5th5: Difference between revisions

Latest revision as of 12:31, 13 August 2026

Crystal Structure of QueE from Bacillus subtilis with 6-carboxypterin-5'-deoxyadenosyl ester bound

Structural highlights

5th5 is a 4 chain structure with sequence from Bacillus subtilis. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	X-ray diffraction, Resolution 2.407Å
Ligands:	7C5, MET
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

QUEE_BACSU Catalyzes the complex heterocyclic radical-mediated conversion of 6-carboxy-5,6,7,8-tetrahydropterin (CPH4) to 7-carboxy-7-deazaguanine (CDG), a step common to the biosynthetic pathways of all 7-deazapurine-containing compounds.[HAMAP-Rule:MF_00917]^[1] ^[2] ^[3]

Publication Abstract from PubMed

Radical S-adenosyl-L-methionine (SAM) enzymes are widely distributed and catalyze diverse reactions. SAM binds to the unique iron atom of a site-differentiated [4Fe-4S] cluster and is reductively cleaved to generate a 5-deoxyadenosyl radical, which initiates turnover. 7-Carboxy-7-deazaguanine (CDG) synthase catalyzes a key step in the biosynthesis of 7-deazapurine containing natural products. 6-Carboxypterin (6-CP), an oxidized analog of the natural substrate 6-carboxy-5,6,7,8-tetrahydropterin (CPH4), is shown to be an alternate substrate for CDG synthase. Under reducing conditions that would promote the reductive cleavage of SAM, 6-CP is turned over to 6-deoxyadenosylpterin, presumably by radical addition of the 5-deoxyadenosine followed by oxidative decarboxylation to the product. By contrast, in the absence of the strong reductant, dithionite, the carboxylate of 6-CP is esterified to generate 6-carboxypterin-5-deoxyadenosyl ester. Structural studies with 6-CP and SAM also reveal electron density consistent with the ester product being formed in crystallo. The differential reactivity of 6-CP under reducing and non-reducing conditions highlights the ability of radical SAM enzymes to carry out both polar and radical transformations in the same active site. .

7-Carboxy-7-deazaguanine synthase - A radical S-adenosyl-L-methionine enzyme with polar tendencies.,Bruender NA, Grell TA, Dowling DP, McCarty RM, Drennan CL, Bandarian V J Am Chem Soc. 2017 Jan 3. doi: 10.1021/jacs.6b11381. PMID:28045519^[4]

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

References

↑ Reader JS, Metzgar D, Schimmel P, de Crecy-Lagard V. Identification of four genes necessary for biosynthesis of the modified nucleoside queuosine. J Biol Chem. 2004 Feb 20;279(8):6280-5. Epub 2003 Dec 2. PMID:14660578 doi:https://dx.doi.org/10.1074/jbc.M310858200
↑ McCarty RM, Somogyi A, Lin G, Jacobsen NE, Bandarian V. The deazapurine biosynthetic pathway revealed: in vitro enzymatic synthesis of PreQ(0) from guanosine 5'-triphosphate in four steps. Biochemistry. 2009 May 12;48(18):3847-52. doi: 10.1021/bi900400e. PMID:19354300 doi:https://dx.doi.org/10.1021/bi900400e
↑ McCarty RM, Krebs C, Bandarian V. Spectroscopic, steady-state kinetic, and mechanistic characterization of the radical SAM enzyme QueE, which catalyzes a complex cyclization reaction in the biosynthesis of 7-deazapurines. Biochemistry. 2013 Jan 8;52(1):188-98. doi: 10.1021/bi301156w. Epub 2012 Dec 24. PMID:23194065 doi:https://dx.doi.org/10.1021/bi301156w
↑ Bruender NA, Grell TA, Dowling DP, McCarty RM, Drennan CL, Bandarian V. 7-Carboxy-7-deazaguanine synthase - A radical S-adenosyl-L-methionine enzyme with polar tendencies. J Am Chem Soc. 2017 Jan 3. doi: 10.1021/jacs.6b11381. PMID:28045519 doi:https://dx.doi.org/10.1021/jacs.6b11381

Proteopedia Page Contributors and Editors (what is this?)

OCA

[1] Reader JS, Metzgar D, Schimmel P, de Crecy-Lagard V. Identification of four genes necessary for biosynthesis of the modified nucleoside queuosine. J Biol Chem. 2004 Feb 20;279(8):6280-5. Epub 2003 Dec 2. PMID:14660578 doi:https://dx.doi.org/10.1074/jbc.M310858200

[2] McCarty RM, Somogyi A, Lin G, Jacobsen NE, Bandarian V. The deazapurine biosynthetic pathway revealed: in vitro enzymatic synthesis of PreQ(0) from guanosine 5'-triphosphate in four steps. Biochemistry. 2009 May 12;48(18):3847-52. doi: 10.1021/bi900400e. PMID:19354300 doi:https://dx.doi.org/10.1021/bi900400e

