1khz: Difference between revisions
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[[Image:1khz.gif|left|200px]] | [[Image:1khz.gif|left|200px]] | ||
'''Structure of the ADPR-ase in complex with AMPCPR and Mg''' | {{Structure | ||
|PDB= 1khz |SIZE=350|CAPTION= <scene name='initialview01'>1khz</scene>, resolution 2.04Å | |||
|SITE= | |||
|LIGAND= <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene> and <scene name='pdbligand=ADV:ALPHA-BETA METHYLENE ADP-RIBOSE'>ADV</scene> | |||
|ACTIVITY= [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] | |||
|GENE= ORF209 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=562 Escherichia coli]) | |||
}} | |||
'''Structure of the ADPR-ase in complex with AMPCPR and Mg''' | |||
==Overview== | ==Overview== | ||
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==About this Structure== | ==About this Structure== | ||
1KHZ is a [ | 1KHZ is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1KHZ OCA]. | ||
==Reference== | ==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:[http:// | 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:[http://www.ncbi.nlm.nih.gov/pubmed/12135348 12135348] | ||
[[Category: ADP-ribose diphosphatase]] | [[Category: ADP-ribose diphosphatase]] | ||
[[Category: Escherichia coli]] | [[Category: Escherichia coli]] | ||
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[[Category: nudix]] | [[Category: nudix]] | ||
''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Mar 20 12:17:44 2008'' | ||
Revision as of 13:17, 20 March 2008
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| , resolution 2.04Å | |||||||
|---|---|---|---|---|---|---|---|
| Ligands: | , and | ||||||
| Gene: | ORF209 (Escherichia coli) | ||||||
| Activity: | ADP-ribose diphosphatase, with EC number 3.6.1.13 | ||||||
| Coordinates: | save as pdb, mmCIF, xml | ||||||
Structure of the ADPR-ase in complex with AMPCPR and Mg
OverviewOverview
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 StructureAbout this Structure
1KHZ is a Single protein structure of sequence from Escherichia coli. Full crystallographic information is available from OCA.
ReferenceReference
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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