1khz | pdb_00001khz

Structure of the ADPR-ase in complex with AMPCPR and Mg

spinqualitylabelsall models 1khz, resolution 2.04Å Show:Asymmetric Unit Biological Assembly Drag the structure with the mouse to rotate   Export Animated Image   Print3D Structural highlights 1khz is a 2 chain structure with sequence from "bacillus_coli"_migula_1895 "bacillus coli" migula 1895. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance. Ligands: ADV, CL, MG Related: 1g0s, 1g9q, 1ga7 Gene: ORF209 ("Bacillus coli" Migula 1895) Activity: ADP-ribose diphosphatase, with EC number 3.6.1.13 Resources: FirstGlance, OCA, PDBe, RCSB, PDBsum Function [ADPP_ECOLI] Acts on ADP-mannose and ADP-glucose as well as ADP-ribose. Prevents glycogen biosynthesis. The reaction catalyzed by this enzyme is a limiting step of the gluconeogenic process. Evolutionary Conservation Check, as determined by ConSurfDB. You may read the explanation of the method and the full data available from ConSurf. Publication Abstract from PubMed 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. 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 From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine. See Also ADP-ribose pyrophosphatase

Proteopedia Page Contributors and Editors (what is this?)

OCA