1sbz

From Proteopedia

(Difference between revisions)

Current revision

Crystal Structure of dodecameric FMN-dependent Ubix-like Decarboxylase from Escherichia coli O157:H7

Structural highlights

1sbz is a 4 chain structure with sequence from Escherichia coli O157:H7. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	X-ray diffraction, Resolution 2Å
Ligands:	,
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT, TOPSAN

Function

PADL_ECO57 Involved in the non-oxidative decarboxylation and detoxification of phenolic derivatives under both aerobic and anaerobic conditions (PubMed:15979273). Flavin prenyltransferase that catalyzes the synthesis of the prenylated FMN cofactor (prenyl-FMN) for phenolic acid decarboxylase (By similarity).[HAMAP-Rule:MF_01986]^[1]

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

The crystal structure of the flavoprotein Pad1 from Escherichia coli O157:H7 complexed with the cofactor FMN has been determined by the multiple anomalous diffraction method and refined at 2.0 A resolution. This protein is a paralog of UbiX (3-octaprenyl-4-hydroxybenzoate carboxylyase, 51% sequence identity) that catalyzes the third step in ubiquinone biosynthesis and to Saccharomyces cerevisiae Pad1 (54% identity), an enzyme that confers resistance to the antimicrobial compounds phenylacrylic acids through decarboxylation of these compounds. Each Pad1 monomer consists of a typical Rossmann fold containing a non-covalently bound molecule of FMN. The fold of Pad1 is similar to MrsD, an enzyme associated with lantibiotic synthesis; EpiD, a peptidyl-cysteine decarboxylase; and AtHAL3a, the enzyme, which decarboxylates 4'-phosphopantothenoylcysteine to 4'-phosphopantetheine during coenzyme A biosynthesis, all with a similar location of the FMN binding site at the interface between two monomers, yet each having little sequence similarity to one another. All of these proteins associate into oligomers, with a trimer forming the common structural unit in each case. In MrsD and EpiD, which belong to the homo-dodecameric flavin-containing cysteine decarboxylase (HFCD) family, these trimers associate further into dodecamers. Pad1 also forms dodecamers, although the association of the trimers is completely different, resulting in exposure of a different side of the trimer unit to the solvent. This exposure affects the location of the substrate binding site and, specifically, its access to the FMN cofactor. Therefore, Pad1 forms a separate family, distinguishable from the HFCD family.

Crystal structure of a dodecameric FMN-dependent UbiX-like decarboxylase (Pad1) from Escherichia coli O157: H7.,Rangarajan ES, Li Y, Iannuzzi P, Tocilj A, Hung LW, Matte A, Cygler M Protein Sci. 2004 Nov;13(11):3006-16. Epub 2004 Sep 30. PMID:15459342^[2]

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

References

↑ Lupa B, Lyon D, Gibbs MD, Reeves RA, Wiegel J. Distribution of genes encoding the microbial non-oxidative reversible hydroxyarylic acid decarboxylases/phenol carboxylases. Genomics. 2005 Sep;86(3):342-51. PMID:15979273 doi:10.1016/j.ygeno.2005.05.002
↑ Rangarajan ES, Li Y, Iannuzzi P, Tocilj A, Hung LW, Matte A, Cygler M. Crystal structure of a dodecameric FMN-dependent UbiX-like decarboxylase (Pad1) from Escherichia coli O157: H7. Protein Sci. 2004 Nov;13(11):3006-16. Epub 2004 Sep 30. PMID:15459342 doi:10.1110/ps.04953004

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

Proteopedia Page Contributors and Editors (what is this?)

OCA

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

@@ Line 3: / Line 3: @@
 <StructureSection load='1sbz' size='340' side='right'caption='[[1sbz]], [[Resolution|resolution]] 2.00&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[1sbz]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Eco57 Eco57]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1SBZ OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1SBZ FirstGlance]. <br>
+<table><tr><td colspan='2'>[[1sbz]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_coli_O157:H7 Escherichia coli O157:H7]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1SBZ OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1SBZ FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=FMN:FLAVIN+MONONUCLEOTIDE'>FMN</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&#8491;</td></tr>
-<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene></td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=FMN:FLAVIN+MONONUCLEOTIDE'>FMN</scene>, <scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene></td></tr>
-<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">PAD1, Z4047, ECS3593 ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=83334 ECO57])</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=1sbz FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1sbz OCA], [https://pdbe.org/1sbz PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1sbz RCSB], [https://www.ebi.ac.uk/pdbsum/1sbz PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1sbz ProSAT], [https://www.topsan.org/Proteins/BSGI/1sbz TOPSAN]</span></td></tr>
 </table>
+== Function ==
+[https://www.uniprot.org/uniprot/PADL_ECO57 PADL_ECO57] Involved in the non-oxidative decarboxylation and detoxification of phenolic derivatives under both aerobic and anaerobic conditions (PubMed:15979273). Flavin prenyltransferase that catalyzes the synthesis of the prenylated FMN cofactor (prenyl-FMN) for phenolic acid decarboxylase (By similarity).[HAMAP-Rule:MF_01986]<ref>PMID:15979273</ref>
 == Evolutionary Conservation ==
 [[Image:Consurf_key_small.gif|200px|right]]
@@ Line 14: / Line 15: @@
   <jmolCheckbox>
     <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/sb/1sbz_consurf.spt"</scriptWhenChecked>
-    <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
+    <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview03.spt</scriptWhenUnchecked>
     <text>to colour the structure by Evolutionary Conservation</text>
   </jmolCheckbox>
@@ Line 32: / Line 33: @@
 __TOC__
 </StructureSection>
-[[Category: Eco57]]
+[[Category: Escherichia coli O157:H7]]
 [[Category: Large Structures]]
-[[Category: Structural genomic]]
+[[Category: Cygler M]]
-[[Category: Cygler, M]]
+[[Category: Hung L-W]]
-[[Category: Hung, L W]]
+[[Category: Iannuzzi P]]
-[[Category: Iannuzzi, P]]
+[[Category: Li Y]]
-[[Category: Li, Y]]
+[[Category: Matte A]]
-[[Category: Matte, A]]
+[[Category: Rangarajan ES]]
-[[Category: Rangarajan, E S]]
+[[Category: Tocilj A]]
-[[Category: Tocilj, A]]
-[[Category: Bsgi]]
-[[Category: Fmn binding]]
-[[Category: Lyase]]
-[[Category: Pad1]]
-[[Category: Ubix]]

1sbz

From Proteopedia

Current revision

Crystal Structure of dodecameric FMN-dependent Ubix-like Decarboxylase from Escherichia coli O157:H7

Structural highlights

Function

Evolutionary Conservation

Publication Abstract from PubMed

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

Views

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