1u08

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(New page: 200px<br /><applet load="1u08" size="450" color="white" frame="true" align="right" spinBox="true" caption="1u08, resolution 2.35&Aring;" /> '''Crystal Structure an...)
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[[Image:1u08.gif|left|200px]]<br /><applet load="1u08" size="450" color="white" frame="true" align="right" spinBox="true"
 
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caption="1u08, resolution 2.35&Aring;" />
 
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'''Crystal Structure and Reactivity of YbdL from Escherichia coli Identify a Methionine Aminotransferase Function.'''<br />
 
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==Overview==
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==Crystal Structure and Reactivity of YbdL from Escherichia coli Identify a Methionine Aminotransferase Function.==
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The ybdL gene of Escherichia coli codes for a protein of unknown function., Sequence analysis showed moderate homology to several vitamin B(6), dependent enzymes, suggesting that it may bind pyridoxal-5'-phosphate. The, structure analysis of YbdL to 2.35 A resolution by protein crystallography, verifies that it is a PLP dependent enzyme of fold type I, the typical, aspartate aminotransferase fold. The active site contains a bound, pyridoxal-5'-phosphate, covalently attached to the conserved active site, lysine residue Lys236. The pattern of conserved amino acids in the, putative substrate binding pocket of the enzyme reveals that it is most, closely related to a hyperthermophilic aromatic residue aminotransferase, from the archeon Pyrococcus horikoshii. Activity tests with 10 amino acids, as amino-donors reveal, however, a preference for Met, followed by His and, Phe, results which can be rationalized by modelization studies.
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<StructureSection load='1u08' size='340' side='right'caption='[[1u08]], [[Resolution|resolution]] 2.35&Aring;' scene=''>
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== Structural highlights ==
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<table><tr><td colspan='2'>[[1u08]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1U08 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1U08 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]] 2.35&#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=PLP:PYRIDOXAL-5-PHOSPHATE'>PLP</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=1u08 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1u08 OCA], [https://pdbe.org/1u08 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1u08 RCSB], [https://www.ebi.ac.uk/pdbsum/1u08 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1u08 ProSAT]</span></td></tr>
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</table>
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== Function ==
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[https://www.uniprot.org/uniprot/YBDL_ECOLI YBDL_ECOLI] Shows aminotransferase activity with methionine and histidine as substrates, and to a lesser extent also with phenylalanine.
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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/u0/1u08_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=1u08 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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The ybdL gene of Escherichia coli codes for a protein of unknown function. Sequence analysis showed moderate homology to several vitamin B(6) dependent enzymes, suggesting that it may bind pyridoxal-5'-phosphate. The structure analysis of YbdL to 2.35 A resolution by protein crystallography verifies that it is a PLP dependent enzyme of fold type I, the typical aspartate aminotransferase fold. The active site contains a bound pyridoxal-5'-phosphate, covalently attached to the conserved active site lysine residue Lys236. The pattern of conserved amino acids in the putative substrate binding pocket of the enzyme reveals that it is most closely related to a hyperthermophilic aromatic residue aminotransferase from the archeon Pyrococcus horikoshii. Activity tests with 10 amino acids as amino-donors reveal, however, a preference for Met, followed by His and Phe, results which can be rationalized by modelization studies.
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==About this Structure==
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Crystal structure and reactivity of YbdL from Escherichia coli identify a methionine aminotransferase function.,Dolzan M, Johansson K, Roig-Zamboni V, Campanacci V, Tegoni M, Schneider G, Cambillau C FEBS Lett. 2004 Jul 30;571(1-3):141-6. PMID:15280032<ref>PMID:15280032</ref>
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1U08 is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli] with PLP as [http://en.wikipedia.org/wiki/ligand ligand]. Full crystallographic information is available from [http://ispc.weizmann.ac.il/oca-bin/ocashort?id=1U08 OCA].
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==Reference==
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From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
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Crystal structure and reactivity of YbdL from Escherichia coli identify a methionine aminotransferase function., Dolzan M, Johansson K, Roig-Zamboni V, Campanacci V, Tegoni M, Schneider G, Cambillau C, FEBS Lett. 2004 Jul 30;571(1-3):141-6. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=15280032 15280032]
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</div>
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<div class="pdbe-citations 1u08" style="background-color:#fffaf0;"></div>
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== References ==
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<references/>
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__TOC__
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</StructureSection>
[[Category: Escherichia coli]]
[[Category: Escherichia coli]]
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[[Category: Single protein]]
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[[Category: Large Structures]]
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[[Category: Cambillau, C.]]
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[[Category: Cambillau C]]
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[[Category: Campanacci, V.]]
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[[Category: Campanacci V]]
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[[Category: Dolzan, M.]]
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[[Category: Dolzan M]]
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[[Category: Johansson, K.]]
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[[Category: Johansson K]]
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[[Category: Roig-Zamboni, V.]]
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[[Category: Roig-Zamboni V]]
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[[Category: Schneider, G.]]
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[[Category: Schneider G]]
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[[Category: Tegoni, M.]]
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[[Category: Tegoni M]]
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[[Category: PLP]]
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[[Category: alpha beta protein]]
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''Page seeded by [http://ispc.weizmann.ac.il/oca OCA ] on Wed Nov 21 03:44:29 2007''
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Current revision

Crystal Structure and Reactivity of YbdL from Escherichia coli Identify a Methionine Aminotransferase Function.

PDB ID 1u08

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