2YB1

Structure of an amidohydrolase from Chromobacterium violaceum (EFI target EFI-500202) with bound Mn, AMP and phosphate.

Summary for 2YB1

• Entry DOI: 10.2210/pdb2yb1/pdb
• Descriptor: AMIDOHYDROLASE, MANGANESE (II) ION, ADENOSINE MONOPHOSPHATE, ... (5 entities in total)
• Functional Keywords: hydrolase
• Biological source: CHROMOBACTERIUM VIOLACEUM
• Total number of polymer chains: 1
• Total formula weight: 31973.45

Authors

Vetting, M.W.,Hillerich, B.,Foti, R.,Seidel, R.D.,Zencheck, W.D.,Toro, R.,Imker, H.J.,Raushel, F.M.,Gerlt, J.A.,Almo, S.C. (deposition date: 2011-02-25, release date: 2011-03-16, Last modification date: 2024-05-08)

Primary citation

Cummings, J.A.,Vetting, M.W.,Ghodge, S.V.,Xu, C.,Hillerich, B.,Seidel, R.D.,Almo, S.C.,Raushel, F.M.
Prospecting for Unannotated Enzymes: Discovery of a 3',5'-Nucleotide Bisphosphate Phosphatase within the Amidohydrolase Superfamily.
Biochemistry, 53:591-, 2014

PubMed Abstract: In bacteria, 3',5'-adenosine bisphosphate (pAp) is generated from 3'-phosphoadenosine 5'-phosphosulfate in the sulfate assimilation pathway, and from coenzyme A by the transfer of the phosphopantetheine group to the acyl-carrier protein. pAp is subsequently hydrolyzed to 5'-AMP and orthophosphate, and this reaction has been shown to be important for superoxide stress tolerance. Herein, we report the discovery of the first instance of an enzyme from the amidohydrolase superfamily that is capable of hydrolyzing pAp. Crystal structures of Cv1693 from Chromobacterium violaceum have been determined to a resolution of 1.9 Å with AMP and orthophosphate bound in the active site. The enzyme has a trinuclear metal center in the active site with three Mn(2+) ions. This enzyme (Cv1693) belongs to the Cluster of Orthologous Groups cog0613 from the polymerase and histidinol phosphatase family of enzymes. The values of kcat and kcat/Km for the hydrolysis of pAp are 22 s(-1) and 1.4 × 10(6) M(-1) s(-1), respectively. The enzyme is promiscuous and is able to hydrolyze other 3',5'-bisphosphonucleotides (pGp, pCp, pUp, and pIp) and 2'-deoxynucleotides with comparable catalytic efficiency. The enzyme is capable of hydrolyzing short oligonucleotides (pdA)5, albeit at rates much lower than that of pAp. Enzymes from two other enzyme families have previously been found to hydrolyze pAp at physiologically significant rates. These enzymes include CysQ from Escherichia coli (cog1218) and YtqI/NrnA from Bacillus subtilis (cog0618). Identification of the functional homologues to the experimentally verified pAp phosphatases from cog0613, cog1218, and cog0618 suggests that there is relatively little overlap of enzymes with this function in sequenced bacterial genomes.

PubMed: 24401123
DOI: 10.1021/BI401640R

Experimental method

X-RAY DIFFRACTION (1.898 Å)