3u1r

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Current revision (10:16, 1 March 2024) (edit) (undo)
 
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<StructureSection load='3u1r' size='340' side='right'caption='[[3u1r]], [[Resolution|resolution]] 2.00&Aring;' scene=''>
<StructureSection load='3u1r' size='340' side='right'caption='[[3u1r]], [[Resolution|resolution]] 2.00&Aring;' scene=''>
== Structural highlights ==
== Structural highlights ==
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<table><tr><td colspan='2'>[[3u1r]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Flavobacterium_sp. Flavobacterium sp.]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3U1R OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3U1R FirstGlance]. <br>
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<table><tr><td colspan='2'>[[3u1r]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Flavobacterium_sp._YS-80-122 Flavobacterium sp. YS-80-122]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3U1R OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3U1R FirstGlance]. <br>
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</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=ZN:ZINC+ION'>ZN</scene></td></tr>
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</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&#8491;</td></tr>
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<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=ZN:ZINC+ION'>ZN</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=3u1r FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3u1r OCA], [https://pdbe.org/3u1r PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3u1r RCSB], [https://www.ebi.ac.uk/pdbsum/3u1r PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3u1r ProSAT]</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=3u1r FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3u1r OCA], [https://pdbe.org/3u1r PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3u1r RCSB], [https://www.ebi.ac.uk/pdbsum/3u1r PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3u1r ProSAT]</span></td></tr>
</table>
</table>
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<div style="background-color:#fffaf0;">
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== Function ==
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== Publication Abstract from PubMed ==
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[https://www.uniprot.org/uniprot/D0VMS8_9FLAO D0VMS8_9FLAO]
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A new psychrophilic marine protease was found from a marine bacterium Flavobacterium YS-80 in the Chinese Yellow Sea. The protease is about 49 kD with an isoelectric point about 4.5. It consists of 480 amino acids and is homologous to a psychrophilic alkaline protease (PAP) from an Antarctic Pseudomonas species. The protein was purified from the natural bacterium fermented and crystallized. Its crystal structure (PDB ID 3U1R) was solved at 2.0 A by Molecular Replacement using a model based on PAP, and was refined to a crystallographic R(work) of 0.16 and an R(free) of 0.21. The marine protease consists of a two domain structure with an N-terminal domain including residues 37-264 and a C-terminal domain including residues 265-480. Similar to PAP, the N-terminal domain is responsible for proteolysis and the C-terminal is for stability. His186, His190, His196 and Tyr226 are ligands for the Zn(2+) ion in the catalytic center. The enzyme's Tyr226 is closer to the Zn(2+) ion than in PAP and it shows a stronger Zn(2+)-Tyr-OH bond. There are eight calcium ions in the marine protease molecule and they have significantly shorter bond distances to their ligands compared to their counterparts in all three crystal forms of PAP. On the other hand, the loops in the marine protease are more compact than in PAP. This makes the total structure stable and less flexible, resulting in higher thermo stability. These properties are consistent with the respective environments of the proteases. The structural analysis of this new marine protease provides new information for the study of psychrophilic proteases and is helpful for elucidating the structure-environment adaptation of these enzymes.
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Structure analysis of a new psychrophilic marine protease.,Zhang SC, Sun M, Li T, Wang QH, Hao JH, Han Y, Hu XJ, Zhou M, Lin SX PLoS One. 2011;6(11):e26939. Epub 2011 Nov 23. PMID:22132082<ref>PMID:22132082</ref>
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From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
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</div>
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<div class="pdbe-citations 3u1r" style="background-color:#fffaf0;"></div>
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== References ==
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<references/>
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__TOC__
__TOC__
</StructureSection>
</StructureSection>
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[[Category: Flavobacterium sp]]
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[[Category: Flavobacterium sp. YS-80-122]]
[[Category: Large Structures]]
[[Category: Large Structures]]
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[[Category: Han, Y]]
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[[Category: Han Y]]
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[[Category: Hao, J H]]
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[[Category: Hao J-H]]
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[[Category: Hu, X J]]
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[[Category: Hu X-J]]
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[[Category: Lin, S X]]
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[[Category: Lin S-X]]
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[[Category: Sun, M]]
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[[Category: Sun M]]
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[[Category: Tang, L]]
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[[Category: Tang L]]
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[[Category: Wang, Q H]]
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[[Category: Wang Q-H]]
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[[Category: Zhang, S C]]
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[[Category: Zhang S-C]]
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[[Category: Zhou, M]]
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[[Category: Zhou M]]
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[[Category: Beta jelly roll]]
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[[Category: Hydrolase]]
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Current revision

Structure Analysis of A New Psychrophilic Marine Protease

PDB ID 3u1r

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