1xdq: Difference between revisions

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-[[Image:1xdq.gif|left|200px]]<br /><applet load="1xdq" size="450" color="white" frame="true" align="right" spinBox="true"
-caption="1xdq, resolution 2.55&Aring;" />
-'''Structural and Biochemical Identification of a Novel Bacterial Oxidoreductase'''<br />
-==Overview==
+==Structural and Biochemical Identification of a Novel Bacterial Oxidoreductase==
-By using a bioinformatics screen of the Escherichia coli genome for, potential molybdenum-containing enzymes, we have identified a novel, oxidoreductase conserved in the majority of Gram-negative bacteria. The, identified operon encodes for a proposed heterodimer, YedYZ in Escherichia, coli, consisting of a soluble catalytic subunit termed YedY, which is, likely anchored to the membrane by a heme-containing trans-membrane, subunit termed YedZ. YedY is uniquely characterized by the presence of one, molybdenum molybdopterin not conjugated by an additional nucleotide, and, it represents the only molybdoenzyme isolated from E. coli characterized, by the presence of this cofactor form. We have further characterized the, catalytic subunit YedY in both the molybdenum- and tungsten-substituted, forms by using crystallographic analysis. YedY is very distinct in overall, architecture from all known bacterial reductases but does show some, similarity with the catalytic domain of the eukaryotic chicken liver, sulfite oxidase. However, the strictly conserved residues involved in the, metal coordination sphere and in the substrate binding pocket of YedY are, strikingly different from that of chicken liver sulfite oxidase, suggesting a catalytic activity more in keeping with a reductase than that, of a sulfite oxidase. Preliminary kinetic analysis of YedY with a variety, of substrates supports our proposal that YedY and its many orthologues may, represent a new type of membrane-associated bacterial reductase.
+<StructureSection load='1xdq' size='340' side='right'caption='[[1xdq]], [[Resolution|resolution]] 2.55&Aring;' scene=''>
+== Structural highlights ==
+<table><tr><td colspan='2'>[[1xdq]] is a 5 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=1XDQ OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1XDQ FirstGlance]. <br>
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.55&#8491;</td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=MO:MOLYBDENUM+ATOM'>MO</scene>, <scene name='pdbligand=MTE:PHOSPHONIC+ACIDMONO-(2-AMINO-5,6-DIMERCAPTO-4-OXO-3,7,8A,9,10,10A-HEXAHYDRO-4H-8-OXA-1,3,9,10-TETRAAZA-ANTHRACEN-7-YLMETHYL)ESTER'>MTE</scene>, <scene name='pdbligand=O:OXYGEN+ATOM'>O</scene>, <scene name='pdbligand=URE:UREA'>URE</scene></td></tr>
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1xdq FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1xdq OCA], [https://pdbe.org/1xdq PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1xdq RCSB], [https://www.ebi.ac.uk/pdbsum/1xdq PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1xdq ProSAT]</span></td></tr>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/MSRP_ECOLI MSRP_ECOLI] Part of the MsrPQ system that repairs oxidized periplasmic proteins containing methionine sulfoxide residues (Met-O), using respiratory chain electrons (PubMed:26641313). Thus protects these proteins from oxidative-stress damage caused by reactive species of oxygen and chlorine (PubMed:26641313). MsrPQ is essential for the maintenance of envelope integrity under bleach stress, rescuing a wide series of structurally unrelated periplasmic proteins from methionine oxidation, including the primary periplasmic chaperone SurA and the lipoprotein Pal (PubMed:26641313). The catalytic subunit MsrP is non-stereospecific, being able to reduce both (R-) and (S-) diastereoisomers of methionine sulfoxide (PubMed:26641313). Can catalyze the reduction of a variety of substrates in vitro, including dimethyl sulfoxide, trimethylamine N-oxide, phenylmethyl sulfoxide and L-methionine sulfoxide (PubMed:15355966). Cannot reduce cyclic N-oxides (PubMed:15355966). Shows no activity as sulfite oxidase (PubMed:15355966).<ref>PMID:15355966</ref> <ref>PMID:26641313</ref>
+== Evolutionary Conservation ==
+[[Image:Consurf_key_small.gif|200px|right]]
+Check<jmol>
+  <jmolCheckbox>
+    <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/xd/1xdq_consurf.spt"</scriptWhenChecked>
+    <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
+    <text>to colour the structure by Evolutionary Conservation</text>
+  </jmolCheckbox>
+</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=1xdq ConSurf].
+<div style="clear:both"></div>
-==About this Structure==
+==See Also==
-XDQ 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 URE, MO, O and MTE as [http://en.wikipedia.org/wiki/ligands ligands]. Full crystallographic information is available from [http://ispc.weizmann.ac.il/oca-bin/ocashort?id=1XDQ OCA].
+*[[Sulfite Oxidase|Sulfite Oxidase]]
+== References ==
-==Reference==
+<references/>
-Structural and biochemical identification of a novel bacterial oxidoreductase., Loschi L, Brokx SJ, Hills TL, Zhang G, Bertero MG, Lovering AL, Weiner JH, Strynadka NC, J Biol Chem. 2004 Nov 26;279(48):50391-400. Epub 2004 Sep 7. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=15355966 15355966]
+__TOC__
+</StructureSection>
 [[Category: Escherichia coli]]
-[[Category: Single protein]]
+[[Category: Large Structures]]
-[[Category: Bertero, M.G.]]
+[[Category: Bertero MG]]
-[[Category: Brokx, S.J.]]
+[[Category: Brokx SJ]]
-[[Category: Hills, T.L.]]
+[[Category: Hills TL]]
-[[Category: Loschi, L.]]
+[[Category: Loschi L]]
-[[Category: Lovering, A.L.]]
+[[Category: Lovering AL]]
-[[Category: Strynadka, N.C.]]
+[[Category: Strynadka NC]]
-[[Category: Weiner, J.H.]]
+[[Category: Weiner JH]]
-[[Category: Zhang, G.]]
+[[Category: Zhang G]]
-[[Category: MO]]
-[[Category: MTE]]
-[[Category: O]]
-[[Category: URE]]
-[[Category: bioinformatics]]
-[[Category: electron transfer]]
-[[Category: molybdoenzymes]]
-[[Category: molybdopterin]]
-[[Category: oxidoreductase]]
-[[Category: sequence analysis]]
-''Page seeded by [http://ispc.weizmann.ac.il/oca OCA ] on Wed Nov 21 06:00:41 2007''