4P56

CRYSTAL STRUCTURE OF A TRAP PERIPLASMIC SOLUTE BINDING PROTEIN FROM BORDETELLA BRONCHISEPTICA, TARGET EFI-510038 (BB2442), WITH BOUND (R)-MANDELATE and (S)-MANDELATE

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 0.201 
  • R-Value Work: 0.150 
  • R-Value Observed: 0.153 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.4 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
Putative extracellular solute-binding proteinA, B, C343Bordetella bronchiseptica RB50Mutation(s): 0 
Gene Names: BB2442
UniProt
Find proteins for A0A0H3LM73 (Bordetella bronchiseptica (strain ATCC BAA-588 / NCTC 13252 / RB50))
Explore A0A0H3LM73 
Go to UniProtKB:  A0A0H3LM73
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A0H3LM73
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SMN
Query on SMN
Download Ideal Coordinates CCD File 
G [auth B],
I [auth C]		(S)-MANDELIC ACID
C8 H8 O3
IWYDHOAUDWTVEP-ZETCQYMHSA-N		 Ligand Interaction
RMN
Query on RMN
Download Ideal Coordinates CCD File 
D [auth A],
H [auth C]		(R)-MANDELIC ACID
C8 H8 O3
IWYDHOAUDWTVEP-SSDOTTSWSA-N		 Ligand Interaction
PGE
Query on PGE
Download Ideal Coordinates CCD File 
E [auth A],
F [auth A]		TRIETHYLENE GLYCOL
C6 H14 O4
ZIBGPFATKBEMQZ-UHFFFAOYSA-N		 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
MSE
Query on MSE		A, B, C L-PEPTIDE LINKINGC5 H11 N O2 SeMET
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 0.201 
  • R-Value Work: 0.150 
  • R-Value Observed: 0.153 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 74.402α = 90
b = 82.635β = 90.84
c = 80.575γ = 90
Software Package:
Software NamePurpose
HKL-3000data reduction
PDB_EXTRACTdata extraction
PHENIXrefinement

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


View more in-depth experimental data
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: 2014-05-07
    Type: Initial release
  • Version 1.1: 2015-02-04
    Changes: Derived calculations
  • Version 1.2: 2015-02-25
    Changes: Database references
  • Version 1.3: 2017-09-27
    Changes: Advisory, Author supporting evidence, Database references, Derived calculations, Other, Source and taxonomy, Structure summary
  • Version 1.4: 2019-12-25
    Changes: Author supporting evidence