2g3f
From Proteopedia
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'''Crystal Structure of imidazolonepropionase complexed with imidazole-4-acetic acid sodium salt, a substrate homologue''' | '''Crystal Structure of imidazolonepropionase complexed with imidazole-4-acetic acid sodium salt, a substrate homologue''' | ||
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| + | ==Overview== | ||
| + | Imidazolonepropionase (EC 3.5.2.7) catalyzes the third step in the universal histidine degradation pathway, hydrolyzing the carbon-nitrogen bonds in 4-imidazolone-5-propionic acid to yield N-formimino-l-glutamic acid. Here we report the crystal structures of the Bacillus subtilis imidazolonepropionase and its complex at 2.0-A resolution with substrate analog imidazole-4-acetic acid sodium (I4AA). The structure of the native enzyme contains two domains, a TIM (triose-phosphate isomerase) barrel domain with two insertions and a small beta-sandwich domain. The TIM barrel domain is quite similar to the members of the alpha/beta barrel metallo-dependent hydrolase superfamily, especially to Escherichia coli cytosine deaminase. A metal ion was found in the central cavity of the TIM barrel and was tightly coordinated to residues His-80, His-82, His-249, Asp-324, and a water molecule. X-ray fluorescence scan analysis confirmed that the bound metal ion was a zinc ion. An acetate ion, 6 A away from the zinc ion, was also found in the potential active site. In the complex structure with I4AA, a substrate analog, I4AA replaced the acetate ion and contacted with Arg-89, Try-102, Tyr-152, His-185, and Glu-252, further defining and confirming the active site. The detailed structural studies allowed us to propose a zinc-activated nucleophilic attack mechanism for the hydrolysis reaction catalyzed by the enzyme. | ||
==About this Structure== | ==About this Structure== | ||
2G3F is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Bacillus_subtilis Bacillus subtilis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2G3F OCA]. | 2G3F is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Bacillus_subtilis Bacillus subtilis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2G3F OCA]. | ||
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| + | ==Reference== | ||
| + | A catalytic mechanism revealed by the crystal structures of the imidazolonepropionase from Bacillus subtilis., Yu Y, Liang YH, Brostromer E, Quan JM, Panjikar S, Dong YH, Su XD, J Biol Chem. 2006 Dec 1;281(48):36929-36. Epub 2006 Sep 21. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/16990261 16990261] | ||
[[Category: Bacillus subtilis]] | [[Category: Bacillus subtilis]] | ||
[[Category: Imidazolonepropionase]] | [[Category: Imidazolonepropionase]] | ||
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[[Category: Liang, Y H.]] | [[Category: Liang, Y H.]] | ||
[[Category: Su, X D.]] | [[Category: Su, X D.]] | ||
| - | [[Category: Yu, Y | + | [[Category: Yu, Y.]] |
| + | [[Category: Hydrolase]] | ||
[[Category: Tim barrel]] | [[Category: Tim barrel]] | ||
| - | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on | + | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Jun 18 12:15:01 2008'' |
Revision as of 09:15, 18 June 2008
Crystal Structure of imidazolonepropionase complexed with imidazole-4-acetic acid sodium salt, a substrate homologue
Overview
Imidazolonepropionase (EC 3.5.2.7) catalyzes the third step in the universal histidine degradation pathway, hydrolyzing the carbon-nitrogen bonds in 4-imidazolone-5-propionic acid to yield N-formimino-l-glutamic acid. Here we report the crystal structures of the Bacillus subtilis imidazolonepropionase and its complex at 2.0-A resolution with substrate analog imidazole-4-acetic acid sodium (I4AA). The structure of the native enzyme contains two domains, a TIM (triose-phosphate isomerase) barrel domain with two insertions and a small beta-sandwich domain. The TIM barrel domain is quite similar to the members of the alpha/beta barrel metallo-dependent hydrolase superfamily, especially to Escherichia coli cytosine deaminase. A metal ion was found in the central cavity of the TIM barrel and was tightly coordinated to residues His-80, His-82, His-249, Asp-324, and a water molecule. X-ray fluorescence scan analysis confirmed that the bound metal ion was a zinc ion. An acetate ion, 6 A away from the zinc ion, was also found in the potential active site. In the complex structure with I4AA, a substrate analog, I4AA replaced the acetate ion and contacted with Arg-89, Try-102, Tyr-152, His-185, and Glu-252, further defining and confirming the active site. The detailed structural studies allowed us to propose a zinc-activated nucleophilic attack mechanism for the hydrolysis reaction catalyzed by the enzyme.
About this Structure
2G3F is a Single protein structure of sequence from Bacillus subtilis. Full crystallographic information is available from OCA.
Reference
A catalytic mechanism revealed by the crystal structures of the imidazolonepropionase from Bacillus subtilis., Yu Y, Liang YH, Brostromer E, Quan JM, Panjikar S, Dong YH, Su XD, J Biol Chem. 2006 Dec 1;281(48):36929-36. Epub 2006 Sep 21. PMID:16990261 Page seeded by OCA on Wed Jun 18 12:15:01 2008
