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1ky4

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(New page: 200px<br /><applet load="1ky4" size="450" color="white" frame="true" align="right" spinBox="true" caption="1ky4, resolution 2.8&Aring;" /> '''S-Adenosylhomocystein...)
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[[Image:1ky4.gif|left|200px]]<br /><applet load="1ky4" size="450" color="white" frame="true" align="right" spinBox="true"
 
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caption="1ky4, resolution 2.8&Aring;" />
 
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'''S-Adenosylhomocysteine hydrolase refined with noncrystallographic restraints'''<br />
 
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==Overview==
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==S-Adenosylhomocysteine hydrolase refined with noncrystallographic restraints==
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S-Adenosylhomocysteine hydrolase (AdoHcyase) catalyzes the hydrolysis of, S-adenosylhomocysteine to form adenosine and homocysteine. On the bases of, crystal structures of the wild type enzyme and the D244E mutated enzyme, complexed with 3'-keto-adenosine (D244E.Ado*), we have identified the, important amino acid residues, Asp-130, Lys-185, Asp-189, and Asn-190, for, the catalytic reaction and have proposed a catalytic mechanism (Komoto, J., Huang, Y., Gomi, T., Ogawa, H., Takata, Y., Fujioka, M., and, Takusagawa, F. (2000) J. Biol. Chem. 275, 32147-32156). To confirm the, proposed catalytic mechanism, we have made the D130N, K185N, D189N, and, N190S mutated enzymes and measured the catalytic activities. The catalytic, rates (k(cat)) of D130N, K185N, D189N, and N190S mutated enzymes are, reduced to 0.7%, 0.5%, 0.1%, and 0.5%, respectively, in comparison with, the wild type enzyme, indicating that Asp-130, Lys-185, Asp-189, and, Asn-190 are involved in the catalytic reaction. K(m) values of the mutated, enzymes are increased significantly, except for the N190S mutation, suggesting that Asp-130, Lys-185, and Asp-189 participate in the substrate, binding. To interpret the kinetic data, the oxidation states of the bound, NAD molecules of the wild type and mutated enzymes were measured during, the catalytic reaction by monitoring the absorbance at 340 nm. The crystal, structures of the WT and D244E.Ado*, containing four subunits in the, crystallographic asymmetric unit, were re-refined to have the same subunit, structures. A detailed catalytic mechanism of AdoHcyase has been revealed, based on the oxidation states of the bound NAD and the re-refined crystal, structures of WT and D244E.Ado*. Lys-185 and Asp-130 abstract hydrogen, atoms from 3'-OH and 4'-CH, respectively. Asp-189 removes a proton from, Lys-185 and produces the neutral N zeta (-NH(2)), and Asn-190 facilitates, formation of the neutral Lys-185. His-54 and His-300 hold and polarize a, water molecule, which nucleophilically attacks the C5'- of, 3'-keto-4',5'-dehydroadenosine to produce 3'-keto-Ado.
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<StructureSection load='1ky4' size='340' side='right'caption='[[1ky4]], [[Resolution|resolution]] 2.80&Aring;' scene=''>
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== Structural highlights ==
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<table><tr><td colspan='2'>[[1ky4]] 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=1KY4 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1KY4 FirstGlance]. <br>
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</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>
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<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>
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<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1ky4 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1ky4 OCA], [https://pdbe.org/1ky4 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1ky4 RCSB], [https://www.ebi.ac.uk/pdbsum/1ky4 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1ky4 ProSAT]</span></td></tr>
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</table>
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== Function ==
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[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.
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== Evolutionary Conservation ==
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[[Image:Consurf_key_small.gif|200px|right]]
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Check<jmol>
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<jmolCheckbox>
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<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/ky/1ky4_consurf.spt"</scriptWhenChecked>
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<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
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<text>to colour the structure by Evolutionary Conservation</text>
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</jmolCheckbox>
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</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=1ky4 ConSurf].
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<div style="clear:both"></div>
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==About this Structure==
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==See Also==
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1KY4 is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Rattus_norvegicus Rattus norvegicus] with NAD as [http://en.wikipedia.org/wiki/ligand ligand]. Active as [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] Full crystallographic information is available from [http://ispc.weizmann.ac.il/oca-bin/ocashort?id=1KY4 OCA].
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*[[S-adenosylhomocysteine hydrolase|S-adenosylhomocysteine hydrolase]]
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__TOC__
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==Reference==
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</StructureSection>
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Catalytic mechanism of S-adenosylhomocysteine hydrolase. Site-directed mutagenesis of Asp-130, Lys-185, Asp-189, and Asn-190., Takata Y, Yamada T, Huang Y, Komoto J, Gomi T, Ogawa H, Fujioka M, Takusagawa F, J Biol Chem. 2002 Jun 21;277(25):22670-6. Epub 2002 Apr 1. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=11927587 11927587]
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[[Category: Large Structures]]
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[[Category: Adenosylhomocysteinase]]
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[[Category: Rattus norvegicus]]
[[Category: Rattus norvegicus]]
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[[Category: Single protein]]
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[[Category: Takata Y]]
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[[Category: Takata, Y.]]
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[[Category: Takusagawa F]]
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[[Category: Takusagawa, F.]]
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[[Category: NAD]]
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[[Category: hydrolase]]
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[[Category: s-adenosylhomocysteine]]
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''Page seeded by [http://ispc.weizmann.ac.il/oca OCA ] on Tue Nov 20 20:03:42 2007''
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Current revision

S-Adenosylhomocysteine hydrolase refined with noncrystallographic restraints

PDB ID 1ky4

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