4PDD

CRYSTAL STRUCTURE OF A TRAP PERIPLASMIC SOLUTE BINDING PROTEIN FROM POLAROMONAS SP JS666 (Bpro_0088, TARGET EFI-510167) BOUND TO D-ERYTHRONATE


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.70 Å
  • R-Value Free: 0.172 
  • R-Value Work: 0.139 
  • R-Value Observed: 0.141 

wwPDB Validation   3D Report Full Report


This is version 2.0 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
  • Primary Citation of Related Structures:  
    4LN5, 4MCO, 4MEV, 4MHF, 4MIJ, 4MNC, 4MNI, 4MX6, 4N15, 4N17, 4N4U, 4N6D, 4N6K, 4N8G, 4N8Y, 4N91, 4NAP, 4NF0, 4NG7, 4NGU, 4NHB, 4NN3, 4NQ8, 4NX1, 4O7M, 4O8M, 4O94, 4OA4, 4OAN, 4OVP, 4OVQ, 4OVR, 4OVS, 4OVT, 4P1E, 4P1L, 4P3L, 4P47, 4P56, 4P8B, 4P9K, 4PAF, 4PAI, 4PAK, 4PBH, 4PBQ, 4PC9, 4PCD, 4PDD, 4PDH

  • 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:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
TRAP dicarboxylate transporter, DctP subunitA, B, C303Polaromonas sp. JS666Mutation(s): 0 
Gene Names: Bpro_0088
UniProt
Find proteins for Q12HD7 (Polaromonas sp. (strain JS666 / ATCC BAA-500))
Explore Q12HD7 
Go to UniProtKB:  Q12HD7
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ12HD7
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
EAX
Query on EAX

Download Ideal Coordinates CCD File 
D [auth A],
J [auth B],
O [auth C]
(2R,3R)-2,3,4-trihydroxybutanoic acid
C4 H8 O5
JPIJQSOTBSSVTP-PWNYCUMCSA-N
 Ligand Interaction
MLA
Query on MLA

Download Ideal Coordinates CCD File 
E [auth A],
F [auth A],
G [auth A],
K [auth B],
L [auth B],
E [auth A],
F [auth A],
G [auth A],
K [auth B],
L [auth B],
P [auth C],
Q [auth C]
MALONIC ACID
C3 H4 O4
OFOBLEOULBTSOW-UHFFFAOYSA-N
 Ligand Interaction
FMT
Query on FMT

Download Ideal Coordinates CCD File 
H [auth A],
I [auth A],
M [auth B],
N [auth B],
R [auth C]
FORMIC ACID
C H2 O2
BDAGIHXWWSANSR-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
PCA
Query on PCA
A, B, C L-PEPTIDE LINKINGC5 H7 N O3GLN
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.70 Å
  • R-Value Free: 0.172 
  • R-Value Work: 0.139 
  • R-Value Observed: 0.141 
  • Space Group: I 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 88.521α = 90
b = 126.647β = 113.21
c = 92.023γ = 90
Software Package:
Software NamePurpose
Aimlessdata scaling
PDB_EXTRACTdata extraction
PHENIXrefinement

Structure Validation

View Full Validation Report




Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesGM093342

Revision History  (Full details and data files)

  • Version 1.0: 2014-05-14
    Type: Initial release
  • Version 1.1: 2015-02-25
    Changes: Database references
  • Version 1.2: 2015-04-29
    Changes: Non-polymer description
  • Version 1.3: 2017-09-27
    Changes: Advisory, Author supporting evidence, Database references, Derived calculations, Other, Refinement description, Source and taxonomy, Structure summary
  • Version 2.0: 2019-12-25
    Changes: Author supporting evidence, Polymer sequence