1d4f: Difference between revisions

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-[[Image:1d4f.gif|left|200px]]
- {{Structure
+==CRYSTAL STRUCTURE OF RECOMBINANT RAT-LIVER D244E MUTANT S-ADENOSYLHOMOCYSTEINE HYDROLASE==
-|PDB= 1d4f |SIZE=350|CAPTION= <scene name='initialview01'>1d4f</scene>, resolution 2.8&Aring;
+<StructureSection load='1d4f' size='340' side='right'caption='[[1d4f]], [[Resolution|resolution]] 2.80&Aring;' scene=''>
-|SITE=
+== Structural highlights ==
-|LIGAND= <scene name='pdbligand=NAD:NICOTINAMIDE-ADENINE-DINUCLEOTIDE'>NAD</scene> and <scene name='pdbligand=ADN:ADENOSINE'>ADN</scene>
+<table><tr><td colspan='2'>[[1d4f]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Rattus_norvegicus Rattus norvegicus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1D4F OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1D4F FirstGlance]. <br>
-|ACTIVITY= [http://en.wikipedia.org/wiki/Adenosylhomocysteinase Adenosylhomocysteinase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.3.1.1 3.3.1.1]
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.8&#8491;</td></tr>
-|GENE=
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ADN:ADENOSINE'>ADN</scene>, <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'>[https://proteopedia.org/fgij/fg.htm?mol=1d4f FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1d4f OCA], [https://pdbe.org/1d4f PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1d4f RCSB], [https://www.ebi.ac.uk/pdbsum/1d4f PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1d4f ProSAT]</span></td></tr>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/SAHH_RAT SAHH_RAT] Adenosylhomocysteine is a competitive inhibitor of S-adenosyl-L-methionine-dependent methyl transferase reactions; therefore adenosylhomocysteinase may play a key role in the control of methylations via regulation of the intracellular concentration of adenosylhomocysteine.
+== Evolutionary Conservation ==
+[[Image:Consurf_key_small.gif|200px|right]]
+Check<jmol>
+  <jmolCheckbox>
+    <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/d4/1d4f_consurf.spt"</scriptWhenChecked>
+    <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
+    <text>to colour the structure by Evolutionary Conservation</text>
+  </jmolCheckbox>
+</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=1d4f ConSurf].
+<div style="clear:both"></div>
-'''CRYSTAL STRUCTURE OF RECOMBINANT RAT-LIVER D244E MUTANT S-ADENOSYLHOMOCYSTEINE HYDROLASE'''
+==See Also==
+*[[S-adenosylhomocysteine hydrolase|S-adenosylhomocysteine hydrolase]]
+__TOC__
-==Overview==
+</StructureSection>
-A site-directed mutagenesis, D244E, of S-adenosylhomocysteine hydrolase (AdoHcyase) changes drastically the nature of the protein, especially the NAD(+) binding affinity. The mutant enzyme contained NADH rather than NAD(+) (Gomi, T., Takata, Y., Date, T., Fujioka, M., Aksamit, R. R., Backlund, P. S., and Cantoni, G. L. (1990) J. Biol. Chem. 265, 16102-16107). In contrast to the site-directed mutagenesis study, the crystal structures of human and rat AdoHcyase recently determined have shown that the carboxyl group of Asp-244 points in a direction opposite to the bound NAD molecule and does not participate in any hydrogen bonds with the NAD molecule. To explain the discrepancy between the mutagenesis study and the x-ray studies, we have determined the crystal structure of the recombinant rat-liver D244E mutant enzyme to 2.8-A resolution. The D244E mutation changes the enzyme structure from the open to the closed conformation by means of a approximately 17 degrees rotation of the individual catalytic domains around the molecular hinge sections. The D244E mutation shifts the catalytic reaction from a reversible to an irreversible fashion. The large affinity difference between NAD(+) and NADH is mainly due to the enzyme conformation, but not to the binding-site geometry; an NAD(+) in the open conformation is readily released from the enzyme, whereas an NADH in the closed conformation is trapped and cannot leave the enzyme. A catalytic mechanism of AdoHcyase has been proposed on the basis of the crystal structures of the wild-type and D244E enzymes.
+[[Category: Large Structures]]
-==About this Structure==
-D4F is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Rattus_norvegicus Rattus norvegicus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1D4F OCA].
-==Reference==
-Effects of site-directed mutagenesis on structure and function of recombinant rat liver S-adenosylhomocysteine hydrolase. Crystal structure of D244E mutant enzyme., Komoto J, Huang Y, Gomi T, Ogawa H, Takata Y, Fujioka M, Takusagawa F, J Biol Chem. 2000 Oct 13;275(41):32147-56. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/10913437 10913437]
-[[Category: Adenosylhomocysteinase]]
 [[Category: Rattus norvegicus]]
-[[Category: Single protein]]
+[[Category: Fujioka M]]
-[[Category: Fujioka, M.]]
+[[Category: Gomi T]]
-[[Category: Gomi, T.]]
+[[Category: Huang Y]]
-[[Category: Huang, Y.]]
+[[Category: Komoto J]]
-[[Category: Komoto, J.]]
+[[Category: Ogawa H]]
-[[Category: Ogawa, H.]]
+[[Category: Takata Y]]
-[[Category: Takata, Y.]]
+[[Category: Takusagawa F]]
-[[Category: Takusagawa, F.]]
-[[Category: ADN]]
-[[Category: NAD]]
-[[Category: adohcy]]
-[[Category: adohcyase]]
-[[Category: enzyme structure]]
-[[Category: mutagenesis]]
-[[Category: s-adenosylhomocysteine hydrolase]]
-[[Category: x-ray crystal structure]]
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Mar 20 10:32:42 2008''