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| | ==Crystal structure of monotopic membrane protein (S)-mandelate dehydrogenase== | | ==Crystal structure of monotopic membrane protein (S)-mandelate dehydrogenase== |
| - | <StructureSection load='6bfg' size='340' side='right' caption='[[6bfg]], [[Resolution|resolution]] 2.20Å' scene=''> | + | <StructureSection load='6bfg' size='340' side='right'caption='[[6bfg]], [[Resolution|resolution]] 2.20Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[6bfg]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/"bacillus_fluorescens_putidus"_flugge_1886 "bacillus fluorescens putidus" flugge 1886]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6BFG OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6BFG FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[6bfg]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Pseudomonas_putida Pseudomonas putida]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6BFG OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6BFG FirstGlance]. <br> |
| - | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CIT:CITRIC+ACID'>CIT</scene>, <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=FMN:FLAVIN+MONONUCLEOTIDE'>FMN</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=LMT:DODECYL-BETA-D-MALTOSIDE'>LMT</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=PEG:DI(HYDROXYETHYL)ETHER'>PEG</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</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]] 2.2Å</td></tr> |
| - | <tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">mdlB ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=303 "Bacillus fluorescens putidus" Flugge 1886])</td></tr>
| + | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CIT:CITRIC+ACID'>CIT</scene>, <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=FMN:FLAVIN+MONONUCLEOTIDE'>FMN</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=LMT:DODECYL-BETA-D-MALTOSIDE'>LMT</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=PEG:DI(HYDROXYETHYL)ETHER'>PEG</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr> |
| - | <tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/(S)-mandelate_dehydrogenase (S)-mandelate dehydrogenase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.1.99.31 1.1.99.31] </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=6bfg FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6bfg OCA], [https://pdbe.org/6bfg PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6bfg RCSB], [https://www.ebi.ac.uk/pdbsum/6bfg PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6bfg 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=6bfg FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6bfg OCA], [http://pdbe.org/6bfg PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6bfg RCSB], [http://www.ebi.ac.uk/pdbsum/6bfg PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6bfg ProSAT]</span></td></tr> | + | |
| | </table> | | </table> |
| | == Function == | | == Function == |
| - | [[http://www.uniprot.org/uniprot/MDLB_PSEPU MDLB_PSEPU]] Reduction of (S)-mandelate to benzoylformate. | + | [https://www.uniprot.org/uniprot/MDLB_PSEPU MDLB_PSEPU] Reduction of (S)-mandelate to benzoylformate. |
| | <div style="background-color:#fffaf0;"> | | <div style="background-color:#fffaf0;"> |
| | == Publication Abstract from PubMed == | | == Publication Abstract from PubMed == |
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| | </div> | | </div> |
| | <div class="pdbe-citations 6bfg" style="background-color:#fffaf0;"></div> | | <div class="pdbe-citations 6bfg" style="background-color:#fffaf0;"></div> |
| | + | |
| | + | ==See Also== |
| | + | *[[Mandelate dehydrogenase|Mandelate dehydrogenase]] |
| | == References == | | == References == |
| | <references/> | | <references/> |
| | __TOC__ | | __TOC__ |
| | </StructureSection> | | </StructureSection> |
| - | [[Category: Bacillus fluorescens putidus flugge 1886]] | + | [[Category: Large Structures]] |
| - | [[Category: Sukumar, N]] | + | [[Category: Pseudomonas putida]] |
| - | [[Category: Alpha-hydroxy acid enzyme]] | + | [[Category: Sukumar N]] |
| - | [[Category: Flavoprotein]]
| + | |
| - | [[Category: Membrane protein]]
| + | |
| - | [[Category: Oxidoreductase]]
| + | |
| - | [[Category: Tim barrel]]
| + | |
| Structural highlights
6bfg is a 2 chain structure with sequence from Pseudomonas putida. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
| | Method: | X-ray diffraction, Resolution 2.2Å |
| Ligands: | , , , , , , , , |
| Resources: | FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT |
Function
MDLB_PSEPU Reduction of (S)-mandelate to benzoylformate.
Publication Abstract from PubMed
The x-ray structure of the monotopic membrane protein (S)-mandelate dehydrogenase (MDH) from Pseudomonas putida reveals an inherent flexibility of its membrane binding segment that might be important for its biological activity. The surface of MDH exhibits a concentration of the positive charges on one side and the negative charges on the other side. The putative membrane binding surface of MDH has a concentric circular ridge, formed by positively charged residues, which projects away from the protein surface by approximately 4A; this is unique structural feature and not observed in other monotopic membrane proteins to our knowledge. There are three alpha-helixes in the membrane binding region. Based on the structure of MDH, it is possible to propose that the interaction of MDH with the membrane is stabilized by coplanar electrostatic interactions, between the positively charged concentric circular ridge and the negatively charged head-groups of the phospholipid bilayer, along with three alpha-helixes that provide additional stability by inserting into the membrane. The structure reveals the possible orientation of these helixes along with possible role for the individual residues which form those helixes. These alpha-helixes may play a role in the enzyme's mobility. The detergent, N-Dodecyl-beta-maltoside, is inserted between the membrane binding region and rest of the molecule and may provide structural stability to intra-protein regions by forming hydrogen bonds and close contacts. From the average B-factor of the MDH structure, it is likely that MDH is highly mobile, which might be essential for its intersection in membrane and non-membrane environments, as its substrate (S)-mandelate, is from the cytoplasm, while its electron acceptor is a component of the membrane electron transport chain.
Structure of the monotopic membrane protein (S)-mandelate dehydrogenase at 2.2A resolution.,Sukumar N, Liu S, Li W, Mathews FS, Mitra B, Kandavelu P Biochimie. 2018 Jul 30. pii: S0300-9084(18)30212-8. doi:, 10.1016/j.biochi.2018.07.017. PMID:30071260[1]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
See Also
References
- ↑ Sukumar N, Liu S, Li W, Mathews FS, Mitra B, Kandavelu P. Structure of the monotopic membrane protein (S)-mandelate dehydrogenase at 2.2A resolution. Biochimie. 2018 Jul 30. pii: S0300-9084(18)30212-8. doi:, 10.1016/j.biochi.2018.07.017. PMID:30071260 doi:http://dx.doi.org/10.1016/j.biochi.2018.07.017
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