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2v7x

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Revision as of 06:17, 8 September 2022

X-RAY CRYSTAL STRUCTURE OF 5'-FLUORODEOXYADENOSINE SYNTHASE S158A mutant FROM STREPTOMYCES CATTLEYA COMPLEXED WITH the PRODUCTS, FDA and Met

Structural highlights

2v7x is a 3 chain structure with sequence from Streptomyces cattleya. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Ligands:	,
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

[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.^[1] ^[2] ^[3] ^[4] ^[5] ^[6]

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

Recently a fluorination enzyme was identified and isolated from Streptomyces cattleya, as the first committed step on the metabolic pathway to the fluorinated metabolites, fluoroacetate and 4-fluorothreonine. This enzyme, 5'-fluoro-5'-deoxy adenosine synthetase (FDAS), has been shown to catalyze C-F bond formation by nucleophilic attack of fluoride ion to S-adenosyl-l-methionine (SAM) with the concomitant displacement of l-methionine to generate 5'-fluoro-5'-deoxy adenosine (5'-FDA). Although the structures of FDAS bound to both SAM and products have been solved, the molecular mechanism remained to be elucidated. We now report site-directed mutagenesis studies, structural analyses, and isothermal calorimetry (ITC) experiments. The data establish the key residues required for catalysis and the order of substrate binding. Fluoride ion is not readily distinguished from water by protein X-ray crystallography; however, using chloride ion (also a substrate) with a mutant of low activity has enabled the halide ion to be located in nonproductive co-complexes with SAH and SAM. The kinetic data suggest the positively charged sulfur of SAM is a key requirement in stabilizing the transition state. We propose a molecular mechanism for FDAS in which fluoride weakly associates with the enzyme exchanging two water molecules for protein ligation. The binding of SAM expels remaining water associated with fluoride ion and traps the ion in a pocket positioned to react with SAM, generating l-methionine and 5'-FDA. l-methionine then dissociates from the enzyme followed by 5'-FDA.

Mechanism of enzymatic fluorination in Streptomyces cattleya.,Zhu X, Robinson DA, McEwan AR, O'Hagan D, Naismith JH J Am Chem Soc. 2007 Nov 28;129(47):14597-604. Epub 2007 Nov 7. PMID:17985882^[7]

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

References

↑ Schaffrath C, Deng H, O'Hagan D. Isolation and characterisation of 5'-fluorodeoxyadenosine synthase, a fluorination enzyme from Streptomyces cattleya. FEBS Lett. 2003 Jul 17;547(1-3):111-4. PMID:12860396
↑ Dong C, Huang F, Deng H, Schaffrath C, Spencer JB, O'Hagan D, Naismith JH. Crystal structure and mechanism of a bacterial fluorinating enzyme. Nature. 2004 Feb 5;427(6974):561-5. PMID:14765200 doi:http://dx.doi.org/10.1038/nature02280
↑ Deng H, Cobb SL, McEwan AR, McGlinchey RP, Naismith JH, O'Hagan D, Robinson DA, Spencer JB. The fluorinase from Streptomyces cattleya is also a chlorinase. Angew Chem Int Ed Engl. 2006 Jan 23;45(5):759-62. PMID:16370017 doi:http://dx.doi.org/10.1002/anie.200503582
↑ Cobb SL, Deng H, McEwan AR, Naismith JH, O'Hagan D, Robinson DA. Substrate specificity in enzymatic fluorination. The fluorinase from Streptomyces cattleya accepts 2'-deoxyadenosine substrates. Org Biomol Chem. 2006 Apr 21;4(8):1458-60. Epub 2006 Mar 8. PMID:16604208 doi:10.1039/b600574h
↑ Huang F, Haydock SF, Spiteller D, Mironenko T, Li TL, O'Hagan D, Leadlay PF, Spencer JB. The gene cluster for fluorometabolite biosynthesis in Streptomyces cattleya: a thioesterase confers resistance to fluoroacetyl-coenzyme A. Chem Biol. 2006 May;13(5):475-84. PMID:16720268 doi:http://dx.doi.org/S1074-5521(06)00084-6
↑ Zhu X, Robinson DA, McEwan AR, O'Hagan D, Naismith JH. Mechanism of enzymatic fluorination in Streptomyces cattleya. J Am Chem Soc. 2007 Nov 28;129(47):14597-604. Epub 2007 Nov 7. PMID:17985882 doi:10.1021/ja0731569
↑ Zhu X, Robinson DA, McEwan AR, O'Hagan D, Naismith JH. Mechanism of enzymatic fluorination in Streptomyces cattleya. J Am Chem Soc. 2007 Nov 28;129(47):14597-604. Epub 2007 Nov 7. PMID:17985882 doi:10.1021/ja0731569

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/2v7x"

@@ Line 3: / Line 3: @@
 <StructureSection load='2v7x' size='340' side='right'caption='[[2v7x]], [[Resolution|resolution]] 1.96&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[2v7x]] is a 3 chain structure with sequence from [https://en.wikipedia.org/wiki/"streptomyces_cattleya"_kahan_et_al._1979 "streptomyces cattleya" kahan et al. 1979]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2V7X OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2V7X FirstGlance]. <br>
+<table><tr><td colspan='2'>[[2v7x]] 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=2V7X OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2V7X FirstGlance]. <br>
 </td></tr><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></td></tr>
-<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[1rqr|1rqr]], [[2c4t|2c4t]], [[2c5b|2c5b]], [[2c5h|2c5h]], [[1rqp|1rqp]], [[2c2w|2c2w]], [[2c4u|2c4u]], [[2cbx|2cbx]], [[2cc2|2cc2]], [[2v7t|2v7t]], [[2v7u|2v7u]], [[2v7v|2v7v]], [[2v7w|2v7w]]</div></td></tr>
-<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/Adenosyl-fluoride_synthase Adenosyl-fluoride synthase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.5.1.63 2.5.1.63] </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=2v7x FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2v7x OCA], [https://pdbe.org/2v7x PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2v7x RCSB], [https://www.ebi.ac.uk/pdbsum/2v7x PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2v7x ProSAT]</span></td></tr>
 </table>
+== 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 ==
 [[Image:Consurf_key_small.gif|200px|right]]
@@ Line 32: / Line 32: @@
 __TOC__
 </StructureSection>
-[[Category: Streptomyces cattleya kahan et al. 1979]]
-[[Category: Adenosyl-fluoride synthase]]
 [[Category: Large Structures]]
-[[Category: Hagan, D O]]
+[[Category: Streptomyces cattleya]]
-[[Category: Naismith, J H]]
+[[Category: Naismith JH]]
-[[Category: Robinson, D A]]
+[[Category: O'Hagan D]]
-[[Category: Zhu, X]]
+[[Category: Robinson DA]]
-[[Category: Biosynthetic protein]]
+[[Category: Zhu X]]
-[[Category: Fluorinase]]
-[[Category: Transferase]]

2v7x

From Proteopedia

Revision as of 06:17, 8 September 2022

X-RAY CRYSTAL STRUCTURE OF 5'-FLUORODEOXYADENOSINE SYNTHASE S158A mutant FROM STREPTOMYCES CATTLEYA COMPLEXED WITH the PRODUCTS, FDA and Met

Structural highlights

Function

Evolutionary Conservation

Publication Abstract from PubMed

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

Views

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