|
|
| Line 3: |
Line 3: |
| <StructureSection load='1wzi' size='340' side='right'caption='[[1wzi]], [[Resolution|resolution]] 2.00Å' scene=''> | | <StructureSection load='1wzi' size='340' side='right'caption='[[1wzi]], [[Resolution|resolution]] 2.00Å' scene=''> |
| == Structural highlights == | | == Structural highlights == |
| <table><tr><td colspan='2'>[[1wzi]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/"flavobacterium_thermophilum"_yoshida_and_oshima_1971 "flavobacterium thermophilum" yoshida and oshima 1971]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1WZI OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1WZI FirstGlance]. <br> | | <table><tr><td colspan='2'>[[1wzi]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Thermus_thermophilus Thermus thermophilus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1WZI OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1WZI FirstGlance]. <br> |
| </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=NDP:NADPH+DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE+PHOSPHATE'>NDP</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]] 2Å</td></tr> |
| <tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[1bmd|1bmd]], [[1y7t|1y7t]], [[1wze|1wze]]</div></td></tr>
| | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=NDP:NADPH+DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE+PHOSPHATE'>NDP</scene></td></tr> |
| <tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">mdh ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=274 "Flavobacterium thermophilum" Yoshida and Oshima 1971])</td></tr> | |
| <tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/Malate_dehydrogenase Malate dehydrogenase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.1.1.37 1.1.1.37] </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=1wzi FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1wzi OCA], [https://pdbe.org/1wzi PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1wzi RCSB], [https://www.ebi.ac.uk/pdbsum/1wzi PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1wzi 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=1wzi FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1wzi OCA], [https://pdbe.org/1wzi PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1wzi RCSB], [https://www.ebi.ac.uk/pdbsum/1wzi PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1wzi ProSAT]</span></td></tr> |
| </table> | | </table> |
| == Function == | | == Function == |
| [[https://www.uniprot.org/uniprot/MDH_THETH MDH_THETH]] Catalyzes the reversible oxidation of malate to oxaloacetate.
| | [https://www.uniprot.org/uniprot/MDH_THETH MDH_THETH] Catalyzes the reversible oxidation of malate to oxaloacetate. |
| == Evolutionary Conservation == | | == Evolutionary Conservation == |
| [[Image:Consurf_key_small.gif|200px|right]] | | [[Image:Consurf_key_small.gif|200px|right]] |
| Line 22: |
Line 20: |
| </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=1wzi 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=1wzi ConSurf]. |
| <div style="clear:both"></div> | | <div style="clear:both"></div> |
| <div style="background-color:#fffaf0;">
| |
| == Publication Abstract from PubMed ==
| |
| A binary complex of malate dehydrogenase from the thermophilic bacterium Thermus flavus (tMDH) with NADH has been crystallized from poly(ethylene glycol) 3500, pH 8.5, yielding diffraction-quality crystals in space group P2(1)2(1)2(1). The structure was solved at 1.9-A resolution using molecular replacement and refined to an R factor of 15.8% with good geometry. The primary sequence of tMDH is 55% identical to that of cytoplasmic malate dehydrogenase (cMDH) [Birktoft, J. J., Rhodes, G., & Banaszak, L. J. (1989) Biochemistry 28, 6065-6081], and overall their three-dimensional structures are very similar. Like cMDH, tMDH crystallized as a dimer with one coenzyme bound per subunit. The coenzyme binds in the extended conformation, and most of the interactions with enzyme are similar to those in cMDH. In tMDH, small local conformational changes are caused by the replacement of a glutamic acid for the aspartic acid involved in hydrogen bonding to the adenine ribose of NADH. Comparison of tMDH with cMDH reveals that both tMDH subunits more closely resemble the B subunit of cMDH which therefore is the more likely representative of the solution conformation. While cMDH is inactivated at temperatures above about 50 degrees C, tMDH is fully active at 90 degrees C. On the basis of the X-ray crystal structure, a number of factors have been identified which are likely to contribute to the relative thermostability of tMDH compared to cMDH. The most striking of the differences involves the introduction of four ion pairs per monomer. All of these ion pairs are solvent-accessible. Three of these ion pairs are located in the dimer interface, Glu27-Lys31, Glu57-Lys168, and Glu57-Arg229, and one ion pair, Glu275-Arg149, is at the domain interface within each subunit. Additionally, we observe incorporation of additional alanines into alpha-helices of tMDH and, in one instance, incorporation of an aspartate that functions as a counterchange to an alpha-helix dipole. The possible contributions of these and other factors to protein thermostability in tMDH are discussed.
| |
|
| |
| Determinants of protein thermostability observed in the 1.9-A crystal structure of malate dehydrogenase from the thermophilic bacterium Thermus flavus.,Kelly CA, Nishiyama M, Ohnishi Y, Beppu T, Birktoft JJ Biochemistry. 1993 Apr 20;32(15):3913-22. PMID:8471603<ref>PMID:8471603</ref>
| |
|
| |
| From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
| |
| </div>
| |
| <div class="pdbe-citations 1wzi" style="background-color:#fffaf0;"></div>
| |
|
| |
|
| ==See Also== | | ==See Also== |
| *[[Malate Dehydrogenase 3D structures|Malate Dehydrogenase 3D structures]] | | *[[Malate Dehydrogenase 3D structures|Malate Dehydrogenase 3D structures]] |
| == References ==
| |
| <references/>
| |
| __TOC__ | | __TOC__ |
| </StructureSection> | | </StructureSection> |
| [[Category: Flavobacterium thermophilum yoshida and oshima 1971]]
| |
| [[Category: Large Structures]] | | [[Category: Large Structures]] |
| [[Category: Malate dehydrogenase]] | | [[Category: Thermus thermophilus]] |
| [[Category: Fushinobu, S]] | | [[Category: Fushinobu S]] |
| [[Category: Kuzuyama, T]] | | [[Category: Kuzuyama T]] |
| [[Category: Nishiyama, M]] | | [[Category: Nishiyama M]] |
| [[Category: Tomita, T]] | | [[Category: Tomita T]] |
| [[Category: Oxidoreductase]]
| |
| [[Category: Protein-nadph complex]]
| |
| [[Category: Seven amino acid residues mutant]]
| |