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| | ==Crystal Structure of QueE from Burkholderia multivorans in complex with AdoMet, 7-carboxy-7-deazaguanine, and Mg2+== | | ==Crystal Structure of QueE from Burkholderia multivorans in complex with AdoMet, 7-carboxy-7-deazaguanine, and Mg2+== |
| - | <StructureSection load='4njk' size='340' side='right' caption='[[4njk]], [[Resolution|resolution]] 1.91Å' scene=''> | + | <StructureSection load='4njk' size='340' side='right'caption='[[4njk]], [[Resolution|resolution]] 1.91Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[4njk]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Burm1 Burm1]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4NJK OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4NJK FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[4njk]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Burkholderia_multivorans_ATCC_17616 Burkholderia multivorans ATCC 17616]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4NJK OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4NJK FirstGlance]. <br> |
| - | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=2KA:2-AMINO-4-OXO-4,7-DIHYDRO-3H-PYRROLO[2,3-D]PYRIMIDINE-5-CARBOXYLIC+ACID'>2KA</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene>, <scene name='pdbligand=SAM:S-ADENOSYLMETHIONINE'>SAM</scene>, <scene name='pdbligand=SF4:IRON/SULFUR+CLUSTER'>SF4</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]] 1.911Å</td></tr> |
| - | <tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[4njg|4njg]], [[4njh|4njh]], [[4nji|4nji]], [[4njj|4njj]]</td></tr>
| + | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=2KA:2-AMINO-4-OXO-4,7-DIHYDRO-3H-PYRROLO[2,3-D]PYRIMIDINE-5-CARBOXYLIC+ACID'>2KA</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene>, <scene name='pdbligand=SAM:S-ADENOSYLMETHIONINE'>SAM</scene>, <scene name='pdbligand=SF4:IRON/SULFUR+CLUSTER'>SF4</scene></td></tr> |
| - | <tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">queE, Bmul_3115, BMULJ_00116 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=395019 BURM1])</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=4njk FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4njk OCA], [https://pdbe.org/4njk PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4njk RCSB], [https://www.ebi.ac.uk/pdbsum/4njk PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4njk ProSAT]</span></td></tr> |
| - | <tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/7-carboxy-7-deazaguanine_synthase 7-carboxy-7-deazaguanine synthase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=4.3.99.3 4.3.99.3] </span></td></tr>
| + | |
| - | <tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4njk FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4njk OCA], [http://pdbe.org/4njk PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4njk RCSB], [http://www.ebi.ac.uk/pdbsum/4njk PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4njk ProSAT]</span></td></tr> | + | |
| | </table> | | </table> |
| | == Function == | | == Function == |
| - | [[http://www.uniprot.org/uniprot/A9AC61_BURM1 A9AC61_BURM1]] Catalyzes the conversion of 6-carboxy-5,6,7,8-tetrahydropterin (CPH4) to 7-carboxy-7-deazaguanine (CDG) (By similarity).[HAMAP-Rule:MF_00917] | + | [https://www.uniprot.org/uniprot/QUEE_BURM1 QUEE_BURM1] 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:24362703</ref> |
| | <div style="background-color:#fffaf0;"> | | <div style="background-color:#fffaf0;"> |
| | == Publication Abstract from PubMed == | | == Publication Abstract from PubMed == |
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| | __TOC__ | | __TOC__ |
| | </StructureSection> | | </StructureSection> |
| - | [[Category: 7-carboxy-7-deazaguanine synthase]] | + | [[Category: Burkholderia multivorans ATCC 17616]] |
| - | [[Category: Burm1]] | + | [[Category: Large Structures]] |
| - | [[Category: Bandarian, V]] | + | [[Category: Bandarian V]] |
| - | [[Category: Bruender, N A]] | + | [[Category: Bruender NA]] |
| - | [[Category: Dowling, D P]] | + | [[Category: Dowling DP]] |
| - | [[Category: Drennan, C L]] | + | [[Category: Drennan CL]] |
| - | [[Category: McCarty, R M]] | + | [[Category: McCarty RM]] |
| - | [[Category: Young, A P]] | + | [[Category: Young AP]] |
| - | [[Category: Adomet radical enzyme]]
| + | |
| - | [[Category: Lyase]]
| + | |
| - | [[Category: Modified partial tim barrel-like structure]]
| + | |
| - | [[Category: Radical adomet fold]]
| + | |
| - | [[Category: Radical sam fold]]
| + | |
| - | [[Category: Synthase]]
| + | |
| Structural highlights
4njk is a 2 chain structure with sequence from Burkholderia multivorans ATCC 17616. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
| | Method: | X-ray diffraction, Resolution 1.911Å |
| Ligands: | , , , , , |
| Resources: | FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT |
Function
QUEE_BURM1 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]
Publication Abstract from PubMed
7-carboxy-7-deazaguanine synthase (QueE) catalyzes a key S-adenosyl-L-methionine (AdoMet)- and Mg(2+)-dependent radical-mediated ring contraction step, which is common to the biosynthetic pathways of all deazapurine-containing compounds. QueE is a member of the AdoMet radical superfamily, which employs the 5'-deoxyadenosyl radical from reductive cleavage of AdoMet to initiate chemistry. To provide a mechanistic rationale for this elaborate transformation, we present the crystal structure of a QueE along with structures of pre- and post-turnover states. We find that substrate binds perpendicular to the [4Fe-4S]-bound AdoMet, exposing its C6 hydrogen atom for abstraction and generating the binding site for Mg(2+), which coordinates directly to the substrate. The Burkholderia multivorans structure reported here varies from all other previously characterized members of the AdoMet radical superfamily in that it contains a hypermodified (beta6/alpha3) protein core and an expanded cluster-binding motif, CX14CX2C.
Radical SAM enzyme QueE defines a new minimal core fold and metal-dependent mechanism.,Dowling DP, Bruender NA, Young AP, McCarty RM, Bandarian V, Drennan CL Nat Chem Biol. 2014 Feb;10(2):106-12. doi: 10.1038/nchembio.1426. Epub 2013 Dec, 22. PMID:24362703[2]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
References
- ↑ Dowling DP, Bruender NA, Young AP, McCarty RM, Bandarian V, Drennan CL. Radical SAM enzyme QueE defines a new minimal core fold and metal-dependent mechanism. Nat Chem Biol. 2014 Feb;10(2):106-12. doi: 10.1038/nchembio.1426. Epub 2013 Dec, 22. PMID:24362703 doi:http://dx.doi.org/10.1038/nchembio.1426
- ↑ Dowling DP, Bruender NA, Young AP, McCarty RM, Bandarian V, Drennan CL. Radical SAM enzyme QueE defines a new minimal core fold and metal-dependent mechanism. Nat Chem Biol. 2014 Feb;10(2):106-12. doi: 10.1038/nchembio.1426. Epub 2013 Dec, 22. PMID:24362703 doi:http://dx.doi.org/10.1038/nchembio.1426
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