2dd4: Difference between revisions

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<StructureSection load='2dd4' size='340' side='right'caption='[[2dd4]], [[Resolution|resolution]] 2.06&Aring;' scene=''>
<StructureSection load='2dd4' size='340' side='right'caption='[[2dd4]], [[Resolution|resolution]] 2.06&Aring;' scene=''>
== Structural highlights ==
== Structural highlights ==
<table><tr><td colspan='2'>[[2dd4]] is a 12 chain structure with sequence from [https://en.wikipedia.org/wiki/"bacterium_thiocyanoxidans"_happold_and_key_1937 "bacterium thiocyanoxidans" happold and key 1937]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2DD4 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2DD4 FirstGlance]. <br>
<table><tr><td colspan='2'>[[2dd4]] is a 12 chain structure with sequence from [https://en.wikipedia.org/wiki/Thiobacillus_thioparus Thiobacillus thioparus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2DD4 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2DD4 FirstGlance]. <br>
</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=FRU:FRUCTOSE'>FRU</scene>, <scene name='pdbligand=TLA:L(+)-TARTARIC+ACID'>TLA</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]] 2.06&#8491;</td></tr>
<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[2dd5|2dd5]]</div></td></tr>
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=FRU:FRUCTOSE'>FRU</scene>, <scene name='pdbligand=TLA:L(+)-TARTARIC+ACID'>TLA</scene></td></tr>
<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/Thiocyanate_hydrolase Thiocyanate hydrolase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.5.5.8 3.5.5.8] </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=2dd4 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2dd4 OCA], [https://pdbe.org/2dd4 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2dd4 RCSB], [https://www.ebi.ac.uk/pdbsum/2dd4 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2dd4 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=2dd4 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2dd4 OCA], [https://pdbe.org/2dd4 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2dd4 RCSB], [https://www.ebi.ac.uk/pdbsum/2dd4 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2dd4 ProSAT]</span></td></tr>
</table>
</table>
== Function ==
== Function ==
[[https://www.uniprot.org/uniprot/SCNA_THITI SCNA_THITI]] Involved in the degradation of thiocyanate. [[https://www.uniprot.org/uniprot/SCNC_THITI SCNC_THITI]] Involved in the degradation of thiocyanate. [[https://www.uniprot.org/uniprot/SCNB_THITI SCNB_THITI]] Involved in the degradation of thiocyanate.  
[https://www.uniprot.org/uniprot/SCNA_THITI SCNA_THITI] Involved in the degradation of thiocyanate.
== Evolutionary Conservation ==
== Evolutionary Conservation ==
[[Image:Consurf_key_small.gif|200px|right]]
[[Image:Consurf_key_small.gif|200px|right]]
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</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=2dd4 ConSurf].
</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=2dd4 ConSurf].
<div style="clear:both"></div>
<div style="clear:both"></div>
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
Thiocyanate hydrolase (SCNase) of Thiobacillus thioparus THI115 is a cobalt(III)-containing enzyme catalyzing the degradation of thiocyanate to carbonyl sulfide and ammonia. We determined the crystal structures of the apo- and native SCNases at a resolution of 2.0 A. SCNases in both forms had a conserved hetero-dodecameric structure, (alphabetagamma)(4). Four alphabetagamma hetero-trimers were structurally equivalent. One alphabetagamma hetero-trimer was composed of the core domain and the betaN domain, which was located at the center of the molecule and linked the hetero-trimers with novel quaternary interfaces. In both the apo- and native SCNases, the core domain was structurally conserved between those of iron and cobalt-types of nitrile hydratase (NHase). Native SCNase possessed the post-translationally modified cysteine ligands, gammaCys131-SO(2)H and gammaCys133-SOH like NHases. However, the low-spin cobalt(III) was found to be in the distorted square-pyramidal geometry, which had not been reported before in any protein. The size as well as the electrostatic properties of the substrate-binding pocket was totally different from NHases with respect to the charge distribution and the substrate accessibility, which rationally explains the differences in the substrate preference between SCNase and NHase.
Structure of thiocyanate hydrolase: a new nitrile hydratase family protein with a novel five-coordinate cobalt(III) center.,Arakawa T, Kawano Y, Kataoka S, Katayama Y, Kamiya N, Yohda M, Odaka M J Mol Biol. 2007 Mar 9;366(5):1497-509. Epub 2006 Dec 8. PMID:17222425<ref>PMID:17222425</ref>
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
</div>
<div class="pdbe-citations 2dd4" style="background-color:#fffaf0;"></div>
== References ==
<references/>
__TOC__
__TOC__
</StructureSection>
</StructureSection>
[[Category: Bacterium thiocyanoxidans happold and key 1937]]
[[Category: Large Structures]]
[[Category: Large Structures]]
[[Category: Thiocyanate hydrolase]]
[[Category: Thiobacillus thioparus]]
[[Category: Arakawa, T]]
[[Category: Arakawa T]]
[[Category: Kamiya, N]]
[[Category: Kamiya N]]
[[Category: Kataoka, S]]
[[Category: Kataoka S]]
[[Category: Katayama, Y]]
[[Category: Katayama Y]]
[[Category: Kawano, Y]]
[[Category: Kawano Y]]
[[Category: Odaka, M]]
[[Category: Odaka M]]
[[Category: Yohda, M]]
[[Category: Yohda M]]
[[Category: Carbonyl sulfide]]
[[Category: Claw setting]]
[[Category: Cobalt]]
[[Category: Complex]]
[[Category: Enzyme]]
[[Category: Hydrolase]]
[[Category: Metalloprotein]]
[[Category: Model complex]]
[[Category: Nitrile hydratase]]
[[Category: Non-corrin]]
[[Category: Protein]]
[[Category: Sulfenic acid]]
[[Category: Sulfinic acid]]
[[Category: Thiocyanate]]

Latest revision as of 16:47, 13 March 2024

Thiocyanate hydrolase (SCNase) from Thiobacillus thioparus recombinant apo-enzymeThiocyanate hydrolase (SCNase) from Thiobacillus thioparus recombinant apo-enzyme

Structural highlights

2dd4 is a 12 chain structure with sequence from Thiobacillus thioparus. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:X-ray diffraction, Resolution 2.06Å
Ligands:,
Resources:FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

SCNA_THITI Involved in the degradation of thiocyanate.

Evolutionary Conservation

Check, as determined by ConSurfDB. You may read the explanation of the method and the full data available from ConSurf.

2dd4, resolution 2.06Å

Drag the structure with the mouse to rotate

Proteopedia Page Contributors and Editors (what is this?)Proteopedia Page Contributors and Editors (what is this?)

OCA
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