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

Experimental Data Snapshot

  • Resolution: 1.95 Å
  • R-Value Free: 0.197 
  • R-Value Work: 0.159 
  • R-Value Observed: 0.160 

Starting Model: experimental
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This is version 1.5 of the entry. See complete history


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: https://doi.org/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, 3RTE, 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 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

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Putative uncharacterized protein502Thermotoga maritima MSB8Mutation(s): 0 
Gene Names: tm0922TM_0922
Find proteins for Q9X024 (Thermotoga maritima (strain ATCC 43589 / DSM 3109 / JCM 10099 / NBRC 100826 / MSB8))
Explore Q9X024 
Go to UniProtKB:  Q9X024
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9X024
Sequence Annotations
  • Reference Sequence

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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Unknown peptide, probably from expression host8Escherichia coli BL21(DE3)Mutation(s): 0 
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on NAP

Download Ideal Coordinates CCD File 
C21 H28 N7 O17 P3
Query on K

Download Ideal Coordinates CCD File 
Experimental Data & Validation

Experimental Data

  • Resolution: 1.95 Å
  • R-Value Free: 0.197 
  • R-Value Work: 0.159 
  • R-Value Observed: 0.160 
  • Space Group: I 4 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 122.271α = 90
b = 122.271β = 90
c = 154.879γ = 90
Software Package:
Software NamePurpose
PDB_EXTRACTdata extraction
HKL-3000data collection
HKL-3000data reduction
HKL-3000data scaling

Structure Validation

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Ligand Structure Quality Assessment 

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2011-06-22
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2012-09-19
    Changes: Database references
  • Version 1.3: 2012-10-31
    Changes: Database references
  • Version 1.4: 2022-04-13
    Changes: Database references, Derived calculations, Structure summary
  • Version 1.5: 2023-09-13
    Changes: Data collection, Refinement description