3RTE

Crystal structure of tm0922, a fusion of a domain of unknown function and ADP/ATP-dependent NAD(P)H-hydrate dehydratase from Thermotoga maritima soaked with NADP and ATP.


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.1 Å
  • R-Value Free: 0.207 
  • R-Value Work: 0.162 

wwPDB Validation 3D Report Full Report


This is version 1.4 of the entry. See complete history

Literature

Identification of unknown protein function using metabolite cocktail screening.

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

(2012) Structure 20: 1715-1725

  • DOI: 10.1016/j.str.2012.07.016
  • Primary Citation of Related Structures:  3RNO, 3RO7, 3ROE, 3ROG, 3ROX, 3ROZ, 3RPH, 3RPZ, 3RQ2, 3RQ5, 3RQ6, 3RQ8, 3RQH, 3RQQ, 3RQX, 3RRB, 3RRE, 3RRF, 3RRJ, 3RS8, 3RS9, 3RSF, 3RSG, 3RSQ, 3RSS, 3RT7, 3RT9, 3RTA, 3RTB, 3RTC, 3RTD, 3RTG, 3RU2, 3RU3

  • 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 identificati ...

    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.


    Organizational Affiliation

    Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, VA 22908, USA. ias2n@virginia.edu




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Putative uncharacterized protein
A
502Thermotoga maritima (strain ATCC 43589 / MSB8 / DSM 3109 / JCM 10099)Gene Names: nnr
EC: 5.1.99.6, 4.2.1.136
Find proteins for Q9X024 (Thermotoga maritima (strain ATCC 43589 / MSB8 / DSM 3109 / JCM 10099))
Go to UniProtKB:  Q9X024
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Unknown peptide, probably from expression host
B
7N/AN/A
Protein Feature View is not available: No corresponding UniProt sequence found.
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
K
Query on K

Download SDF File 
Download CCD File 
A
POTASSIUM ION
K
NPYPAHLBTDXSSS-UHFFFAOYSA-N
 Ligand Interaction
ATP
Query on ATP

Download SDF File 
Download CCD File 
A
ADENOSINE-5'-TRIPHOSPHATE
C10 H16 N5 O13 P3
ZKHQWZAMYRWXGA-KQYNXXCUSA-N
 Ligand Interaction
NAP
Query on NAP

Download SDF File 
Download CCD File 
A
NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE
2'-MONOPHOSPHOADENOSINE 5'-DIPHOSPHORIBOSE
C21 H28 N7 O17 P3
XJLXINKUBYWONI-NNYOXOHSSA-N
 Ligand Interaction
MG
Query on MG

Download SDF File 
Download CCD File 
A
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.1 Å
  • R-Value Free: 0.207 
  • R-Value Work: 0.162 
  • Space Group: I 4 2 2
Unit Cell:
Length (Å)Angle (°)
a = 122.441α = 90.00
b = 122.441β = 90.00
c = 155.050γ = 90.00
Software Package:
Software NamePurpose
HKL-3000data collection
HKL-3000phasing
HKL-3000data scaling
HKL-3000data reduction
PDB_EXTRACTdata extraction
REFMACrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2011-06-22
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Version format compliance
  • Version 1.2: 2012-09-19
    Type: Database references
  • Version 1.3: 2012-10-31
    Type: Database references
  • Version 1.4: 2015-01-21
    Type: Database references