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| | ==Catalytic domain of beta-agarase from Microbulbifer thermotolerans JAMB-A94== | | ==Catalytic domain of beta-agarase from Microbulbifer thermotolerans JAMB-A94== |
| - | <StructureSection load='3wz1' size='340' side='right' caption='[[3wz1]], [[Resolution|resolution]] 1.60Å' scene=''> | + | <StructureSection load='3wz1' size='340' side='right'caption='[[3wz1]], [[Resolution|resolution]] 1.60Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[3wz1]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Dsm_19189 Dsm 19189]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3WZ1 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3WZ1 FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[3wz1]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Microbulbifer_thermotolerans Microbulbifer thermotolerans]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3WZ1 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3WZ1 FirstGlance]. <br> |
| - | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</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]] 1.6Å</td></tr> |
| - | <tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">agaA ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=252514 DSM 19189])</td></tr> | + | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene></td></tr> |
| - | <tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Beta-agarase Beta-agarase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.2.1.81 3.2.1.81] </span></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=3wz1 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3wz1 OCA], [https://pdbe.org/3wz1 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3wz1 RCSB], [https://www.ebi.ac.uk/pdbsum/3wz1 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3wz1 ProSAT]</span></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=3wz1 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3wz1 OCA], [http://pdbe.org/3wz1 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3wz1 RCSB], [http://www.ebi.ac.uk/pdbsum/3wz1 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=3wz1 ProSAT]</span></td></tr> | + | |
| | </table> | | </table> |
| | + | == Function == |
| | + | [https://www.uniprot.org/uniprot/Q6F4N4_9GAMM Q6F4N4_9GAMM] |
| | <div style="background-color:#fffaf0;"> | | <div style="background-color:#fffaf0;"> |
| | == Publication Abstract from PubMed == | | == Publication Abstract from PubMed == |
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| | __TOC__ | | __TOC__ |
| | </StructureSection> | | </StructureSection> |
| - | [[Category: Beta-agarase]] | + | [[Category: Large Structures]] |
| - | [[Category: Dsm 19189]] | + | [[Category: Microbulbifer thermotolerans]] |
| - | [[Category: Akita, M]] | + | [[Category: Akita M]] |
| - | [[Category: Hatada, Y]] | + | [[Category: Hatada Y]] |
| - | [[Category: Miyazaki, T]] | + | [[Category: Miyazaki T]] |
| - | [[Category: Nishikawa, A]] | + | [[Category: Nishikawa A]] |
| - | [[Category: Ohta, Y]] | + | [[Category: Ohta Y]] |
| - | [[Category: Takagi, E]] | + | [[Category: Takagi E]] |
| - | [[Category: Tonozuka, T]] | + | [[Category: Tonozuka T]] |
| - | [[Category: Yokoi, G]] | + | [[Category: Yokoi G]] |
| - | [[Category: Agarose]]
| + | |
| - | [[Category: Beta-jelly roll fold]]
| + | |
| - | [[Category: Glycoside hydrolase family 16]]
| + | |
| - | [[Category: Hydrolase]]
| + | |
| Structural highlights
Function
Q6F4N4_9GAMM
Publication Abstract from PubMed
A deep-sea bacterium, Microbulbifer thermotolerans JAMB-A94, has a beta-agarase (MtAgaA) belonging to the glycoside hydrolase family (GH) 16. The optimal temperature of this bacterium for growth is 43-49 degrees C, and MtAgaA is stable at 60 degrees C, which is one of the most thermostable enzymes among GH16 beta-agarases. Here, we determined the catalytic domain structure of MtAgaA. MtAgaA consists of a beta-jelly roll fold, as observed in other GH16 enzymes. The structure of MtAgaA was most similar to two beta-agarases from Zobellia galactanivorans, ZgAgaA, and ZgAgaB. Although the catalytic cleft structure of MtAgaA was similar to ZgAgaA and ZgAgaB, residues at subsite -4 of MtAgaA were not conserved between them. Also, an alpha-helix, designated as alpha4', was uniquely located near the catalytic cleft of MtAgaA. A comparison of the structures of the three enzymes suggested that multiple factors, including increased numbers of arginine and proline residues, could contribute to the thermostability of MtAgaA.
Crystal structure of the catalytic domain of a GH16 beta-agarase from a deep-sea bacterium, Microbulbifer thermotolerans JAMB-A94.,Takagi E, Hatada Y, Akita M, Ohta Y, Yokoi G, Miyazaki T, Nishikawa A, Tonozuka T Biosci Biotechnol Biochem. 2015 Apr;79(4):625-32. doi:, 10.1080/09168451.2014.988680. Epub 2014 Dec 6. PMID:25483365[1]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
References
- ↑ Takagi E, Hatada Y, Akita M, Ohta Y, Yokoi G, Miyazaki T, Nishikawa A, Tonozuka T. Crystal structure of the catalytic domain of a GH16 beta-agarase from a deep-sea bacterium, Microbulbifer thermotolerans JAMB-A94. Biosci Biotechnol Biochem. 2015 Apr;79(4):625-32. doi:, 10.1080/09168451.2014.988680. Epub 2014 Dec 6. PMID:25483365 doi:http://dx.doi.org/10.1080/09168451.2014.988680
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