[3] McCarty RM, Krebs C, Bandarian V. Spectroscopic, steady-state kinetic, and mechanistic characterization of the radical SAM enzyme QueE, which catalyzes a complex cyclization reaction in the biosynthesis of 7-deazapurines. Biochemistry. 2013 Jan 8;52(1):188-98. doi: 10.1021/bi301156w. Epub 2012 Dec 24. PMID:23194065 doi:https://dx.doi.org/10.1021/bi301156w

[4] Bruender NA, Grell TA, Dowling DP, McCarty RM, Drennan CL, Bandarian V. 7-Carboxy-7-deazaguanine synthase - A radical S-adenosyl-L-methionine enzyme with polar tendencies. J Am Chem Soc. 2017 Jan 3. doi: 10.1021/jacs.6b11381. PMID:28045519 doi:https://dx.doi.org/10.1021/jacs.6b11381

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[2]

[3]

[4]

@@ Line 1: / Line 1: @@
-'''Unreleased structure'''
-The entry 5th5 is ON HOLD
+==Crystal Structure of QueE from Bacillus subtilis with 6-carboxypterin-5'-deoxyadenosyl ester bound==
+<StructureSection load='5th5' size='340' side='right'caption='[[5th5]], [[Resolution|resolution]] 2.41&Aring;' scene=''>
+== Structural highlights ==
+<table><tr><td colspan='2'>[[5th5]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Bacillus_subtilis Bacillus subtilis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5TH5 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5TH5 FirstGlance]. <br>
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.407&#8491;</td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=7C5:5-O-(2-AMINO-4-OXO-1,4-DIHYDROPTERIDINE-6-CARBONYL)ADENOSINE'>7C5</scene>, <scene name='pdbligand=MET:METHIONINE'>MET</scene></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=5th5 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5th5 OCA], [https://pdbe.org/5th5 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5th5 RCSB], [https://www.ebi.ac.uk/pdbsum/5th5 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5th5 ProSAT]</span></td></tr>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/QUEE_BACSU QUEE_BACSU] Catalyzes the complex heterocyclic radical-mediated conversion of 6-carboxy-5,6,7,8-tetrahydropterin (CPH4) to 7-carboxy-7-deazaguanine (CDG), a step common to the biosynthetic pathways of all 7-deazapurine-containing compounds.[HAMAP-Rule:MF_00917]<ref>PMID:14660578</ref> <ref>PMID:19354300</ref> <ref>PMID:23194065</ref>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+Radical S-adenosyl-L-methionine (SAM) enzymes are widely distributed and catalyze diverse reactions. SAM binds to the unique iron atom of a site-differentiated [4Fe-4S] cluster and is reductively cleaved to generate a 5-deoxyadenosyl radical, which initiates turnover. 7-Carboxy-7-deazaguanine (CDG) synthase catalyzes a key step in the biosynthesis of 7-deazapurine containing natural products. 6-Carboxypterin (6-CP), an oxidized analog of the natural substrate 6-carboxy-5,6,7,8-tetrahydropterin (CPH4), is shown to be an alternate substrate for CDG synthase. Under reducing conditions that would promote the reductive cleavage of SAM, 6-CP is turned over to 6-deoxyadenosylpterin, presumably by radical addition of the 5-deoxyadenosine followed by oxidative decarboxylation to the product. By contrast, in the absence of the strong reductant, dithionite, the carboxylate of 6-CP is esterified to generate 6-carboxypterin-5-deoxyadenosyl ester. Structural studies with 6-CP and SAM also reveal electron density consistent with the ester product being formed in crystallo. The differential reactivity of 6-CP under reducing and non-reducing conditions highlights the ability of radical SAM enzymes to carry out both polar and radical transformations in the same active site. .
-Authors:
+-Carboxy-7-deazaguanine synthase - A radical S-adenosyl-L-methionine enzyme with polar tendencies.,Bruender NA, Grell TA, Dowling DP, McCarty RM, Drennan CL, Bandarian V J Am Chem Soc. 2017 Jan 3. doi: 10.1021/jacs.6b11381. PMID:28045519<ref>PMID:28045519</ref>
-Description:
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-[[Category: Unreleased Structures]]
+</div>
+<div class="pdbe-citations 5th5" style="background-color:#fffaf0;"></div>
+== References ==
+<references/>
+__TOC__
+</StructureSection>
+[[Category: Bacillus subtilis]]
+[[Category: Large Structures]]
+[[Category: Dowling DP]]
+[[Category: Drennan CL]]
+[[Category: Grell TAJ]]

5th5: Difference between revisions

Latest revision as of 12:31, 13 August 2026

Crystal Structure of QueE from Bacillus subtilis with 6-carboxypterin-5'-deoxyadenosyl ester bound

Structural highlights

Function

Publication Abstract from PubMed

References

Contents

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