1khz
From Proteopedia
(New page: 200px<br /><applet load="1khz" size="450" color="white" frame="true" align="right" spinBox="true" caption="1khz, resolution 2.04Å" /> '''Structure of the ADP...) |
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| - | [[Image:1khz.gif|left|200px]]<br /><applet load="1khz" size=" | + | [[Image:1khz.gif|left|200px]]<br /><applet load="1khz" size="350" color="white" frame="true" align="right" spinBox="true" |
caption="1khz, resolution 2.04Å" /> | caption="1khz, resolution 2.04Å" /> | ||
'''Structure of the ADPR-ase in complex with AMPCPR and Mg'''<br /> | '''Structure of the ADPR-ase in complex with AMPCPR and Mg'''<br /> | ||
==Overview== | ==Overview== | ||
| - | Escherichia coli ADP-ribose (ADPR) pyrophosphatase (ADPRase), a Nudix | + | Escherichia coli ADP-ribose (ADPR) pyrophosphatase (ADPRase), a Nudix enzyme, catalyzes the Mg(2+)-dependent hydrolysis of ADP-ribose to AMP and ribose 5-phosphate. ADPR hydrolysis experiments conducted in the presence of H(2)(18)O and analyzed by electrospray mass spectrometry showed that the ADPRase-catalyzed reaction takes place through nucleophilic attack at the adenosyl phosphate. The structure of ADPRase in complex with Mg(2+) and a nonhydrolyzable ADPR analogue, alpha,beta-methylene ADP-ribose, reveals an active site water molecule poised for nucleophilic attack on the adenosyl phosphate. This water molecule is activated by two magnesium ions, and its oxygen contacts the target phosphorus (P-O distance of 3.0 A) and forms an angle of 177 degrees with the scissile bond, suggesting an associative mechanism. A third Mg(2+) ion bridges the two phosphates and could stabilize the negative charge of the leaving group, ribose 5-phosphate. The structure of the ternary complex also shows that loop L9 moves fully 10 A from its position in the free enzyme, forming a tighter turn and bringing Glu 162 to its catalytic position. These observations indicate that as part of the catalytic mechanism, the ADPRase cycles between an open (free enzyme) and a closed (substrate-metal complex) conformation. This cycling may be important in preventing nonspecific hydrolysis of other nucleotides. |
==About this Structure== | ==About this Structure== | ||
| - | 1KHZ is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli] with CL, MG and ADV as [http://en.wikipedia.org/wiki/ligands ligands]. Active as [http://en.wikipedia.org/wiki/ADP-ribose_diphosphatase ADP-ribose diphosphatase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.6.1.13 3.6.1.13] Full crystallographic information is available from [http:// | + | 1KHZ is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli] with <scene name='pdbligand=CL:'>CL</scene>, <scene name='pdbligand=MG:'>MG</scene> and <scene name='pdbligand=ADV:'>ADV</scene> as [http://en.wikipedia.org/wiki/ligands ligands]. Active as [http://en.wikipedia.org/wiki/ADP-ribose_diphosphatase ADP-ribose diphosphatase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.6.1.13 3.6.1.13] Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1KHZ OCA]. |
==Reference== | ==Reference== | ||
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[[Category: Escherichia coli]] | [[Category: Escherichia coli]] | ||
[[Category: Single protein]] | [[Category: Single protein]] | ||
| - | [[Category: Amzel, L | + | [[Category: Amzel, L M.]] |
| - | [[Category: Bessman, M | + | [[Category: Bessman, M J.]] |
| - | [[Category: Bianchet, M | + | [[Category: Bianchet, M A.]] |
| - | [[Category: Gabelli, S | + | [[Category: Gabelli, S B.]] |
[[Category: ADV]] | [[Category: ADV]] | ||
[[Category: CL]] | [[Category: CL]] | ||
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[[Category: nudix]] | [[Category: nudix]] | ||
| - | ''Page seeded by [http:// | + | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Feb 21 13:34:21 2008'' |
Revision as of 11:34, 21 February 2008
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Structure of the ADPR-ase in complex with AMPCPR and Mg
Overview
Escherichia coli ADP-ribose (ADPR) pyrophosphatase (ADPRase), a Nudix enzyme, catalyzes the Mg(2+)-dependent hydrolysis of ADP-ribose to AMP and ribose 5-phosphate. ADPR hydrolysis experiments conducted in the presence of H(2)(18)O and analyzed by electrospray mass spectrometry showed that the ADPRase-catalyzed reaction takes place through nucleophilic attack at the adenosyl phosphate. The structure of ADPRase in complex with Mg(2+) and a nonhydrolyzable ADPR analogue, alpha,beta-methylene ADP-ribose, reveals an active site water molecule poised for nucleophilic attack on the adenosyl phosphate. This water molecule is activated by two magnesium ions, and its oxygen contacts the target phosphorus (P-O distance of 3.0 A) and forms an angle of 177 degrees with the scissile bond, suggesting an associative mechanism. A third Mg(2+) ion bridges the two phosphates and could stabilize the negative charge of the leaving group, ribose 5-phosphate. The structure of the ternary complex also shows that loop L9 moves fully 10 A from its position in the free enzyme, forming a tighter turn and bringing Glu 162 to its catalytic position. These observations indicate that as part of the catalytic mechanism, the ADPRase cycles between an open (free enzyme) and a closed (substrate-metal complex) conformation. This cycling may be important in preventing nonspecific hydrolysis of other nucleotides.
About this Structure
1KHZ is a Single protein structure of sequence from Escherichia coli with , and as ligands. Active as ADP-ribose diphosphatase, with EC number 3.6.1.13 Full crystallographic information is available from OCA.
Reference
Mechanism of the Escherichia coli ADP-ribose pyrophosphatase, a Nudix hydrolase., Gabelli SB, Bianchet MA, Ohnishi Y, Ichikawa Y, Bessman MJ, Amzel LM, Biochemistry. 2002 Jul 30;41(30):9279-85. PMID:12135348
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