1wkq
From Proteopedia
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|PDB= 1wkq |SIZE=350|CAPTION= <scene name='initialview01'>1wkq</scene>, resolution 1.17Å | |PDB= 1wkq |SIZE=350|CAPTION= <scene name='initialview01'>1wkq</scene>, resolution 1.17Å | ||
|SITE= | |SITE= | ||
| - | |LIGAND= <scene name='pdbligand= | + | |LIGAND= <scene name='pdbligand=IMD:IMIDAZOLE'>IMD</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene> |
| - | |ACTIVITY= [http://en.wikipedia.org/wiki/Guanine_deaminase Guanine deaminase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.5.4.3 3.5.4.3] | + | |ACTIVITY= <span class='plainlinks'>[http://en.wikipedia.org/wiki/Guanine_deaminase Guanine deaminase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.5.4.3 3.5.4.3] </span> |
|GENE= guanine deaminase ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1423 Bacillus subtilis]) | |GENE= guanine deaminase ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1423 Bacillus subtilis]) | ||
| + | |DOMAIN= | ||
| + | |RELATEDENTRY= | ||
| + | |RESOURCES=<span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1wkq FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1wkq OCA], [http://www.ebi.ac.uk/pdbsum/1wkq PDBsum], [http://www.rcsb.org/pdb/explore.do?structureId=1wkq RCSB]</span> | ||
}} | }} | ||
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[[Category: Lai, C T.]] | [[Category: Lai, C T.]] | ||
[[Category: Liaw, S H.]] | [[Category: Liaw, S H.]] | ||
| - | [[Category: IMD]] | ||
| - | [[Category: ZN]] | ||
[[Category: domain swap]] | [[Category: domain swap]] | ||
[[Category: guanine deaminase]] | [[Category: guanine deaminase]] | ||
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[[Category: the cytidine deaminase superfamily]] | [[Category: the cytidine deaminase superfamily]] | ||
| - | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on | + | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Mon Mar 31 00:37:33 2008'' |
Revision as of 21:37, 30 March 2008
| |||||||
| , resolution 1.17Å | |||||||
|---|---|---|---|---|---|---|---|
| Ligands: | , | ||||||
| Gene: | guanine deaminase (Bacillus subtilis) | ||||||
| Activity: | Guanine deaminase, with EC number 3.5.4.3 | ||||||
| Resources: | FirstGlance, OCA, PDBsum, RCSB | ||||||
| Coordinates: | save as pdb, mmCIF, xml | ||||||
Crystal Structure of Bacillus subtilis Guanine Deaminase. The first domain-swapped structure in the cytidine deaminase superfamily
Overview
Guanine deaminase, a key enzyme in the nucleotide metabolism, catalyzes the hydrolytic deamination of guanine into xanthine. The crystal structure of the 156-residue guanine deaminase from Bacillus subtilis has been solved at 1.17-A resolution. Unexpectedly, the C-terminal segment is swapped to form an intersubunit active site and an intertwined dimer with an extensive interface of 3900 A(2) per monomer. The essential zinc ion is ligated by a water molecule together with His(53), Cys(83), and Cys(86). A transition state analog was modeled into the active site cavity based on the tightly bound imidazole and water molecules, allowing identification of the conserved deamination mechanism and specific substrate recognition by Asp(114) and Tyr(156'). The closed conformation also reveals that substrate binding seals the active site entrance, which is controlled by the C-terminal tail. Therefore, the domain swapping has not only facilitated the dimerization but has also ensured specific substrate recognition. Finally, a detailed structural comparison of the cytidine deaminase superfamily illustrates the functional versatility of the divergent active sites found in the guanine, cytosine, and cytidine deaminases and suggests putative specific substrate-interacting residues for other members such as dCMP deaminases.
About this Structure
1WKQ is a Single protein structure of sequence from Bacillus subtilis. Full crystallographic information is available from OCA.
Reference
Crystal structure of Bacillus subtilis guanine deaminase: the first domain-swapped structure in the cytidine deaminase superfamily., Liaw SH, Chang YJ, Lai CT, Chang HC, Chang GG, J Biol Chem. 2004 Aug 20;279(34):35479-85. Epub 2004 Jun 4. PMID:15180998
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