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1r8g

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[[Image:1r8g.jpg|left|200px]]
 
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{{Structure
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==Structure and function of YbdK==
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|PDB= 1r8g |SIZE=350|CAPTION= <scene name='initialview01'>1r8g</scene>, resolution 2.15&Aring;
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<StructureSection load='1r8g' size='340' side='right'caption='[[1r8g]], [[Resolution|resolution]] 2.15&Aring;' scene=''>
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|SITE=
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== Structural highlights ==
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|LIGAND=
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<table><tr><td colspan='2'>[[1r8g]] 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=1R8G OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1R8G 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]] 2.15&#8491;</td></tr>
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|GENE= YBDK, B0581 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=562 Escherichia coli])
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<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene></td></tr>
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}}
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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=1r8g FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1r8g OCA], [https://pdbe.org/1r8g PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1r8g RCSB], [https://www.ebi.ac.uk/pdbsum/1r8g PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1r8g ProSAT]</span></td></tr>
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</table>
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'''Structure and function of YbdK'''
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== Function ==
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[https://www.uniprot.org/uniprot/GCS2_ECOLI GCS2_ECOLI] ATP-dependent carboxylate-amine ligase which exhibits weak glutamate--cysteine ligase activity. However, because of the low catalytic rate, the question remains whether L-cysteine is the actual biological substrate.[HAMAP-Rule:MF_01609]<ref>PMID:15211520</ref>
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== Evolutionary Conservation ==
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==Overview==
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[[Image:Consurf_key_small.gif|200px|right]]
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The Escherichia coli open reading frame YbdK encodes a member of a large bacterial protein family of unknown biological function. The sequences within this family are remotely related to the sequence of gamma-glutamate-cysteine ligase (gamma-GCS), an enzyme in the glutathione biosynthetic pathway. A gene encoding gamma-GCS in E. coli is already known. The 2.15 A resolution crystal structure of YbdK reveals an overall fold similar to that of glutamine synthetase (GS), a nitrogen metabolism enzyme that ligates glutamate and ammonia to yield glutamine. GS and gamma-GCS perform related chemical reactions and require ATP and Mg2+ for their activity. The Mg2+-dependent binding of ATP to YbdK was confirmed by fluorescence spectroscopy employing 2'(or 3')-O-(trinitrophenyl)adenosine 5'-triphosphate, and yielding a dissociation constant of 3 +/- 0.5 microM. The structure of YbdK contains a crevice that corresponds to the binding sites of ATP, Mg2+ and glutamate in GS. Many of the GS residues that coordinate the metal ions and interact with glutamic acid and the phosphoryl and ribosyl groups of ATP are also present in YbdK. GS amino acids that have been associated with ammonia binding have no obvious counterparts in YbdK, consistent with a substrate specificity that is different from that of GS. Ligase activity between glutamic acid and each of the twenty amino acid residues was tested on high performance liquid chromatography (HPLC) by following the hydrolysis of ATP to ADP. Catalysis was observed only with cysteine. A pyruvate kinase/lactic acid dehydrogenase coupled assay was used to rule out GS activity and to determine that YbdK exhibits gamma-GCS activity. The catalytic rate was found to be approximately 500-fold slower than that reported for authentic gamma-GCS.
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Check<jmol>
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<jmolCheckbox>
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==About this Structure==
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<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/r8/1r8g_consurf.spt"</scriptWhenChecked>
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1R8G 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=1R8G OCA].
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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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==Reference==
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</jmolCheckbox>
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YbdK is a carboxylate-amine ligase with a gamma-glutamyl:Cysteine ligase activity: crystal structure and enzymatic assays., Lehmann C, Doseeva V, Pullalarevu S, Krajewski W, Howard A, Herzberg O, Proteins. 2004 Aug 1;56(2):376-83. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/15211520 15211520]
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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=1r8g ConSurf].
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<div style="clear:both"></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: Doseeva, V.]]
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[[Category: Doseeva V]]
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[[Category: Herzberg, O.]]
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[[Category: Herzberg O]]
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[[Category: Howard, A.]]
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[[Category: Howard A]]
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[[Category: Krajewski, W.]]
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[[Category: Krajewski W]]
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[[Category: Lehmann, C.]]
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[[Category: Lehmann C]]
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[[Category: Pullalarevu, S.]]
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[[Category: Pullalarevu S]]
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[[Category: S2F, Structure 2.Function Project.]]
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[[Category: carboxylate-amine ligase]]
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[[Category: hypothetical protein]]
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[[Category: s2f]]
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[[Category: structural genomic]]
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[[Category: structure 2 function project]]
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[[Category: unknown function]]
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[[Category: ybdk]]
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''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Mar 20 13:48:16 2008''
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Current revision

Structure and function of YbdK

PDB ID 1r8g

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