1qae
From Proteopedia
(New page: 200px<br /><applet load="1qae" size="450" color="white" frame="true" align="right" spinBox="true" caption="1qae, resolution 2.05Å" /> '''THE ACTIVE SITE OF S...) |
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| - | [[Image:1qae.gif|left|200px]]<br /><applet load="1qae" size=" | + | [[Image:1qae.gif|left|200px]]<br /><applet load="1qae" size="350" color="white" frame="true" align="right" spinBox="true" |
caption="1qae, resolution 2.05Å" /> | caption="1qae, resolution 2.05Å" /> | ||
'''THE ACTIVE SITE OF SERRATIA ENDONUCLEASE CONTAINS A CONSERVED MAGNESIUM-WATER CLUSTER'''<br /> | '''THE ACTIVE SITE OF SERRATIA ENDONUCLEASE CONTAINS A CONSERVED MAGNESIUM-WATER CLUSTER'''<br /> | ||
==Overview== | ==Overview== | ||
| - | Serratia endonuclease is an important member of a class of magnesium | + | Serratia endonuclease is an important member of a class of magnesium dependent nucleases that are widely distributed in nature. Here, we describe the location and geometry of a magnesium-water cluster within the active site of this enzyme. The sole protein ligand of the magnesium atom is Asn119; this metal ion is also associated with five water molecules to complete an octahedral coordination complex. These water molecules are very well ordered and there is no evidence of rotational disorder or motion. Glu127 and His89 are located nearby and each is hydrogen bonded to water molecules in the coordination sphere. Asp86 is not chelated to the magnesium or its surrounding water molecules. Results of kinetics and site-specific mutagenesis experiments suggest that this metal-water cluster contains the catalytic metal ion of this enzyme. All residues which hydrogen bond to the water molecules that coordinate the magnesium atom are conserved in nucleases homologous to Serratia endonuclease, suggesting that the water cluster is a conserved feature of this family of enzymes. We offer a detailed structural comparison to one other nuclease, the homing endonuclease I-PpoI, that has recently been shown, in spite of a lack of sequence homology, to share a similar active site geometry to Serratia endonuclease. Evidence from both of these structures suggests that the magnesium of Serratia nuclease participates in catalysis via an inner sphere mechanism. |
==About this Structure== | ==About this Structure== | ||
| - | 1QAE is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Serratia_marcescens Serratia marcescens] with MG as [http://en.wikipedia.org/wiki/ligand ligand]. Active as [http://en.wikipedia.org/wiki/Serratia_marcescens_nuclease Serratia marcescens nuclease], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.1.30.2 3.1.30.2] Full crystallographic information is available from [http:// | + | 1QAE is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Serratia_marcescens Serratia marcescens] with <scene name='pdbligand=MG:'>MG</scene> as [http://en.wikipedia.org/wiki/ligand ligand]. Active as [http://en.wikipedia.org/wiki/Serratia_marcescens_nuclease Serratia marcescens nuclease], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.1.30.2 3.1.30.2] Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1QAE OCA]. |
==Reference== | ==Reference== | ||
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[[Category: Serratia marcescens nuclease]] | [[Category: Serratia marcescens nuclease]] | ||
[[Category: Single protein]] | [[Category: Single protein]] | ||
| - | [[Category: Krause, K | + | [[Category: Krause, K L.]] |
| - | [[Category: Miller, M | + | [[Category: Miller, M D.]] |
[[Category: MG]] | [[Category: MG]] | ||
[[Category: dnase]] | [[Category: dnase]] | ||
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[[Category: sugar-nonspecific nuclease]] | [[Category: sugar-nonspecific nuclease]] | ||
| - | ''Page seeded by [http:// | + | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Feb 21 14:37:33 2008'' |
Revision as of 12:37, 21 February 2008
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THE ACTIVE SITE OF SERRATIA ENDONUCLEASE CONTAINS A CONSERVED MAGNESIUM-WATER CLUSTER
Overview
Serratia endonuclease is an important member of a class of magnesium dependent nucleases that are widely distributed in nature. Here, we describe the location and geometry of a magnesium-water cluster within the active site of this enzyme. The sole protein ligand of the magnesium atom is Asn119; this metal ion is also associated with five water molecules to complete an octahedral coordination complex. These water molecules are very well ordered and there is no evidence of rotational disorder or motion. Glu127 and His89 are located nearby and each is hydrogen bonded to water molecules in the coordination sphere. Asp86 is not chelated to the magnesium or its surrounding water molecules. Results of kinetics and site-specific mutagenesis experiments suggest that this metal-water cluster contains the catalytic metal ion of this enzyme. All residues which hydrogen bond to the water molecules that coordinate the magnesium atom are conserved in nucleases homologous to Serratia endonuclease, suggesting that the water cluster is a conserved feature of this family of enzymes. We offer a detailed structural comparison to one other nuclease, the homing endonuclease I-PpoI, that has recently been shown, in spite of a lack of sequence homology, to share a similar active site geometry to Serratia endonuclease. Evidence from both of these structures suggests that the magnesium of Serratia nuclease participates in catalysis via an inner sphere mechanism.
About this Structure
1QAE is a Single protein structure of sequence from Serratia marcescens with as ligand. Active as Serratia marcescens nuclease, with EC number 3.1.30.2 Full crystallographic information is available from OCA.
Reference
The active site of Serratia endonuclease contains a conserved magnesium-water cluster., Miller MD, Cai J, Krause KL, J Mol Biol. 1999 May 21;288(5):975-87. PMID:10329193
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