1bs1: Difference between revisions

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New page: left|200px<br /><applet load="1bs1" size="450" color="white" frame="true" align="right" spinBox="true" caption="1bs1, resolution 1.8Å" /> '''DETHIOBIOTIN SYNTHETA...
 
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[[Image:1bs1.jpg|left|200px]]<br /><applet load="1bs1" size="450" color="white" frame="true" align="right" spinBox="true"
caption="1bs1, resolution 1.8&Aring;" />
'''DETHIOBIOTIN SYNTHETASE COMPLEXED WITH DETHIOBIOTIN, ADP , INORGANIC PHOSPHATE AND MAGNESIUM'''<br />


==Overview==
==DETHIOBIOTIN SYNTHETASE COMPLEXED WITH DETHIOBIOTIN, ADP , INORGANIC PHOSPHATE AND MAGNESIUM==
The crystal structures of two complexes of dethiobiotin synthetase, enzyme-diaminopelargonic acid-MgADP-AlF3 and enzyme-dethiobiotin-MgADP-Pi, respectively, have been determined to 1.8 A resolution. In dethiobiotin, synthetase, AlF3 together with carbamylated diaminopelargonic acid mimics, the phosphorylated reaction intermediate rather than the transition state, complex for phosphoryl transfer. Observed differences in the binding of, substrate, diaminopelargonic acid, and the product, dethiobiotin, suggest, considerable displacements of substrate atoms during the ring closure step, of the catalytic reaction. In both complexes, two metal ions are observed, at the active site, providing evidence for a two-metal mechanism for this, enzyme.
<StructureSection load='1bs1' size='340' side='right'caption='[[1bs1]], [[Resolution|resolution]] 1.80&Aring;' scene=''>
== Structural highlights ==
<table><tr><td colspan='2'>[[1bs1]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1BS1 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1BS1 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]] 1.8&#8491;</td></tr>
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ADP:ADENOSINE-5-DIPHOSPHATE'>ADP</scene>, <scene name='pdbligand=DAA:8-AMINO-7-CARBOXYAMINO-NONANOIC+ACID+WITH+ALUMINUM+FLUORIDE'>DAA</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</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=1bs1 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1bs1 OCA], [https://pdbe.org/1bs1 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1bs1 RCSB], [https://www.ebi.ac.uk/pdbsum/1bs1 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1bs1 ProSAT]</span></td></tr>
</table>
== Function ==
[https://www.uniprot.org/uniprot/BIOD1_ECOLI BIOD1_ECOLI] 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. Only CTP can partially replace ATP while diaminobiotin is only 37% as effective as 7,8-diaminopelargonic acid.<ref>PMID:4892372</ref> <ref>PMID:4921568</ref>
== Evolutionary Conservation ==
[[Image:Consurf_key_small.gif|200px|right]]
Check<jmol>
  <jmolCheckbox>
    <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/bs/1bs1_consurf.spt"</scriptWhenChecked>
    <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
    <text>to colour the structure by Evolutionary Conservation</text>
  </jmolCheckbox>
</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=1bs1 ConSurf].
<div style="clear:both"></div>


==About this Structure==
==See Also==
1BS1 is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli] with MG, ADP and DAA as [http://en.wikipedia.org/wiki/ligands ligands]. Active as [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] Full crystallographic information is available from [http://ispc.weizmann.ac.il/oca-bin/ocashort?id=1BS1 OCA].
*[[Dethiobiotin synthetase 3D structures|Dethiobiotin synthetase 3D structures]]
 
== References ==
==Reference==
<references/>
Crystal structure of two quaternary complexes of dethiobiotin synthetase, enzyme-MgADP-AlF3-diaminopelargonic acid and enzyme-MgADP-dethiobiotin-phosphate; implications for catalysis., Kack H, Sandmark J, Gibson KJ, Schneider G, Lindqvist Y, Protein Sci. 1998 Dec;7(12):2560-6. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=9865950 9865950]
__TOC__
[[Category: Dethiobiotin synthase]]
</StructureSection>
[[Category: Escherichia coli]]
[[Category: Escherichia coli]]
[[Category: Single protein]]
[[Category: Large Structures]]
[[Category: Gibson, K.J.]]
[[Category: Gibson KJ]]
[[Category: Kaeck, H.]]
[[Category: Kaeck H]]
[[Category: Lindqvist, Y.]]
[[Category: Lindqvist Y]]
[[Category: Sandmark, J.]]
[[Category: Sandmark J]]
[[Category: Schneider, G.]]
[[Category: Schneider G]]
[[Category: ADP]]
[[Category: DAA]]
[[Category: MG]]
[[Category: aluminum flouride]]
[[Category: atp-binding]]
[[Category: biotin biosynthesis]]
[[Category: ligase]]
[[Category: phosphoryl transfer]]
 
''Page seeded by [http://ispc.weizmann.ac.il/oca OCA ] on Tue Nov 20 11:52:22 2007''

Latest revision as of 09:38, 7 February 2024

DETHIOBIOTIN SYNTHETASE COMPLEXED WITH DETHIOBIOTIN, ADP , INORGANIC PHOSPHATE AND MAGNESIUMDETHIOBIOTIN SYNTHETASE COMPLEXED WITH DETHIOBIOTIN, ADP , INORGANIC PHOSPHATE AND MAGNESIUM

Structural highlights

1bs1 is a 1 chain structure with sequence from Escherichia coli. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:X-ray diffraction, Resolution 1.8Å
Ligands:, ,
Resources:FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

BIOD1_ECOLI 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. Only CTP can partially replace ATP while diaminobiotin is only 37% as effective as 7,8-diaminopelargonic acid.[1] [2]

Evolutionary Conservation

Check, as determined by ConSurfDB. You may read the explanation of the method and the full data available from ConSurf.

See Also

References

  1. ↑ Eisenberg MA, Krell K. Synthesis of desthiobiotin from 7,8-diaminopelargonic acid in biotin auxotrophs of Escherichia coli K-12. J Bacteriol. 1969 Jun;98(3):1227-31. PMID:4892372
  2. ↑ Krell K, Eisenberg MA. The purification and properties of dethiobiotin synthetase. J Biol Chem. 1970 Dec 25;245(24):6558-66. PMID:4921568

1bs1, resolution 1.80Å

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