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| | <StructureSection load='4wop' size='340' side='right'caption='[[4wop]], [[Resolution|resolution]] 2.39Å' scene=''> | | <StructureSection load='4wop' size='340' side='right'caption='[[4wop]], [[Resolution|resolution]] 2.39Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[4wop]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Mycta Mycta]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4WOP OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4WOP FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[4wop]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Mycobacterium_tuberculosis_H37Ra Mycobacterium tuberculosis H37Ra]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4WOP OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4WOP FirstGlance]. <br> |
| - | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CTP:CYTIDINE-5-TRIPHOSPHATE'>CTP</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</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]] 2.393Å</td></tr> |
| - | <tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">bioD, MRA_1582 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=419947 MYCTA])</td></tr> | + | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CTP:CYTIDINE-5-TRIPHOSPHATE'>CTP</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr> |
| - | <tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Dethiobiotin_synthase Dethiobiotin synthase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=6.3.3.3 6.3.3.3] </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=4wop FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4wop OCA], [https://pdbe.org/4wop PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4wop RCSB], [https://www.ebi.ac.uk/pdbsum/4wop PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4wop ProSAT]</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=4wop FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4wop OCA], [http://pdbe.org/4wop PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4wop RCSB], [http://www.ebi.ac.uk/pdbsum/4wop PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4wop ProSAT]</span></td></tr> | + | |
| | </table> | | </table> |
| | == Function == | | == Function == |
| - | [[http://www.uniprot.org/uniprot/BIOD_MYCTA BIOD_MYCTA]] Catalyzes a mechanistically unusual reaction, the ATP-dependent insertion of CO2 between the N7 and N8 nitrogen atoms of 7,8-diaminopelargonic acid (DAPA) to form an ureido ring. | + | [https://www.uniprot.org/uniprot/BIOD_MYCTU BIOD_MYCTU] Catalyzes a mechanistically unusual reaction, the ATP-dependent insertion of CO2 between the N7 and N8 nitrogen atoms of 7,8-diaminopelargonic acid (DAPA) to form an ureido ring.<ref>PMID:20565114</ref> |
| | <div style="background-color:#fffaf0;"> | | <div style="background-color:#fffaf0;"> |
| | == Publication Abstract from PubMed == | | == Publication Abstract from PubMed == |
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| | | | |
| | ==See Also== | | ==See Also== |
| - | *[[Dethiobiotin synthetase|Dethiobiotin synthetase]] | + | *[[Dethiobiotin synthetase 3D structures|Dethiobiotin synthetase 3D structures]] |
| | == References == | | == References == |
| | <references/> | | <references/> |
| | __TOC__ | | __TOC__ |
| | </StructureSection> | | </StructureSection> |
| - | [[Category: Dethiobiotin synthase]] | |
| | [[Category: Large Structures]] | | [[Category: Large Structures]] |
| - | [[Category: Mycta]] | + | [[Category: Mycobacterium tuberculosis H37Ra]] |
| - | [[Category: Booker, G W]] | + | [[Category: Booker GW]] |
| - | [[Category: Polyak, S W]] | + | [[Category: Polyak SW]] |
| - | [[Category: Salaemae, W]] | + | [[Category: Salaemae W]] |
| - | [[Category: Wegener, K L]] | + | [[Category: Wegener KL]] |
| - | [[Category: Wilce, M C.J]] | + | [[Category: Wilce MCJ]] |
| - | [[Category: Yap, M Y]] | + | [[Category: Yap MY]] |
| - | [[Category: Biotin protein ligase]]
| + | |
| - | [[Category: Ligase]]
| + | |
| Structural highlights
Function
BIOD_MYCTU Catalyzes a mechanistically unusual reaction, the ATP-dependent insertion of CO2 between the N7 and N8 nitrogen atoms of 7,8-diaminopelargonic acid (DAPA) to form an ureido ring.[1]
Publication Abstract from PubMed
Dethiobiotin synthetase (DTBS) plays a crucial role in biotin biosynthesis in microorganisms, fungi, and plants. Due to its importance in bacterial pathogenesis, and the absence of a human homologue, DTBS is a promising target for the development of new antibacterials desperately needed to combat antibiotic resistance. Here we report the first X-ray structure of DTBS from Mycobacterium tuberculosis (MtDTBS) bound to a nucleotide triphosphate (CTP). The nucleoside base is stabilized in its pocket through hydrogen-bonding interactions with the protein backbone, rather than amino acid side chains. This resulted in the unexpected finding that MtDTBS could utilise ATP, CTP, GTP, ITP, TTP, or UTP with similar Km and kcat values, although the enzyme had the highest affinity for CTP in competitive binding and surface plasmon resonance assays. This is in contrast to other DTBS homologues that preferentially bind ATP primarily through hydrogen-bonds between the purine base and the carboxamide side chain of a key asparagine. Mutational analysis performed alongside in silico experiments revealed a gate-keeper role for Asn175 in Escherichia coli DTBS that excludes binding of other nucleotide triphosphates. Here we provide evidence to show that MtDTBS has a broad nucleotide specificity due to the absence of the gate-keeper residue.
Nucleotide triphosphate promiscuity in Mycobacterium tuberculosis dethiobiotin synthetase.,Salaemae W, Yap MY, Wegener KL, Booker GW, Wilce MC, Polyak SW Tuberculosis (Edinb). 2015 Mar 6. pii: S1472-9792(15)20712-3. doi:, 10.1016/j.tube.2015.02.046. PMID:25801336[2]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
See Also
References
- ↑ Dey S, Lane JM, Lee RE, Rubin EJ, Sacchettini JC. Structural characterization of the Mycobacterium tuberculosis biotin biosynthesis enzymes 7,8-diaminopelargonic acid synthase and dethiobiotin synthetase . Biochemistry. 2010 Aug 10;49(31):6746-60. PMID:20565114 doi:10.1021/bi902097j
- ↑ Salaemae W, Yap MY, Wegener KL, Booker GW, Wilce MC, Polyak SW. Nucleotide triphosphate promiscuity in Mycobacterium tuberculosis dethiobiotin synthetase. Tuberculosis (Edinb). 2015 Mar 6. pii: S1472-9792(15)20712-3. doi:, 10.1016/j.tube.2015.02.046. PMID:25801336 doi:http://dx.doi.org/10.1016/j.tube.2015.02.046
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