>
-
'''THE THREE-DIMENSIONAL STRUCTURE OF BETA-AGARASE B FROM ZOBELLIA GALACTANIVORANS'''
+
== Function ==
-
 
+
[https://www.uniprot.org/uniprot/AGAB_ZOBGA AGAB_ZOBGA] Cleaves the beta-1,4-linkages between beta-D-galactose and alpha-L-3,6-anhydro-galactose residues in agarose. Cleaves agarose in a random manner with retention of the anomeric-bond configuration, producing beta-anomers that give rise progressively to alpha-anomers when mutarotation takes place. Also tolerant to hybrid substrates containing C6-sulfate groups at the -4, +1, and +3 positions.<ref>PMID:15456406</ref> <ref>PMID:22778272</ref>
-
 
+
== Evolutionary Conservation ==
-
==Overview==
+
[[Image:Consurf_key_small.gif|200px|right]]
-
Agars are important gelifying agents for biochemical use and the food industry. To cleave the beta-1,4-linkages between beta-d-galactose and alpha-l-3,6-anhydro-galactose residues in the red algal galactans known as agars, marine bacteria produce polysaccharide hydrolases called beta-agarases. Beta-agarases A and B from Zobellia galactanivorans Dsij have recently been biochemically characterized. Here we report the first crystal structure of these two beta-agarases. The two proteins were overproduced in Escherichia coli and crystallized, and the crystal structures were determined at 1.48 and 2.3 A for beta-agarases A and B, respectively. The structure of beta-agarase A was solved by the multiple anomalous diffraction method, whereas beta-agarase B was solved with molecular replacement using beta-agarase A as model. Their structures adopt a jelly roll fold with a deep active site channel harboring the catalytic machinery, namely the nucleophilic residues Glu-147 and Glu-184 and the acid/base residues Glu-152 and Glu-189 for beta-agarases A and B, respectively. The structures of the agarases were compared with those of two lichenases and of a kappa-carrageenase, which all belong to family 16 of the glycoside hydrolases in order to pinpoint the residues responsible for their widely differing substrate specificity. The relationship between structure and enzymatic activity of the two beta-agarases from Z. galactanivorans Dsij was studied by analysis of the degradation products starting with different oligosaccharides. The combination of the structural and biochemical results allowed the determination of the number of subsites present in the catalytic cleft of the beta-agarases.
+
Check<jmol>
-
 
+
<jmolCheckbox>
-
==About this Structure==
+
<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/o4/1o4z_consurf.spt"</scriptWhenChecked>
-
1O4Z is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Zobellia_galactanivorans Zobellia galactanivorans]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1O4Z OCA].
+
<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
-
 
+
<text>to colour the structure by Evolutionary Conservation</text>
-
==Reference==
+
</jmolCheckbox>
-
The three-dimensional structures of two beta-agarases., Allouch J, Jam M, Helbert W, Barbeyron T, Kloareg B, Henrissat B, Czjzek M, J Biol Chem. 2003 Nov 21;278(47):47171-80. Epub 2003 Sep 11. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/12970344 12970344]
+
</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=1o4z ConSurf].
-
[[Category: Beta-agarase]]
+
<div style="clear:both"></div>
-
[[Category: Single protein]]
+
== References ==
 +
<references/>
 +
__TOC__
 +
</StructureSection>
 +
[[Category: Large Structures]]
[[Category: Zobellia galactanivorans]]
[[Category: Zobellia galactanivorans]]
-
[[Category: Allouch, J.]]
+
[[Category: Allouch J]]
-
[[Category: Barbeyron, T.]]
+
[[Category: Barbeyron T]]
-
[[Category: Czjzek, M.]]
+
[[Category: Czjzek M]]
-
[[Category: Helbert, W.]]
+
[[Category: Helbert W]]
-
[[Category: Henrissat, B.]]
+
[[Category: Henrissat B]]
-
[[Category: Jam, M.]]
+
[[Category: Jam M]]
-
[[Category: Kloareg, B.]]
+
[[Category: Kloareg B]]
-
[[Category: 4-d-galactose linkage]]
+
-
[[Category: Agarose degradation]]
+
-
[[Category: Beta-agarase]]
+
-
[[Category: Cleavage of beta-1]]
+
-
[[Category: Glycoside hydrolase family 16]]
+
-
''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sat May 3 03:23:23 2008''
+

Current revision

THE THREE-DIMENSIONAL STRUCTURE OF BETA-AGARASE B FROM ZOBELLIA GALACTANIVORANS

PDB ID 1o4z

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/1o4z"
Personal tools