This old version of Proteopedia is provided for student assignments while the new version is undergoing repairs. Content and edits done in this old version of Proteopedia after March 1, 2026 will eventually be lost when it is retired in about June of 2026.

Apply for new accounts at the new Proteopedia. Your logins will work in both the old and new versions.


1rqr

From Proteopedia

(Difference between revisions)
Jump to: navigation, search
Current revision (08:26, 1 May 2024) (edit) (undo)
 
(12 intermediate revisions not shown.)
Line 1: Line 1:
-
[[Image:1rqr.gif|left|200px]]
 
-
{{Structure
+
==Crystal structure and mechanism of a bacterial fluorinating enzyme, product complex==
-
|PDB= 1rqr |SIZE=350|CAPTION= <scene name='initialview01'>1rqr</scene>, resolution 2.67&Aring;
+
<StructureSection load='1rqr' size='340' side='right'caption='[[1rqr]], [[Resolution|resolution]] 2.67&Aring;' scene=''>
-
|SITE=
+
== Structural highlights ==
-
|LIGAND= <scene name='pdbligand=5FD:5&#39;-FLUORO-5&#39;-DEOXYADENOSINE'>5FD</scene>, <scene name='pdbligand=MET:METHIONINE'>MET</scene>, <scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene>
+
<table><tr><td colspan='2'>[[1rqr]] is a 3 chain structure with sequence from [https://en.wikipedia.org/wiki/Streptomyces_cattleya Streptomyces cattleya]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1RQR OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1RQR FirstGlance]. <br>
-
|ACTIVITY= <span class='plainlinks'>[http://en.wikipedia.org/wiki/Adenosyl-fluoride_synthase Adenosyl-fluoride synthase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.5.1.63 2.5.1.63] </span>
+
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.67&#8491;</td></tr>
-
|GENE= fla ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=29303 Streptomyces cattleya])
+
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=5FD:5-FLUORO-5-DEOXYADENOSINE'>5FD</scene>, <scene name='pdbligand=MET:METHIONINE'>MET</scene>, <scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene></td></tr>
-
|DOMAIN=
+
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1rqr FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1rqr OCA], [https://pdbe.org/1rqr PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1rqr RCSB], [https://www.ebi.ac.uk/pdbsum/1rqr PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1rqr ProSAT]</span></td></tr>
-
|RELATEDENTRY=[[1rqp|1RQP]]
+
</table>
-
|RESOURCES=<span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1rqr FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1rqr OCA], [http://www.ebi.ac.uk/pdbsum/1rqr PDBsum], [http://www.rcsb.org/pdb/explore.do?structureId=1rqr RCSB]</span>
+
== Function ==
-
}}
+
[https://www.uniprot.org/uniprot/FLA_STRCT FLA_STRCT] Involved in the biosynthesis of fluorometabolites. Catalyzes the formation of a C-F bond by combining S-adenosyl-L-methionine (SAM) and fluoride to generate 5'-fluoro-5'-deoxyadenosine (5'-FDA) and L-methionine. It can also use 2'-deoxyadenosine in place of adenosine as substrate.<ref>PMID:12860396</ref> <ref>PMID:14765200</ref> <ref>PMID:16370017</ref> <ref>PMID:16604208</ref> <ref>PMID:16720268</ref> <ref>PMID:17985882</ref>
-
 
+
== Evolutionary Conservation ==
-
'''Crystal structure and mechanism of a bacterial fluorinating enzyme, product complex'''
+
[[Image:Consurf_key_small.gif|200px|right]]
-
 
+
Check<jmol>
-
 
+
<jmolCheckbox>
-
==Overview==
+
<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/rq/1rqr_consurf.spt"</scriptWhenChecked>
-
Fluorine is the thirteenth most abundant element in the earth's crust, but fluoride concentrations in surface water are low and fluorinated metabolites are extremely rare. The fluoride ion is a potent nucleophile in its desolvated state, but is tightly hydrated in water and effectively inert. Low availability and a lack of chemical reactivity have largely excluded fluoride from biochemistry: in particular, fluorine's high redox potential precludes the haloperoxidase-type mechanism used in the metabolic incorporation of chloride and bromide ions. But fluorinated chemicals are growing in industrial importance, with applications in pharmaceuticals, agrochemicals and materials products. Reactive fluorination reagents requiring specialist process technologies are needed in industry and, although biological catalysts for these processes are highly sought after, only one enzyme that can convert fluoride to organic fluorine has been described. Streptomyces cattleya can form carbon-fluorine bonds and must therefore have evolved an enzyme able to overcome the chemical challenges of using aqueous fluoride. Here we report the sequence and three-dimensional structure of the first native fluorination enzyme, 5'-fluoro-5'-deoxyadenosine synthase, from this organism. Both substrate and products have been observed bound to the enzyme, enabling us to propose a nucleophilic substitution mechanism for this biological fluorination reaction.
+
<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
-
 
+
<text>to colour the structure by Evolutionary Conservation</text>
-
==About this Structure==
+
</jmolCheckbox>
-
1RQR is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Streptomyces_cattleya Streptomyces cattleya]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1RQR OCA].
+
</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=1rqr ConSurf].
-
 
+
<div style="clear:both"></div>
-
==Reference==
+
== References ==
-
Crystal structure and mechanism of a bacterial fluorinating enzyme., Dong C, Huang F, Deng H, Schaffrath C, Spencer JB, O'Hagan D, Naismith JH, Nature. 2004 Feb 5;427(6974):561-5. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/14765200 14765200]
+
<references/>
-
[[Category: Adenosyl-fluoride synthase]]
+
__TOC__
-
[[Category: Single protein]]
+
</StructureSection>
 +
[[Category: Large Structures]]
[[Category: Streptomyces cattleya]]
[[Category: Streptomyces cattleya]]
-
[[Category: Deng, H.]]
+
[[Category: Deng H]]
-
[[Category: Dong, C.]]
+
[[Category: Dong C]]
-
[[Category: Hagan, D O.]]
+
[[Category: Huang F]]
-
[[Category: Huang, F.]]
+
[[Category: Naismith JH]]
-
[[Category: Naismith, J H.]]
+
[[Category: O'Hagan D]]
-
[[Category: Schaffrath, C.]]
+
[[Category: Schaffrath C]]
-
[[Category: Spencer, J B.]]
+
[[Category: Spencer JB]]
-
[[Category: anti-parallel beta sheet]]
+
-
[[Category: central 7 stranded beta sheet]]
+
-
[[Category: fluorinase]]
+
-
 
+
-
''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sun Mar 30 23:31:47 2008''
+

Current revision

Crystal structure and mechanism of a bacterial fluorinating enzyme, product complex

PDB ID 1rqr

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/1rqr"
Personal tools