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1pwe

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(New page: 200px<br /><applet load="1pwe" size="450" color="white" frame="true" align="right" spinBox="true" caption="1pwe, resolution 2.80&Aring;" /> '''Rat Liver L-Serine D...)
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[[Image:1pwe.gif|left|200px]]<br /><applet load="1pwe" size="450" color="white" frame="true" align="right" spinBox="true"
 
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caption="1pwe, resolution 2.80&Aring;" />
 
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'''Rat Liver L-Serine Dehydratase Apo Enzyme'''<br />
 
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==Overview==
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==Rat Liver L-Serine Dehydratase Apo Enzyme==
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SDH (L-serine dehydratase, EC 4.3.1.17) catalyzes the pyridoxal, 5'-phosphate (PLP)-dependent dehydration of L-serine to yield pyruvate and, ammonia. Liver SDH plays an important role in gluconeogenesis. Formation, of pyruvate by SDH is a two-step reaction in which the hydroxyl group of, serine is cleaved to produce aminoacrylate, and then the aminoacrylate is, deaminated by nonenzymatic hydrolysis to produce pyruvate. The crystal, structure of rat liver apo-SDH was determined by single isomorphous, replacement at 2.8 A resolution. The holo-SDH crystallized with, O-methylserine (OMS) was also determined at 2.6 A resolution by molecular, replacement. SDH is composed of two domains, and each domain has a typical, alphabeta-open structure. The active site is located in the cleft between, the two domains. The holo-SDH contained PLP-OMS aldimine in the active, site, indicating that OMS can form the Schiff base linkage with PLP, but, the subsequent dehydration did not occur. Apo-SDH forms a dimer by, inserting the small domain into the catalytic cleft of the partner subunit, so that the active site is closed. Holo-SDH also forms a dimer by making, contacts at the back of the clefts so that the dimerization does not close, the catalytic cleft. The phosphate group of PLP is surrounded by a, characteristic G-rich sequence ((168)GGGGL(172)) and forms hydrogen bonds, with the amide groups of those amino acid residues, suggesting that the, phosphate group can be protonated. N(1) of PLP participates in a hydrogen, bond with Cys303, and similar hydrogen bonds with N(1) participating are, seen in other beta-elimination enzymes. These hydrogen bonding schemes, indicate that N(1) is not protonated, and thus, the pyridine ring cannot, take a quinone-like structure. These characteristics of the bound PLP, suggest that SDH catalysis is not facilitated by forming the, resonance-stabilized structure of the PLP-Ser aldimine as seen in, aminotransferases. A possible catalytic mechanism involves the phosphate, group, surrounded by the characteristic sequence, acting as a general acid, to donate a proton to the leaving hydroxyl group of serine.
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<StructureSection load='1pwe' size='340' side='right'caption='[[1pwe]], [[Resolution|resolution]] 2.80&Aring;' scene=''>
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== Structural highlights ==
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<table><tr><td colspan='2'>[[1pwe]] is a 6 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=1PWE OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1PWE 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='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1pwe FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1pwe OCA], [https://pdbe.org/1pwe PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1pwe RCSB], [https://www.ebi.ac.uk/pdbsum/1pwe PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1pwe ProSAT]</span></td></tr>
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</table>
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== Function ==
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[https://www.uniprot.org/uniprot/SDHL_RAT SDHL_RAT]
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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/pw/1pwe_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=1pwe 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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1PWE is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Rattus_norvegicus Rattus norvegicus]. Active as [http://en.wikipedia.org/wiki/L-serine_ammonia-lyase L-serine ammonia-lyase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=4.3.1.17 4.3.1.17] Full crystallographic information is available from [http://ispc.weizmann.ac.il/oca-bin/ocashort?id=1PWE OCA].
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*[[Deaminase 3D structures|Deaminase 3D structures]]
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__TOC__
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==Reference==
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</StructureSection>
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Crystal structure of serine dehydratase from rat liver., Yamada T, Komoto J, Takata Y, Ogawa H, Pitot HC, Takusagawa F, Biochemistry. 2003 Nov 11;42(44):12854-65. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=14596599 14596599]
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[[Category: Large Structures]]
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[[Category: L-serine ammonia-lyase]]
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[[Category: Rattus norvegicus]]
[[Category: Rattus norvegicus]]
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[[Category: Single protein]]
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[[Category: Komoto J]]
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[[Category: Komoto, J.]]
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[[Category: Ogawa H]]
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[[Category: Ogawa, H.]]
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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: Yamada T]]
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[[Category: Yamada, T.]]
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[[Category: apo enzyme]]
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[[Category: l-serine dehydratase]]
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[[Category: rat liver]]
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''Page seeded by [http://ispc.weizmann.ac.il/oca OCA ] on Wed Nov 21 00:10:56 2007''
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Current revision

Rat Liver L-Serine Dehydratase Apo Enzyme

PDB ID 1pwe

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