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| | ==Crystal structure of dethiobiotin synthetase (BioD) from Helicobacter pylori cocrystallized with ATP== | | ==Crystal structure of dethiobiotin synthetase (BioD) from Helicobacter pylori cocrystallized with ATP== |
| - | <StructureSection load='3mle' size='340' side='right' caption='[[3mle]], [[Resolution|resolution]] 2.80Å' scene=''> | + | <StructureSection load='3mle' size='340' side='right'caption='[[3mle]], [[Resolution|resolution]] 2.80Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[3mle]] is a 6 chain structure with sequence from [http://en.wikipedia.org/wiki/Campylobacter_pylori Campylobacter pylori]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3MLE OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3MLE FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[3mle]] is a 6 chain structure with sequence from [https://en.wikipedia.org/wiki/Helicobacter_pylori_26695 Helicobacter pylori 26695]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3MLE OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3MLE FirstGlance]. <br> |
| - | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=8AC:8-AMINOOCTANOIC+ACID'>8AC</scene>, <scene name='pdbligand=ADP:ADENOSINE-5-DIPHOSPHATE'>ADP</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=NO3:NITRATE+ION'>NO3</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</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]] 2.8Å</td></tr> |
| - | <tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">bioD, HP0029, HP_0029 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=85962 Campylobacter pylori])</td></tr>
| + | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=8AC:8-AMINOOCTANOIC+ACID'>8AC</scene>, <scene name='pdbligand=ADP:ADENOSINE-5-DIPHOSPHATE'>ADP</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=NO3:NITRATE+ION'>NO3</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</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=3mle FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3mle OCA], [https://pdbe.org/3mle PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3mle RCSB], [https://www.ebi.ac.uk/pdbsum/3mle PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3mle 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=3mle FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3mle OCA], [http://pdbe.org/3mle PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3mle RCSB], [http://www.ebi.ac.uk/pdbsum/3mle PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=3mle ProSAT]</span></td></tr> | + | |
| | </table> | | </table> |
| | == Function == | | == Function == |
| - | [[http://www.uniprot.org/uniprot/BIOD_HELPY BIOD_HELPY]] 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 (By similarity).[HAMAP-Rule:MF_00336] | + | [https://www.uniprot.org/uniprot/BIOD_HELPY BIOD_HELPY] 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 (By similarity).[HAMAP-Rule:MF_00336] |
| | == Evolutionary Conservation == | | == Evolutionary Conservation == |
| | [[Image:Consurf_key_small.gif|200px|right]] | | [[Image:Consurf_key_small.gif|200px|right]] |
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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: Campylobacter pylori]] | + | [[Category: Helicobacter pylori 26695]] |
| - | [[Category: Dethiobiotin synthase]] | + | [[Category: Large Structures]] |
| - | [[Category: Chruszcz, M]] | + | [[Category: Chruszcz M]] |
| - | [[Category: Joachimiak, A]] | + | [[Category: Joachimiak A]] |
| - | [[Category: Klimecka, M M]] | + | [[Category: Klimecka MM]] |
| - | [[Category: Structural genomic]]
| + | [[Category: Minor W]] |
| - | [[Category: Minor, W]] | + | [[Category: Murshudov G]] |
| - | [[Category: Murshudov, G]] | + | [[Category: Murzyn K]] |
| - | [[Category: Murzyn, K]] | + | [[Category: Nicholls R]] |
| - | [[Category: Nicholls, R]] | + | [[Category: Porebski PJ]] |
| - | [[Category: Porebski, P J]] | + | |
| - | [[Category: Dethiobiotin synthetase]]
| + | |
| - | [[Category: Dtb]]
| + | |
| - | [[Category: Ligase]]
| + | |
| - | [[Category: Mcsg]]
| + | |
| - | [[Category: PSI, Protein structure initiative]]
| + | |
| Structural highlights
3mle is a 6 chain structure with sequence from Helicobacter pylori 26695. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
| | Method: | X-ray diffraction, Resolution 2.8Å |
| Ligands: | , , , , , |
| Resources: | FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT |
Function
BIOD_HELPY 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 (By similarity).[HAMAP-Rule:MF_00336]
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
Dethiobiotin synthetase (DTBS) is involved in the biosynthesis of biotin in bacteria, fungi, and plants. As humans lack this pathway, DTBS is a promising antimicrobial drug target. We determined structures of DTBS from Helicobacter pylori (hpDTBS) bound with cofactors and a substrate analog, and described its unique characteristics relative to other DTBS proteins. Comparison with bacterial DTBS orthologs revealed considerable structural differences in nucleotide recognition. The C-terminal region of DTBS proteins, which contains two nucleotide-recognition motifs, differs greatly among DTBS proteins from different species. The structure of hpDTBS revealed that this protein is unique and does not contain a C-terminal region containing one of the motifs. The single nucleotide-binding motif in hpDTBS is similar to its counterpart in GTPases; however, isothermal titration calorimetry binding studies showed that hpDTBS has a strong preference for ATP. The structural determinants of ATP specificity were assessed with X-ray crystallographic studies of hpDTBS.ATP and hpDTBS.GTP complexes. The unique mode of nucleotide recognition in hpDTBS makes this protein a good target for H. pylori-specific inhibitors of the biotin synthesis pathway. Database Coordinates and structure factors for structures presented in this article have been deposited in the Protein Data Bank under the following accession codes: 2QMO - apo-form; 3MLE - hpDTBS.8-ac.ADP. in P2(1) 2(1) 2(1) form; 3QXC - hpDTBS.ATP; 3QXH - hpDTBS.8-ac:ADP. in C2 form; 3QXJ - hpDTBS.GTP; 3QXS - hpDTBS.ANP; 3QXX - 8-ac.GDP.; and 3QY0 - hpDTBS.GDP.. Structured digital abstract * hpDTBS and hpDTBS bind by x-ray crystallography (View interaction).
Structural characterization of Helicobacter pylori dethiobiotin synthetase reveals differences between family members.,Porebski PJ, Klimecka M, Chruszcz M, Nicholls RA, Murzyn K, Cuff ME, Xu X, Cymborowski M, Murshudov GN, Savchenko A, Edwards A, Minor W FEBS J. 2012 Jan 27. doi: 10.1111/j.1742-4658.2012.08506.x. PMID:22284390[1]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
See Also
References
- ↑ Porebski PJ, Klimecka M, Chruszcz M, Nicholls RA, Murzyn K, Cuff ME, Xu X, Cymborowski M, Murshudov GN, Savchenko A, Edwards A, Minor W. Structural characterization of Helicobacter pylori dethiobiotin synthetase reveals differences between family members. FEBS J. 2012 Jan 27. doi: 10.1111/j.1742-4658.2012.08506.x. PMID:22284390 doi:10.1111/j.1742-4658.2012.08506.x
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