1q3k
From Proteopedia
(New page: 200px<br /><applet load="1q3k" size="450" color="white" frame="true" align="right" spinBox="true" caption="1q3k, resolution 2.10Å" /> '''Crystal structure of...) |
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| - | [[Image:1q3k.jpg|left|200px]]<br /><applet load="1q3k" size=" | + | [[Image:1q3k.jpg|left|200px]]<br /><applet load="1q3k" size="350" color="white" frame="true" align="right" spinBox="true" |
caption="1q3k, resolution 2.10Å" /> | caption="1q3k, resolution 2.10Å" /> | ||
'''Crystal structure of creatinine amidohydrolase (creatininase)'''<br /> | '''Crystal structure of creatinine amidohydrolase (creatininase)'''<br /> | ||
==Overview== | ==Overview== | ||
| - | Creatinine amidohydrolase (creatininase; EC 3.5.2.10) from Pseudomonas | + | Creatinine amidohydrolase (creatininase; EC 3.5.2.10) from Pseudomonas putida, a homohexameric enzyme with a molecular mass of 28.4 kDa per subunit, is a cyclic amidohydrolase catalysing the reversible conversion of creatinine to creatine. The enzyme plays a key role in the bacterial degradation of creatinine. The three-dimensional structure of creatininase from P.putida was determined and refined to 2.1A. The structure shows the six subunits arranged as a trimer of dimers and definitely disproves previous reports that the enzyme has an octameric quaternary structure. Each monomer consists of a central, four-stranded, parallel beta-sheet flanked by two alpha-helices on both sides of the beta-sheet. This topology is unique within the superfamily of amidohydrolases. Moreover, creatininase possesses a novel fold with no close structural relatives within the Protein Data Bank. Each creatininase monomer contains a binuclear zinc centre near the C termini of the beta-strands and the N termini of the main alpha-helices. These zinc ions indicate the location of the active site unambiguously. The active site is entirely buried and is not accessible from the solution without movement of parts of the protein. The two zinc ions are bridged by a water molecule and by an aspartate residue, which acts as a bidentate ligand. They differ from each other in the number and the spatial arrangement of their ligands. One of them is tetrahedrally and the other trigonal-bipyramidally ligated. Using two water molecules of the first coordination sphere as anchor points, a creatinine-water adduct resembling the transition state of the hydrolysation reaction was modelled into the active site. The resulting complex in combination with structural comparisons with other amidohydrolases enabled us to identify the most probable candidate for the catalytic base and to suggest a putative reaction mechanism. Surprisingly these structural comparisons revealed a similarity in the active-site arrangement between creatininase and the hydantoinase-like cyclic amidohydrolases that was unexpected, given the completely unrelated primary and tertiary structures. In particular, the zinc-bridging aspartate residue of creatininase is a spatially and functionally analogue to a carboxylated lysine residue found in dihydroorotase and the hydantoinases. Hence, creatininase and the hydantoinase-like cyclic amidohydrolases represent a further example of convergent evolution within the enzyme class of hydrolases. |
==About this Structure== | ==About this Structure== | ||
| - | 1Q3K is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Pseudomonas_putida Pseudomonas putida] with ZN and GOL as [http://en.wikipedia.org/wiki/ligands ligands]. Active as [http://en.wikipedia.org/wiki/Creatininase Creatininase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.5.2.10 3.5.2.10] Full crystallographic information is available from [http:// | + | 1Q3K is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Pseudomonas_putida Pseudomonas putida] with <scene name='pdbligand=ZN:'>ZN</scene> and <scene name='pdbligand=GOL:'>GOL</scene> as [http://en.wikipedia.org/wiki/ligands ligands]. Active as [http://en.wikipedia.org/wiki/Creatininase Creatininase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.5.2.10 3.5.2.10] Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1Q3K OCA]. |
==Reference== | ==Reference== | ||
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[[Category: alpha-beta-fold]] | [[Category: alpha-beta-fold]] | ||
| - | ''Page seeded by [http:// | + | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Feb 21 14:35:33 2008'' |
Revision as of 12:35, 21 February 2008
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Crystal structure of creatinine amidohydrolase (creatininase)
Overview
Creatinine amidohydrolase (creatininase; EC 3.5.2.10) from Pseudomonas putida, a homohexameric enzyme with a molecular mass of 28.4 kDa per subunit, is a cyclic amidohydrolase catalysing the reversible conversion of creatinine to creatine. The enzyme plays a key role in the bacterial degradation of creatinine. The three-dimensional structure of creatininase from P.putida was determined and refined to 2.1A. The structure shows the six subunits arranged as a trimer of dimers and definitely disproves previous reports that the enzyme has an octameric quaternary structure. Each monomer consists of a central, four-stranded, parallel beta-sheet flanked by two alpha-helices on both sides of the beta-sheet. This topology is unique within the superfamily of amidohydrolases. Moreover, creatininase possesses a novel fold with no close structural relatives within the Protein Data Bank. Each creatininase monomer contains a binuclear zinc centre near the C termini of the beta-strands and the N termini of the main alpha-helices. These zinc ions indicate the location of the active site unambiguously. The active site is entirely buried and is not accessible from the solution without movement of parts of the protein. The two zinc ions are bridged by a water molecule and by an aspartate residue, which acts as a bidentate ligand. They differ from each other in the number and the spatial arrangement of their ligands. One of them is tetrahedrally and the other trigonal-bipyramidally ligated. Using two water molecules of the first coordination sphere as anchor points, a creatinine-water adduct resembling the transition state of the hydrolysation reaction was modelled into the active site. The resulting complex in combination with structural comparisons with other amidohydrolases enabled us to identify the most probable candidate for the catalytic base and to suggest a putative reaction mechanism. Surprisingly these structural comparisons revealed a similarity in the active-site arrangement between creatininase and the hydantoinase-like cyclic amidohydrolases that was unexpected, given the completely unrelated primary and tertiary structures. In particular, the zinc-bridging aspartate residue of creatininase is a spatially and functionally analogue to a carboxylated lysine residue found in dihydroorotase and the hydantoinases. Hence, creatininase and the hydantoinase-like cyclic amidohydrolases represent a further example of convergent evolution within the enzyme class of hydrolases.
About this Structure
1Q3K is a Single protein structure of sequence from Pseudomonas putida with and as ligands. Active as Creatininase, with EC number 3.5.2.10 Full crystallographic information is available from OCA.
Reference
Crystal structure of creatininase from Pseudomonas putida: a novel fold and a case of convergent evolution., Beuth B, Niefind K, Schomburg D, J Mol Biol. 2003 Sep 5;332(1):287-301. PMID:12946365
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