5gkd

From Proteopedia

(Difference between revisions)
Jump to: navigation, search
Current revision (09:12, 20 March 2024) (edit) (undo)
 
(2 intermediate revisions not shown.)
Line 1: Line 1:
==Structure of PL6 family alginate lyase AlyGC==
==Structure of PL6 family alginate lyase AlyGC==
-
<StructureSection load='5gkd' size='340' side='right' caption='[[5gkd]], [[Resolution|resolution]] 2.19&Aring;' scene=''>
+
<StructureSection load='5gkd' size='340' side='right'caption='[[5gkd]], [[Resolution|resolution]] 2.19&Aring;' scene=''>
== Structural highlights ==
== Structural highlights ==
-
<table><tr><td colspan='2'>[[5gkd]] is a 4 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5GKD OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5GKD FirstGlance]. <br>
+
<table><tr><td colspan='2'>[[5gkd]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Paraglaciecola_chathamensis Paraglaciecola chathamensis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5GKD OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5GKD FirstGlance]. <br>
-
</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=CO3:CARBONATE+ION'>CO3</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene></td></tr>
+
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.194&#8491;</td></tr>
-
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5gkd FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5gkd OCA], [http://pdbe.org/5gkd PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5gkd RCSB], [http://www.ebi.ac.uk/pdbsum/5gkd PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5gkd ProSAT]</span></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=CO3:CARBONATE+ION'>CO3</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</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=5gkd FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5gkd OCA], [https://pdbe.org/5gkd PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5gkd RCSB], [https://www.ebi.ac.uk/pdbsum/5gkd PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5gkd ProSAT]</span></td></tr>
</table>
</table>
-
<div style="background-color:#fffaf0;">
+
== Function ==
-
== Publication Abstract from PubMed ==
+
[https://www.uniprot.org/uniprot/A0A1S4NYD7_9ALTE A0A1S4NYD7_9ALTE]
-
Alginate lyases that degrade alginate via a beta-elimination reaction fall into seven polysaccharide lyase (PL) families. Although the structures and catalytic mechanisms of alginate lyases in the other PL families have been clarified, those in family PL6 have yet to be revealed. Here, the crystal structure of AlyGC, a PL6 alginate lyase from marine bacterium Glaciecola chathamensis S18K6T, was solved, and its catalytic mechanism was illustrated. AlyGC is a homodimeric enzyme and adopts a structure distinct from other alginate lyases. Each monomer contains a catalytic N-terminal domain and a functionally unknown C-terminal domain. A combined structural and mutational analysis using the structures of AlyGC and of an inactive mutant R241A in complex with an alginate tetrasaccharide indicates that conformational changes occur in AlyGC when a substrate is bound and that the two active centers in AlyGC may not bind substrates simultaneously. The C-terminal domain is shown to be essential for the dimerization and the catalytic activity of AlyGC. Residues Tyr130, Arg187, His242, Arg265, and Tyr304 in the active center are also important for the activity of AlyGC. In catalysis, Lys220 and Arg241 function as the Bronsted base and acid, respectively, and a Ca2+ in the active center neutralizes the negative charge of the C5 carboxyl group of the substrate. Finally, based on our data, we propose a metal ion-assisted catalytic mechanism of AlyGC for alginate cleavage with a state change mode, which provides a better understanding for polysaccharide lyases and alginate degradation.
+
-
 
+
-
Novel Molecular Insights into the Catalytic Mechanism of Marine Bacterial Alginate Lyase AlyGC from Polysaccharide Lyase Family 6.,Xu F, Dong F, Wang P, Cao HY, Li CY, Li PY, Pang XH, Zhang YZ, Chen XL J Biol Chem. 2017 Mar 17;292(11):4457-4468. doi: 10.1074/jbc.M116.766030. Epub, 2017 Feb 1. PMID:28154171<ref>PMID:28154171</ref>
+
-
 
+
-
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
+
-
</div>
+
-
<div class="pdbe-citations 5gkd" style="background-color:#fffaf0;"></div>
+
-
== References ==
+
-
<references/>
+
__TOC__
__TOC__
</StructureSection>
</StructureSection>
-
[[Category: Wang, P]]
+
[[Category: Large Structures]]
-
[[Category: Xu, F]]
+
[[Category: Paraglaciecola chathamensis]]
-
[[Category: Zhang, Y Z]]
+
[[Category: Wang P]]
-
[[Category: Alginate lyase]]
+
[[Category: Xu F]]
-
[[Category: Lyase]]
+
[[Category: Zhang YZ]]
-
[[Category: Pl6]]
+

Current revision

Structure of PL6 family alginate lyase AlyGC

PDB ID 5gkd

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/5gkd"
Personal tools