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6dka

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Yeast Ddi2 Cyanamide Hydratase

Structural highlights

6dka is a 9 chain structure with sequence from Saccharomyces cerevisiae YJM789. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	X-ray diffraction, Resolution 2.901Å
Ligands:	, ,
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

A7A1Y4_YEAS7

Publication Abstract from PubMed

Cyanamide (H2N-CN) is used to break bud dormancy in woody plants and to deter alcohol use in humans. The biological effects of cyanamide in both these cases require the enzyme catalase. We previously demonstrated that Saccharomyces cerevisiae exposed to cyanamide resulted in strong induction of DDI2 gene expression. Ddi2 enzymatically hydrates cyanamide to urea and belongs to the family of HD-domain metalloenzymes (named after conserved active-site metal-binding His and Asp residues). Here, we report the X-ray structure of yeast Ddi2 to 2.6 A resolution, revealing that Ddi2 is a dimeric zinc metalloenzyme. We also confirm that Ddi2 shares structural similarity with other known HD-domain proteins. HD residues His-55, His-88, and Asp-89 coordinate the active-site zinc, and the fourth zinc ligand is a water/hydroxide molecule. Other HD domain enzymes have a second aspartate metal ligand, but in Ddi2 this residue (Thr-157) does not interact with the zinc ion. Several Ddi2 active-site point mutations exhibited reduced catalytic activity. We kinetically and structurally characterized H137N and T157V mutants of Ddi2. A cyanamide soak of the Ddi2-T157V enzyme revealed cyanamide bound directly to the Zn(2+) ion, having displaced the zinc-bound water molecule. The mode of cyanamide binding to Ddi2 resembles cyanamide binding to the active-site zinc of carbonic anhydrase, a known cyanamide hydratase. Finally, we observed that the sensitivity of ddi2Delta ddi3Delta to cyanamide was not rescued by plasmids harboring ddi2-H137N or ddi2-TI57V variants, demonstrating that yeast cells require a functioning cyanamide hydratase to overcome cyanamide-induced growth defects.

Structure of Ddi2, a highly inducible detoxifying metalloenzyme from Saccharomyces cerevisiae.,Li J, Jia Y, Lin A, Hanna M, Chelico L, Xiao W, Moore SA J Biol Chem. 2019 Jul 5;294(27):10674-10685. doi: 10.1074/jbc.RA118.006394. Epub , 2019 May 31. PMID:31152065^[1]

From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.

References

↑ Li J, Jia Y, Lin A, Hanna M, Chelico L, Xiao W, Moore SA. Structure of Ddi2, a highly inducible detoxifying metalloenzyme from Saccharomyces cerevisiae. J Biol Chem. 2019 Jul 5;294(27):10674-10685. doi: 10.1074/jbc.RA118.006394. Epub , 2019 May 31. PMID:31152065 doi:http://dx.doi.org/10.1074/jbc.RA118.006394

1 Structural highlights
2 Function
3 Publication Abstract from PubMed
4 References

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/6dka"

Categories: Large Structures | Saccharomyces cerevisiae YJM789 | Li J | Moore SA | Xiao W

@@ Line 3: / Line 3: @@
 <StructureSection load='6dka' size='340' side='right'caption='[[6dka]], [[Resolution|resolution]] 2.90&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[6dka]] is a 9 chain structure with sequence from [http://en.wikipedia.org/wiki/Baker's_yeast Baker's yeast]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6DKA OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6DKA FirstGlance]. <br>
+<table><tr><td colspan='2'>[[6dka]] is a 9 chain structure with sequence from [https://en.wikipedia.org/wiki/Saccharomyces_cerevisiae_YJM789 Saccharomyces cerevisiae YJM789]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6DKA OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6DKA FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CNN:CYANAMIDE'>CNN</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</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]] 2.901&#8491;</td></tr>
-<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">SCY_1694 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=307796 Baker's yeast])</td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CNN:CYANAMIDE'>CNN</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</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'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6dka FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6dka OCA], [http://pdbe.org/6dka PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6dka RCSB], [http://www.ebi.ac.uk/pdbsum/6dka PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6dka 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=6dka FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6dka OCA], [https://pdbe.org/6dka PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6dka RCSB], [https://www.ebi.ac.uk/pdbsum/6dka PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6dka ProSAT]</span></td></tr>
 </table>
+== Function ==
+[https://www.uniprot.org/uniprot/A7A1Y4_YEAS7 A7A1Y4_YEAS7]
 <div style="background-color:#fffaf0;">
 == Publication Abstract from PubMed ==
@@ Line 21: / Line 23: @@
 __TOC__
 </StructureSection>
-[[Category: Baker's yeast]]
 [[Category: Large Structures]]
-[[Category: Li, J]]
+[[Category: Saccharomyces cerevisiae YJM789]]
-[[Category: Moore, S A]]
+[[Category: Li J]]
-[[Category: Xiao, W]]
+[[Category: Moore SA]]
-[[Category: Cyanamide]]
+[[Category: Xiao W]]
-[[Category: Hd-domain]]
-[[Category: Hydratase]]
-[[Category: Lyase]]
-[[Category: Metal binding protein]]
-[[Category: Zn-metalloprotein]]

6dka

From Proteopedia

Current revision

Yeast Ddi2 Cyanamide Hydratase

Structural highlights

Function

Publication Abstract from PubMed

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

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