1xdy

From Proteopedia

(Difference between revisions)

Current revision

Structural and Biochemical Identification of a Novel Bacterial Oxidoreductase, W-containing cofactor

Structural highlights

1xdy is a 10 chain structure with sequence from Escherichia coli. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	X-ray diffraction, Resolution 2.2Å
Ligands:	,
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

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).^[1] ^[2]

Evolutionary Conservation

Check, as determined by ConSurfDB. You may read the explanation of the method and the full data available from ConSurf.

Publication Abstract from PubMed

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.

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:15355966^[3]

From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.

References

↑ Loschi L, Brokx SJ, Hills TL, Zhang G, Bertero MG, Lovering AL, Weiner JH, Strynadka NC. Structural and biochemical identification of a novel bacterial oxidoreductase. J Biol Chem. 2004 Nov 26;279(48):50391-400. Epub 2004 Sep 7. PMID:15355966 doi:10.1074/jbc.M408876200
↑ Gennaris A, Ezraty B, Henry C, Agrebi R, Vergnes A, Oheix E, Bos J, Leverrier P, Espinosa L, Szewczyk J, Vertommen D, Iranzo O, Collet JF, Barras F. Repairing oxidized proteins in the bacterial envelope using respiratory chain electrons. Nature. 2015 Dec 17;528(7582):409-412. PMID:26641313 doi:10.1038/nature15764
↑ Loschi L, Brokx SJ, Hills TL, Zhang G, Bertero MG, Lovering AL, Weiner JH, Strynadka NC. Structural and biochemical identification of a novel bacterial oxidoreductase. J Biol Chem. 2004 Nov 26;279(48):50391-400. Epub 2004 Sep 7. PMID:15355966 doi:10.1074/jbc.M408876200

1 Structural highlights
2 Function
3 Evolutionary Conservation
4 Publication Abstract from PubMed
5 See Also
6 References

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/1xdy"

@@ Line 1: / Line 1: @@
 ==Structural and Biochemical Identification of a Novel Bacterial Oxidoreductase, W-containing cofactor==
-<StructureSection load='1xdy' size='340' side='right' caption='[[1xdy]], [[Resolution|resolution]] 2.20&Aring;' scene=''>
+<StructureSection load='1xdy' size='340' side='right'caption='[[1xdy]], [[Resolution|resolution]] 2.20&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[1xdy]] is a 10 chain structure with sequence from [http://en.wikipedia.org/wiki/"bacillus_coli"_migula_1895 "bacillus coli" migula 1895]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1XDY OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1XDY FirstGlance]. <br>
+<table><tr><td colspan='2'>[[1xdy]] is a 10 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=1XDY OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1XDY FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><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=W:TUNGSTEN+ION'>W</scene></td></tr>
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.2&#8491;</td></tr>
-<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[1xdq|1xdq]]</td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><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=W:TUNGSTEN+ION'>W</scene></td></tr>
-<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1xdy FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1xdy OCA], [http://pdbe.org/1xdy PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1xdy RCSB], [http://www.ebi.ac.uk/pdbsum/1xdy PDBsum]</span></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=1xdy FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1xdy OCA], [https://pdbe.org/1xdy PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1xdy RCSB], [https://www.ebi.ac.uk/pdbsum/1xdy PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1xdy ProSAT]</span></td></tr>
 </table>
 == Function ==
-[[http://www.uniprot.org/uniprot/YEDY_ECOLI YEDY_ECOLI]] The exact function is not known. Can catalyze the reduction of a variety of substrates like dimethyl sulfoxide, trimethylamine N-oxide, phenylmethyl sulfoxide and L-methionine sulfoxide. Cannot reduce cyclic N-oxides. Shows no activity as sulfite oxidase.<ref>PMID:15355966</ref>
+[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/1xdy_consurf.spt"</scriptWhenChecked>
+    <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/xd/1xdy_consurf.spt"</scriptWhenChecked>
     <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
     <text>to colour the structure by Evolutionary Conservation</text>
@@ Line 35: / Line 36: @@
 __TOC__
 </StructureSection>
-[[Category: Bacillus coli migula 1895]]
+[[Category: Escherichia coli]]
-[[Category: Bertero, M G]]
+[[Category: Large Structures]]
-[[Category: Brokx, S J]]
+[[Category: Bertero MG]]
-[[Category: Hills, T L]]
+[[Category: Brokx SJ]]
-[[Category: Loschi, L]]
+[[Category: Hills TL]]
-[[Category: Lovering, A L]]
+[[Category: Loschi L]]
-[[Category: Strynadka, N C]]
+[[Category: Lovering AL]]
-[[Category: Weiner, J H]]
+[[Category: Strynadka NC]]
-[[Category: Zhang, G]]
+[[Category: Weiner JH]]
-[[Category: Bioinformatic]]
+[[Category: Zhang G]]
-[[Category: Electron transfer]]
-[[Category: Molybdoenzyme]]
-[[Category: Molybdopterin]]
-[[Category: Oxidoreductase]]
-[[Category: Sequence analysis]]

1xdy

From Proteopedia

Current revision

Structural and Biochemical Identification of a Novel Bacterial Oxidoreductase, W-containing cofactor

Structural highlights

Function

Evolutionary Conservation

Publication Abstract from PubMed

See Also

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

Views

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