4N91

Crystal structure of a trap periplasmic solute binding protein from anaerococcus prevotii dsm 20548 (Apre_1383), target EFI-510023, with bound alpha/beta d-glucuronate


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.70 Å
  • R-Value Free: 0.172 
  • R-Value Work: 0.147 
  • R-Value Observed: 0.148 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Experimental strategies for functional annotation and metabolism discovery: targeted screening of solute binding proteins and unbiased panning of metabolomes.

Vetting, M.W.Al-Obaidi, N.Zhao, S.San Francisco, B.Kim, J.Wichelecki, D.J.Bouvier, J.T.Solbiati, J.O.Vu, H.Zhang, X.Rodionov, D.A.Love, J.D.Hillerich, B.S.Seidel, R.D.Quinn, R.J.Osterman, A.L.Cronan, J.E.Jacobson, M.P.Gerlt, J.A.Almo, S.C.

(2015) Biochemistry 54: 909-931

  • DOI: 10.1021/bi501388y
  • Structures With Same Primary Citation

  • PubMed Abstract: 
  • The rate at which genome sequencing data is accruing demands enhanced methods for functional annotation and metabolism discovery. Solute binding proteins (SBPs) facilitate the transport of the first reactant in a metabolic pathway, thereby constraining the regions of chemical space and the chemistries that must be considered for pathway reconstruction ...

    The rate at which genome sequencing data is accruing demands enhanced methods for functional annotation and metabolism discovery. Solute binding proteins (SBPs) facilitate the transport of the first reactant in a metabolic pathway, thereby constraining the regions of chemical space and the chemistries that must be considered for pathway reconstruction. We describe high-throughput protein production and differential scanning fluorimetry platforms, which enabled the screening of 158 SBPs against a 189 component library specifically tailored for this class of proteins. Like all screening efforts, this approach is limited by the practical constraints imposed by construction of the library, i.e., we can study only those metabolites that are known to exist and which can be made in sufficient quantities for experimentation. To move beyond these inherent limitations, we illustrate the promise of crystallographic- and mass spectrometric-based approaches for the unbiased use of entire metabolomes as screening libraries. Together, our approaches identified 40 new SBP ligands, generated experiment-based annotations for 2084 SBPs in 71 isofunctional clusters, and defined numerous metabolic pathways, including novel catabolic pathways for the utilization of ethanolamine as sole nitrogen source and the use of d-Ala-d-Ala as sole carbon source. These efforts begin to define an integrated strategy for realizing the full value of amassing genome sequence data.


    Organizational Affiliation

    Department of Biochemistry, Albert Einstein College of Medicine , Bronx, New York 10461, United States.



Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
TRAP dicarboxylate transporter, DctP subunitA347Anaerococcus prevotii DSM 20548Mutation(s): 0 
Gene Names: Apre_1383
Find proteins for C7RDZ3 (Anaerococcus prevotii (strain ATCC 9321 / DSM 20548 / JCM 6508 / PC1))
Explore C7RDZ3 
Go to UniProtKB:  C7RDZ3
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
PG4
Query on PG4

Download CCD File 
A
TETRAETHYLENE GLYCOL
C8 H18 O5
UWHCKJMYHZGTIT-UHFFFAOYSA-N
 Ligand Interaction
GCU
Query on GCU

Download CCD File 
A
alpha-D-glucopyranuronic acid
C6 H10 O7
AEMOLEFTQBMNLQ-WAXACMCWSA-N
 Ligand Interaction
BDP
Query on BDP

Download CCD File 
A
beta-D-glucopyranuronic acid
C6 H10 O7
AEMOLEFTQBMNLQ-QIUUJYRFSA-N
 Ligand Interaction
CL
Query on CL

Download CCD File 
A
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
MSE
Query on MSE
AL-PEPTIDE LINKINGC5 H11 N O2 SeMET
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.70 Å
  • R-Value Free: 0.172 
  • R-Value Work: 0.147 
  • R-Value Observed: 0.148 
  • Space Group: P 31 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 107.216α = 90
b = 107.216β = 90
c = 66.417γ = 120
Software Package:
Software NamePurpose
SCALAdata scaling
PHENIXrefinement
PDB_EXTRACTdata extraction
MOSFLMdata reduction
PHENIXphasing

Structure Validation

View Full Validation Report



Entry History 

Revision History 

  • Version 1.0: 2013-11-13
    Type: Initial release
  • Version 1.1: 2015-02-25
    Changes: Database references
  • Version 1.2: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Data collection, Database references, Derived calculations, Structure summary