PDBsum entry 3rqq

Lyase/lyase substrate

PDB id: 3rqq

Contents

Protein chain

277 a.a.

Ligands

BA3

Metals

_MG

Waters ×202

PDB id:

3rqq

Name:

Lyase/lyase substrate

Title:

Crystal structure of adp/atp-dependent NAD(p)h-hydrate dehydratase from bacillus subtilis in complex with p1,p3-di(adenosine-5') triphosphate

Structure:

Adp/atp-dependent NAD(p)h-hydrate dehydratase. Chain: a. Engineered: yes

Source:

Bacillus subtilis. Organism_taxid: 1423. Gene: bsu38720, yxko. Expressed in: escherichia coli. Expression_system_taxid: 511693.

Resolution:

1.60Å R-factor: 0.151 R-free: 0.162

Authors:

I.A.Shumilin,M.Cymborowski,A.Joachimiak,W.Minor,Midwest Center For Structural Genomics (Mcsg)

Key ref:

I.A.Shumilin et al. (2012). Identification of unknown protein function using metabolite cocktail screening. Structure, 20, 1715-1725. PubMed id: 22940582

Date:

28-Apr-11 Release date: 27-Jul-11

Protein chain

P94368  (NNRD_BACSU) -  ADP-dependent (S)-NAD(P)H-hydrate dehydratase from Bacillus subtilis (strain 168)

Seq: 276 a.a.

Struc: 277 a.a.

Enzyme reactions

• Enzyme class: E.C.4.2.1.136 - ADP-dependent NAD(P)H-hydrate dehydratase.
• Reaction:
  1. (6S)-NADHX + ADP = AMP + phosphate + NADH + H⁺
  2. (6S)-NADPHX + ADP = AMP + phosphate + NADPH + H⁺

(6S)-NADHX + ADP (Bound ligand (Het Group name = BA3) corresponds exactly) = AMP + phosphate + NADH + H(+)

(6S)-NADPHX + ADP (Bound ligand (Het Group name = BA3) corresponds exactly) = AMP + phosphate + NADPH + H(+)

Molecule diagrams generated from .mol files obtained from the KEGG ftp site

reference

Structure 20:1715-1725 (2012)

PubMed id: 22940582

Identification of unknown protein function using metabolite cocktail screening.

I.A.Shumilin, M.Cymborowski, O.Chertihin, K.N.Jha, J.C.Herr, S.A.Lesley, A.Joachimiak, W.Minor.

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.