4zz7: Difference between revisions

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<StructureSection load='4zz7' size='340' side='right'caption='[[4zz7]], [[Resolution|resolution]] 2.90&Aring;' scene=''>
<StructureSection load='4zz7' size='340' side='right'caption='[[4zz7]], [[Resolution|resolution]] 2.90&Aring;' scene=''>
== Structural highlights ==
== Structural highlights ==
<table><tr><td colspan='2'>[[4zz7]] is a 12 chain structure with sequence from [http://en.wikipedia.org/wiki/Atcc_27123 Atcc 27123]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4ZZ7 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4ZZ7 FirstGlance]. <br>
<table><tr><td colspan='2'>[[4zz7]] is a 12 chain structure with sequence from [https://en.wikipedia.org/wiki/Oceanimonas_doudoroffii Oceanimonas doudoroffii]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4ZZ7 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4ZZ7 FirstGlance]. <br>
</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=NAD:NICOTINAMIDE-ADENINE-DINUCLEOTIDE'>NAD</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]] 2.9&#8491;</td></tr>
<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">dddC ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=84158 ATCC 27123])</td></tr>
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=NAD:NICOTINAMIDE-ADENINE-DINUCLEOTIDE'>NAD</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=4zz7 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4zz7 OCA], [http://pdbe.org/4zz7 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4zz7 RCSB], [http://www.ebi.ac.uk/pdbsum/4zz7 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4zz7 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=4zz7 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4zz7 OCA], [https://pdbe.org/4zz7 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4zz7 RCSB], [https://www.ebi.ac.uk/pdbsum/4zz7 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4zz7 ProSAT]</span></td></tr>
</table>
</table>
<div style="background-color:#fffaf0;">
== Function ==
== Publication Abstract from PubMed ==
[https://www.uniprot.org/uniprot/G5CZI2_9GAMM G5CZI2_9GAMM]
The gene product of dddC (Uniprot code G5CZI2), from the Gram-negative marine bacterium Oceanimonas doudoroffii, is a methylmalonate-semialdehyde dehydrogenase (OdoMMSDH) enzyme. MMSDH is a member of the aldehyde dehydrogenase superfamily, and it catalyzes the NADdependent decarboxylation of methylmalonate semialdehyde to propionyl-CoA. We determined the crystal structure of OdoMMSDH at 2.9 A resolution. Among the twelve molecules in the asymmetric unit, six subunits complexed with NAD, which was carried along the protein purification steps. OdoMMSDH exists as a stable homodimer in solution; each subunit consists of three distinct domains: an NAD-binding domain, a catalytic domain, and an oligomerization domain. Computational modeling studies of the OdoMMSDH structure revealed key residues important for substrate recognition and tetrahedral intermediate stabilization. Two basic residues (Arg103 and Arg279) and six hydrophobic residues (Phe150, Met153, Val154, Trp157, Met281, and Phe449) were found to be important for tetrahedral intermediate binding. Modeling data also suggested that the backbone amide of Cys280 and the side chain amine of Asn149 function as the oxyanion hole during the enzymatic reaction. Our results provide useful insights into the substrate recognition site residues and catalytic mechanism of OdoMMSDH.
 
Crystal structure and modeling of the tetrahedral intermediate state of methylmalonate-semialdehyde dehydrogenase (MMSDH) from Oceanimonas doudoroffii.,Do H, Lee CW, Lee SG, Kang H, Park CM, Kim HJ, Park H, Park H, Lee JH J Microbiol. 2016 Feb;54(2):114-21. doi: 10.1007/s12275-016-5549-2. Epub 2016 Feb, 2. PMID:26832667<ref>PMID:26832667</ref>
 
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
</div>
<div class="pdbe-citations 4zz7" style="background-color:#fffaf0;"></div>
== References ==
<references/>
__TOC__
__TOC__
</StructureSection>
</StructureSection>
[[Category: Atcc 27123]]
[[Category: Large Structures]]
[[Category: Large Structures]]
[[Category: Do, H]]
[[Category: Oceanimonas doudoroffii]]
[[Category: Kang, H]]
[[Category: Do H]]
[[Category: Kim, H J]]
[[Category: Kang H]]
[[Category: Lee, C W]]
[[Category: Kim HJ]]
[[Category: Lee, J H]]
[[Category: Lee CW]]
[[Category: Lee, S G]]
[[Category: Lee JH]]
[[Category: Park, C M]]
[[Category: Lee SG]]
[[Category: Park, H]]
[[Category: Park CM]]
[[Category: Dddc]]
[[Category: Park H]]
[[Category: Oxidoreductase]]

Latest revision as of 12:05, 20 March 2024

Crystal structure of methylmalonate-semialdehyde dehydrogenase (DddC) from Oceanimonas doudoroffiiCrystal structure of methylmalonate-semialdehyde dehydrogenase (DddC) from Oceanimonas doudoroffii

Structural highlights

4zz7 is a 12 chain structure with sequence from Oceanimonas doudoroffii. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:X-ray diffraction, Resolution 2.9Å
Ligands:
Resources:FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

G5CZI2_9GAMM

4zz7, resolution 2.90Å

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