2rkb

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{{Seed}}
 
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[[Image:2rkb.png|left|200px]]
 
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==Serine dehydratase like-1 from human cancer cells==
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The line below this paragraph, containing "STRUCTURE_2rkb", creates the "Structure Box" on the page.
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<StructureSection load='2rkb' size='340' side='right'caption='[[2rkb]], [[Resolution|resolution]] 2.80&Aring;' scene=''>
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You may change the PDB parameter (which sets the PDB file loaded into the applet)
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== Structural highlights ==
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or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
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<table><tr><td colspan='2'>[[2rkb]] is a 5 chain structure with sequence from [https://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2RKB OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2RKB FirstGlance]. <br>
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or leave the SCENE parameter empty for the default display.
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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=K:POTASSIUM+ION'>K</scene>, <scene name='pdbligand=PLP:PYRIDOXAL-5-PHOSPHATE'>PLP</scene></td></tr>
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{{STRUCTURE_2rkb| PDB=2rkb | SCENE= }}
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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=2rkb FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2rkb OCA], [https://pdbe.org/2rkb PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2rkb RCSB], [https://www.ebi.ac.uk/pdbsum/2rkb PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2rkb ProSAT]</span></td></tr>
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</table>
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== Function ==
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[https://www.uniprot.org/uniprot/SDSL_HUMAN SDSL_HUMAN] Has low serine dehydratase and threonine dehydratase activity.
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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/rk/2rkb_consurf.spt"</scriptWhenChecked>
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<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview03.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=2rkb ConSurf].
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<div style="clear:both"></div>
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<div style="background-color:#fffaf0;">
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== Publication Abstract from PubMed ==
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SDH (l-serine dehydratase, EC 4.3.1.17) is a pyridoxal-5'-phosphate (PLP)-dependent enzyme that catalyzes dehydration of l-Ser/Thr to yield pyruvate/ketobutyrate and ammonia. A SDH isoform (cSDH) found in human cancer cell lines has relatively low catalytic activity in comparison with the liver enzyme (hSDH). The crystal structure of cSDH has been determined at 2.8 angstroms resolution. A PLP is covalently attached to K48 by Schiff-base linkage in the active site. The ring nitrogen of PLP is involved in a H-bonding with C309, but is apparently not protonated. Twenty-three amino residues that compose the active site surfaces were identified. The human and rat liver enzymes (hSDH and rSDH) have the same residues, while residues G72, A172, and S228 in cSDH are replaced with A66, S166, and A222, respectively, in hSDH. These residues in hSDH and cSDH were mutated to make complementary pairs of mutated enzymes, and their kinetic parameters were determined. C303 of hSDH and C309 of cSDH which are H-bonding partner of the ring nitrogen of PLP were mutated to alanine and their kinetic parameters were also determined. The crystal structures and the mutation data suggest that having a glycine at residue 72 of cSDH is the major reason for the reduction of catalytic activity of cSDH. Changing alanine to glycine at residue 72 increases the flexibility of the substrate binding-loop (71S(G/A)GN74), so that the bound substrate and PLP are not pushed deep into the active cleft. Consequently, the proton transfer rate from S(G) of C309 to N1 of the bound PLP is decreased, which determines the rate of catalytic reaction.
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===Serine dehydratase like-1 from human cancer cells===
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A catalytic mechanism that explains a low catalytic activity of serine dehydratase like-1 from human cancer cells: crystal structure and site-directed mutagenesis studies.,Yamada T, Komoto J, Kasuya T, Takata Y, Ogawa H, Mori H, Takusagawa F Biochim Biophys Acta. 2008 May;1780(5):809-18. Epub 2008 Feb 19. PMID:18342636<ref>PMID:18342636</ref>
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From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
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</div>
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<div class="pdbe-citations 2rkb" style="background-color:#fffaf0;"></div>
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==See Also==
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The line below this paragraph, {{ABSTRACT_PUBMED_18342636}}, adds the Publication Abstract to the page
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*[[Deaminase 3D structures|Deaminase 3D structures]]
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(as it appears on PubMed at http://www.pubmed.gov), where 18342636 is the PubMed ID number.
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== References ==
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<references/>
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{{ABSTRACT_PUBMED_18342636}}
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__TOC__
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</StructureSection>
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==About this Structure==
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2RKB is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2RKB OCA].
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==Reference==
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A catalytic mechanism that explains a low catalytic activity of serine dehydratase like-1 from human cancer cells: Crystal structure and site-directed mutagenesis studies., Yamada T, Komoto J, Kasuya T, Takata Y, Ogawa H, Mori H, Takusagawa F, Biochim Biophys Acta. 2008 Feb 19;. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/18342636 18342636]
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[[Category: Homo sapiens]]
[[Category: Homo sapiens]]
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[[Category: Single protein]]
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[[Category: Large Structures]]
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[[Category: Kasuya, T.]]
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[[Category: Kasuya T]]
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[[Category: Komoto, J.]]
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[[Category: Komoto J]]
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[[Category: Mori, H.]]
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[[Category: Mori H]]
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[[Category: Ogawa, H.]]
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[[Category: Ogawa H]]
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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: Enzyme found in human cancer cell]]
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[[Category: Lyase]]
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[[Category: Plp bound enzyme]]
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[[Category: Pyridoxal phosphate]]
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[[Category: Serine dehydratase]]
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''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Mon Jul 28 03:00:06 2008''
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Current revision

Serine dehydratase like-1 from human cancer cells

PDB ID 2rkb

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