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3mle

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Revision as of 09:56, 13 April 2022

Crystal structure of dethiobiotin synthetase (BioD) from Helicobacter pylori cocrystallized with ATP

Structural highlights

3mle is a 6 chain structure with sequence from Campylobacter pylori. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Ligands:	, , , , ,
Gene:	bioD, HP0029, HP_0029 (Campylobacter pylori)
Activity:	Dethiobiotin synthase, with EC number 6.3.3.3
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.

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

1 Structural highlights
2 Function
3 Evolutionary Conservation
4 Publication Abstract from PubMed
5 See Also
6 References

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/3mle"

@@ Line 1: / Line 1: @@
 ==Crystal structure of dethiobiotin synthetase (BioD) from Helicobacter pylori cocrystallized with ATP==
-<StructureSection load='3mle' size='340' side='right' caption='[[3mle]], [[Resolution|resolution]] 2.80&Aring;' scene=''>
+<StructureSection load='3mle' size='340' side='right'caption='[[3mle]], [[Resolution|resolution]] 2.80&Aring;' scene=''>
 == 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/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 [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='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='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='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">bioD, HP0029, HP_0029 ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=85962 Campylobacter pylori])</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='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/Dethiobiotin_synthase Dethiobiotin synthase], with EC number [https://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'>[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>
+<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>
 </table>
 == 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 ==
 [[Image:Consurf_key_small.gif|200px|right]]
@@ Line 32: / Line 32: @@
 ==See Also==
-*[[Dethiobiotin synthetase|Dethiobiotin synthetase]]
+*[[Dethiobiotin synthetase 3D structures|Dethiobiotin synthetase 3D structures]]
 == References ==
 <references/>
@@ Line 39: / Line 39: @@
 [[Category: Campylobacter pylori]]
 [[Category: Dethiobiotin synthase]]
+[[Category: Large Structures]]
 [[Category: Chruszcz, M]]
 [[Category: Joachimiak, A]]

3mle

From Proteopedia

Revision as of 09:56, 13 April 2022

Crystal structure of dethiobiotin synthetase (BioD) from Helicobacter pylori cocrystallized with ATP

Structural highlights

Function

Evolutionary Conservation

Publication Abstract from PubMed

See Also

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

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