1sbz

From Proteopedia

(Difference between revisions)
Jump to: navigation, search
Current revision (08:48, 6 November 2024) (edit) (undo)
 
(9 intermediate revisions not shown.)
Line 1: Line 1:
-
{{Seed}}
 
-
[[Image:1sbz.png|left|200px]]
 
-
<!--
+
==Crystal Structure of dodecameric FMN-dependent Ubix-like Decarboxylase from Escherichia coli O157:H7==
-
The line below this paragraph, containing "STRUCTURE_1sbz", creates the "Structure Box" on the page.
+
<StructureSection load='1sbz' size='340' side='right'caption='[[1sbz]], [[Resolution|resolution]] 2.00&Aring;' scene=''>
-
You may change the PDB parameter (which sets the PDB file loaded into the applet)
+
== Structural highlights ==
-
or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
+
<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>
-
or leave the SCENE parameter empty for the default display.
+
</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='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>
-
{{STRUCTURE_1sbz| PDB=1sbz | SCENE= }}
+
<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]]
 +
Check<jmol>
 +
<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/initialview03.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=1sbz ConSurf].
 +
<div style="clear:both"></div>
 +
<div style="background-color:#fffaf0;">
 +
== 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 dodecameric FMN-dependent Ubix-like Decarboxylase from Escherichia coli O157:H7===
+
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<ref>PMID:15459342</ref>
-
 
+
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-
<!--
+
</div>
-
The line below this paragraph, {{ABSTRACT_PUBMED_15459342}}, adds the Publication Abstract to the page
+
<div class="pdbe-citations 1sbz" style="background-color:#fffaf0;"></div>
-
(as it appears on PubMed at http://www.pubmed.gov), where 15459342 is the PubMed ID number.
+
== References ==
-
-->
+
<references/>
-
{{ABSTRACT_PUBMED_15459342}}
+
__TOC__
-
 
+
</StructureSection>
-
==About this Structure==
+
[[Category: Escherichia coli O157:H7]]
-
1SBZ is a 4 chains structure of sequences 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=1SBZ OCA].
+
[[Category: Large Structures]]
-
 
+
[[Category: Cygler M]]
-
==Reference==
+
[[Category: Hung L-W]]
-
<ref group="xtra">PMID:15459342</ref><references group="xtra"/>
+
[[Category: Iannuzzi P]]
-
[[Category: Escherichia coli]]
+
[[Category: Li Y]]
-
[[Category: BSGI, Montreal-Kingston Bacterial Structural Genomics Initiative.]]
+
[[Category: Matte A]]
-
[[Category: Cygler, M.]]
+
[[Category: Rangarajan ES]]
-
[[Category: Hung, L W.]]
+
[[Category: Tocilj A]]
-
[[Category: Iannuzzi, P.]]
+
-
[[Category: Li, Y.]]
+
-
[[Category: Matte, A.]]
+
-
[[Category: Rangarajan, E S.]]
+
-
[[Category: Tocilj, A.]]
+
-
[[Category: Bsgi]]
+
-
[[Category: Fmn binding]]
+
-
[[Category: Montreal-kingston bacterial structural genomics initiative]]
+
-
[[Category: Pad1]]
+
-
[[Category: Structural genomic]]
+
-
[[Category: Ubix]]
+
-
 
+
-
''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Feb 18 09:13:15 2009''
+

Current revision

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

PDB ID 1sbz

Drag the structure with the mouse to rotate

Proteopedia Page Contributors and Editors (what is this?)

OCA

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