3RQQ

Crystal Structure of ADP/ATP-dependent NAD(P)H-hydrate dehydratase from Bacillus subtilis in complex with P1,P3-Di(adenosine-5') triphosphate

Summary for 3RQQ

• Entry DOI: 10.2210/pdb3rqq/pdb
• Related: 1KYH 3RPZ 3RQ5 3RQ6 3RQ8 3RQH 3RQX
• Descriptor: ADP/ATP-DEPENDENT NAD(P)H-HYDRATE DEHYDRATASE, MAGNESIUM ION, BIS(ADENOSINE)-5'-TRIPHOSPHATE, ... (4 entities in total)
• Functional Keywords: structural genomics, psi-biology, protein structure initiative, midwest center for structural genomics, mcsg, lyase-lyase substrate complex, lyase/lyase substrate
• Biological source: Bacillus subtilis
• Total number of polymer chains: 1
• Total formula weight: 30957.15

Authors

Shumilin, I.A.,Cymborowski, M.,Joachimiak, A.,Minor, W.,Midwest Center for Structural Genomics (MCSG) (deposition date: 2011-04-28, release date: 2011-07-27, Last modification date: 2023-09-13)

Primary citation

Shumilin, I.A.,Cymborowski, M.,Chertihin, O.,Jha, K.N.,Herr, J.C.,Lesley, S.A.,Joachimiak, A.,Minor, W.
Identification of unknown protein function using metabolite cocktail screening.
Structure, 20:1715-1725, 2012

PubMed Abstract: Proteins of unknown function comprise a significant fraction of sequenced genomes. Defining the roles of these proteins is vital to understanding cellular processes. Here, we describe a method to determine a protein function based on the identification of its natural ligand(s) by the crystallographic screening of the binding of a metabolite library, followed by a focused search in the metabolic space. The method was applied to two protein families with unknown function, PF01256 and YjeF_N. The PF01256 proteins, represented by YxkO from Bacillus subtilis and the C-terminal domain of Tm0922 from Thermotoga maritima, were shown to catalyze ADP/ATP-dependent NAD(P)H-hydrate dehydratation, a previously described orphan activity. The YjeF_N proteins, represented by mouse apolipoprotein A-I binding protein and the N-terminal domain of Tm0922, were found to interact with an adenosine diphosphoribose-related substrate and likely serve as ADP-ribosyltransferases. Crystallographic screening of metabolites serves as an efficient tool in functional analyses of uncharacterized proteins.

PubMed: 22940582
DOI: 10.1016/j.str.2012.07.016

Experimental method

X-RAY DIFFRACTION (1.6 Å)