2rkb

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(New page: 200px {{Structure |PDB= 2rkb |SIZE=350|CAPTION= <scene name='initialview01'>2rkb</scene>, resolution 2.80&Aring; |SITE= <scene name='pdbsite=AC1:K+Binding+Site+Fo...)
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[[Image:2rkb.jpg|left|200px]]
 
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{{Structure
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==Serine dehydratase like-1 from human cancer cells==
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|PDB= 2rkb |SIZE=350|CAPTION= <scene name='initialview01'>2rkb</scene>, resolution 2.80&Aring;
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<StructureSection load='2rkb' size='340' side='right'caption='[[2rkb]], [[Resolution|resolution]] 2.80&Aring;' scene=''>
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|SITE= <scene name='pdbsite=AC1:K+Binding+Site+For+Residue+A+401'>AC1</scene>, <scene name='pdbsite=AC2:K+Binding+Site+For+Residue+B+401'>AC2</scene>, <scene name='pdbsite=AC3:K+Binding+Site+For+Residue+C+401'>AC3</scene>, <scene name='pdbsite=AC4:K+Binding+Site+For+Residue+D+401'>AC4</scene>, <scene name='pdbsite=AC5:K+Binding+Site+For+Residue+E+401'>AC5</scene>, <scene name='pdbsite=AC6:Plp+Binding+Site+For+Residue+A+400'>AC6</scene>, <scene name='pdbsite=AC7:Plp+Binding+Site+For+Residue+B+400'>AC7</scene>, <scene name='pdbsite=AC8:Plp+Binding+Site+For+Residue+C+400'>AC8</scene>, <scene name='pdbsite=AC9:Plp+Binding+Site+For+Residue+D+400'>AC9</scene> and <scene name='pdbsite=BC1:Plp+Binding+Site+For+Residue+E+400'>BC1</scene>
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== Structural highlights ==
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|LIGAND= <scene name='pdbligand=K:POTASSIUM+ION'>K</scene>, <scene name='pdbligand=PLP:PYRIDOXAL-5&#39;-PHOSPHATE'>PLP</scene>
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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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|ACTIVITY=
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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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|GENE=
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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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|DOMAIN=<span class='plainlinks'>[http://www.ncbi.nlm.nih.gov/Structure/cdd/cddsrv.cgi?uid=COG1171 IlvA]</span>
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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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|RELATEDENTRY=
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</table>
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|RESOURCES=<span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2rkb FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2rkb OCA], [http://www.ebi.ac.uk/pdbsum/2rkb PDBsum], [http://www.rcsb.org/pdb/explore.do?structureId=2rkb RCSB]</span>
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== Function ==
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}}
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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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==Overview==
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==See Also==
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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 A 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 ((71)S(G/A)GN(74)), 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 N(1) of the bound PLP is decreased, which determines the rate of catalytic reaction.
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*[[Deaminase 3D structures|Deaminase 3D structures]]
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== References ==
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==About this Structure==
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<references/>
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2RKB is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2RKB OCA].
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__TOC__
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</StructureSection>
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==Reference==
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[[Category: Homo sapiens]]
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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: Large Structures]]
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[[Category: Escherichia coli]]
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[[Category: Kasuya T]]
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[[Category: Single protein]]
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[[Category: Komoto J]]
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[[Category: Kasuya, T.]]
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[[Category: Mori H]]
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[[Category: Komoto, J.]]
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[[Category: Ogawa H]]
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[[Category: Mori, H.]]
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[[Category: Takusagawa F]]
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[[Category: Ogawa, H.]]
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[[Category: Yamada T]]
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[[Category: Takusagawa, F.]]
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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 Wed Apr 2 11:58:30 2008''
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Current revision

Serine dehydratase like-1 from human cancer cells

PDB ID 2rkb

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