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1lkm

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Current revision

Crystal structure of Desulfovibrio vulgaris rubrerythrin all-iron(III) form

Structural highlights

1lkm is a 1 chain structure with sequence from Desulfovibrio vulgaris. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	X-ray diffraction, Resolution 1.69Å
Ligands:
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

RUBY_DESVH May provide oxidative stress protection via catalytic reduction of intracellular hydrogen peroxide (By similarity).

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

Rubrerythrin (Rbr) is a 44-kDa homodimeric protein, found in many air-sensitive bacteria and archaea, which contains a unique combination of a rubredoxin-like [Fe(SCys)(4)] site and a non-sulfur, oxo/dicarboxylato-bridged diiron site. The diiron site structure resembles those found in O2-activating diiron enzymes. However, Rbr instead appears to function as a hydrogen peroxide reductase (peroxidase). The diferrous site in all-ferrous Rbr (Rbr(red)) shows a much greater reactivity with H2O2 than does the diferric site in all-ferric Rbr (Rbr(ox)), but only the latter structure has been reported. Here we report the X-ray crystal structures of the recombinant Rbr(red) from the sulfate reducing bacterium, Desulfovibrio vulgaris, as well as its azide adduct (Rbr(red)N3). We have also redetermined the structure of Rbr(ox) to a higher resolution than previously reported. The structural differences between Rbr(ox) and Rbr(red) are localized entirely at the diiron site. The most striking structural change upon reduction of the diferric to the diferrous site of Rbr is a 1.8-A movement of one iron away from a unique glutamate carboxylate ligand and toward a trans-disposed histidine side chain, which replaces the glutamate as a ligand. This movement increases the inter-iron distance from 3.3 to 4 A. Rbr(red)N(3) shows this same iron movement and His-->Glu ligand replacement relative to Rbr(ox), and, in addition, an azide coordinated to the diiron site in a cis mu-1,3 fashion, replacing two solvent ligands in Rbr(red). Relative to those in O2-activating enzymes, the bridging carboxylate ligation of the Rbr diiron site is less flexible upon diferric/diferrous interconversion. The diferrous site is also much more rigid, symmetrical, and solvent-exposed than those in O2-activating enzymes. On the basis of these unique structural features, a mechanism is proposed for facile reduction of hydrogen peroxide by Rbr involving a cis mu-eta(2) H2O2 diferrous intermediate.

X-ray crystal structures of reduced rubrerythrin and its azide adduct: a structure-based mechanism for a non-heme diiron peroxidase.,Jin S, Kurtz DM Jr, Liu ZJ, Rose J, Wang BC J Am Chem Soc. 2002 Aug 21;124(33):9845-55. PMID:12175244^[1]

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

References

↑ Jin S, Kurtz DM Jr, Liu ZJ, Rose J, Wang BC. X-ray crystal structures of reduced rubrerythrin and its azide adduct: a structure-based mechanism for a non-heme diiron peroxidase. J Am Chem Soc. 2002 Aug 21;124(33):9845-55. PMID:12175244

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/1lkm"

@@ Line 1: / Line 1: @@
 ==Crystal structure of Desulfovibrio vulgaris rubrerythrin all-iron(III) form==
-<StructureSection load='1lkm' size='340' side='right' caption='[[1lkm]], [[Resolution|resolution]] 1.69&Aring;' scene=''>
+<StructureSection load='1lkm' size='340' side='right'caption='[[1lkm]], [[Resolution|resolution]] 1.69&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[1lkm]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Atcc_29579 Atcc 29579]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1LKM OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1LKM FirstGlance]. <br>
+<table><tr><td colspan='2'>[[1lkm]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Desulfovibrio_vulgaris Desulfovibrio vulgaris]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1LKM OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1LKM FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=FE:FE+(III)+ION'>FE</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]] 1.69&#8491;</td></tr>
-<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[1lko|1lko]], [[1lkp|1lkp]]</td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=FE:FE+(III)+ION'>FE</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=1lkm FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1lkm OCA], [http://pdbe.org/1lkm PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1lkm RCSB], [http://www.ebi.ac.uk/pdbsum/1lkm 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=1lkm FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1lkm OCA], [https://pdbe.org/1lkm PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1lkm RCSB], [https://www.ebi.ac.uk/pdbsum/1lkm PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1lkm ProSAT]</span></td></tr>
 </table>
 == Function ==
-[[http://www.uniprot.org/uniprot/RUBY_DESVH RUBY_DESVH]] May provide oxidative stress protection via catalytic reduction of intracellular hydrogen peroxide (By similarity).
+[https://www.uniprot.org/uniprot/RUBY_DESVH RUBY_DESVH] May provide oxidative stress protection via catalytic reduction of intracellular hydrogen peroxide (By similarity).
 == 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/lk/1lkm_consurf.spt"</scriptWhenChecked>
+    <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/lk/1lkm_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/chain_selection.php?pdb_ID=2ata ConSurf].
+</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=1lkm ConSurf].
 <div style="clear:both"></div>
 <div style="background-color:#fffaf0;">
@@ Line 30: / Line 31: @@
 ==See Also==
-*[[Myosin|Myosin]]
+*[[Myosin 3D Structures|Myosin 3D Structures]]
 == References ==
 <references/>
 __TOC__
 </StructureSection>
-[[Category: Atcc 29579]]
+[[Category: Desulfovibrio vulgaris]]
-[[Category: Jin, S]]
+[[Category: Large Structures]]
-[[Category: Kurtz, D M]]
+[[Category: Jin S]]
-[[Category: Liu, Z J]]
+[[Category: Kurtz Jr DM]]
-[[Category: Rose, J]]
+[[Category: Liu ZJ]]
-[[Category: Wang, B C]]
+[[Category: Rose J]]
-[[Category: Diiron]]
+[[Category: Wang BC]]
-[[Category: Electron transport]]
-[[Category: Four-helix bundle]]
-[[Category: Oxidized form]]
-[[Category: Rubredoxin-like]]
-[[Category: Rubrerythrin]]

1lkm

From Proteopedia

Current revision

Crystal structure of Desulfovibrio vulgaris rubrerythrin all-iron(III) form

Structural highlights

Function

Evolutionary Conservation

Publication Abstract from PubMed

See Also

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

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