1a82
From Proteopedia
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|PDB= 1a82 |SIZE=350|CAPTION= <scene name='initialview01'>1a82</scene>, resolution 1.8Å | |PDB= 1a82 |SIZE=350|CAPTION= <scene name='initialview01'>1a82</scene>, resolution 1.8Å | ||
|SITE= | |SITE= | ||
| - | |LIGAND= <scene name='pdbligand= | + | |LIGAND= <scene name='pdbligand=ATP:ADENOSINE-5'-TRIPHOSPHATE'>ATP</scene>, <scene name='pdbligand=DNN:7,8-DIAMINO-NONANOIC+ACID'>DNN</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene> |
| - | |ACTIVITY= [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] | + | |ACTIVITY= <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> |
|GENE= | |GENE= | ||
| + | |DOMAIN= | ||
| + | |RELATEDENTRY= | ||
| + | |RESOURCES=<span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1a82 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1a82 OCA], [http://www.ebi.ac.uk/pdbsum/1a82 PDBsum], [http://www.rcsb.org/pdb/explore.do?structureId=1a82 RCSB]</span> | ||
}} | }} | ||
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[[Category: Lindqvist, Y.]] | [[Category: Lindqvist, Y.]] | ||
[[Category: Schneider, G.]] | [[Category: Schneider, G.]] | ||
| - | [[Category: ATP]] | ||
| - | [[Category: DNN]] | ||
| - | [[Category: MG]] | ||
[[Category: atp]] | [[Category: atp]] | ||
[[Category: biotin biosynthesis]] | [[Category: biotin biosynthesis]] | ||
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[[Category: phosphoryl transfer]] | [[Category: phosphoryl transfer]] | ||
| - | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sun Mar | + | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sun Mar 30 18:35:15 2008'' |
Revision as of 15:35, 30 March 2008
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| , resolution 1.8Å | |||||||
|---|---|---|---|---|---|---|---|
| Ligands: | , , | ||||||
| Activity: | Dethiobiotin synthase, with EC number 6.3.3.3 | ||||||
| Resources: | FirstGlance, OCA, PDBsum, RCSB | ||||||
| Coordinates: | save as pdb, mmCIF, xml | ||||||
DETHIOBIOTIN SYNTHETASE FROM ESCHERICHIA COLI, COMPLEX WITH SUBSTRATES ATP AND DIAMINOPELARGONIC ACID
Overview
The ATP-dependent enzyme dethiobiotin synthetase from Escherichia coli catalyses the formation of dethiobiotin from CO2 and 7, 8-diaminopelargonic acid. The reaction is initiated by the formation of a carbamate and proceeds through a phosphorylated intermediate, a mixed carbamic phosphoric anhydride. Here, we report the crystal structures at 1.9- and 1.6-A resolution, respectively, of the enzyme-MgATP-diaminopelargonic acid and enzyme-MgADP-carbamic-phosphoric acid anhydride complexes, observed by using kinetic crystallography. Reaction initiation by addition of either NaHCO3 or diaminopelargonic acid to crystals already containing cosubstrates resulted in the accumulation of the phosphorylated intermediate at the active site. The phosphoryl transfer step shows inversion of the configuration at the phosphorus atom, consistent with an in-line attack by the carbamate oxygen onto the phosphorus atom of ATP. A key feature in the structure of the complex of the enzyme with the reaction intermediate is two magnesium ions, bridging the phosphates at the cleavage site. These magnesium ions compensate the negative charges at both phosphate groups after phosphoryl transfer and contribute to the stabilization of the reaction intermediate.
About this Structure
1A82 is a Single protein structure of sequence from Escherichia coli. Full crystallographic information is available from OCA.
Reference
Snapshot of a phosphorylated substrate intermediate by kinetic crystallography., Kack H, Gibson KJ, Lindqvist Y, Schneider G, Proc Natl Acad Sci U S A. 1998 May 12;95(10):5495-500. PMID:9576910
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