5KC4

Structure of TmRibU, orthorhombic crystal form

  • Classification: Transport Protein, Membrane Protein
  • Organism(s): Thermotoga maritima MSB8
  • Expression System: Escherichia coli BL21(DE3)
  • Mutation(s): No 

  • Deposited: 2016-06-04 Released: 2016-06-29 
  • Deposition Author(s): Karpowich, N.K., Wang, D.N., Song, J.M.
  • Funding Organization(s): National Institutes of Health/National Institute of Diabetes and Digestive and Kidney Disease (NIH/NIDDK), National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS), National Institutes of Health/National Institute of Mental Health (NIH/NIMH), National Institutes of Health/National Institute on Drug Abuse (NIH/NIDA)

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.40 Å
  • R-Value Free: 0.270 
  • R-Value Work: 0.249 
  • R-Value Observed: 0.250 

wwPDB Validation   3D Report Full Report


This is version 1.5 of the entry. See complete history


Literature

An Aromatic Cap Seals the Substrate Binding Site in an ECF-Type S Subunit for Riboflavin.

Karpowich, N.K.Song, J.Wang, D.N.

(2016) J Mol Biol 428: 3118-3130

  • DOI: 10.1016/j.jmb.2016.06.003
  • Primary Citation of Related Structures:  
    5KBW, 5KC0, 5KC4

  • PubMed Abstract: 
  • ECF transporters are a family of active membrane transporters for essential micronutrients, such as vitamins and trace metals. Found exclusively in archaea and bacteria, these transporters are composed of four subunits: an integral membrane substrate-binding subunit (EcfS), a transmembrane coupling subunit (EcfT), and two ATP-binding cassette ATPases (EcfA and EcfA') ...

    ECF transporters are a family of active membrane transporters for essential micronutrients, such as vitamins and trace metals. Found exclusively in archaea and bacteria, these transporters are composed of four subunits: an integral membrane substrate-binding subunit (EcfS), a transmembrane coupling subunit (EcfT), and two ATP-binding cassette ATPases (EcfA and EcfA'). We have characterized the structural basis of substrate binding by the EcfS subunit for riboflavin from Thermotoga maritima, TmRibU. TmRibU binds riboflavin with high affinity, and the protein-substrate complex is exceptionally stable in solution. The crystal structure of riboflavin-bound TmRibU reveals an electronegative binding pocket at the extracellular surface in which the substrate is completely buried. Analysis of the intermolecular contacts indicates that nearly every available substrate hydrogen bond is satisfied. A conserved aromatic residue at the extracellular end of TM5, Tyr130, caps the binding site to generate a substrate-bound, occluded state, and non-conservative mutation of Tyr130 reduces the stability of this conformation. Using a novel fluorescence binding assay, we find that an aromatic residue at this position is essential for high-affinity substrate binding. Comparison with other S subunit structures suggests that TM5 and Loop5-6 contain a dynamic, conserved motif that plays a key role in gating substrate entry and release by S subunits of ECF transporters.


    Organizational Affiliation

    The Helen L. and Martin S. Kimmel Center for Biology and Medicine at the Skirball Institute of Biomolecular Medicine, and Department of Cell Biology, New York University School of Medicine, 540 First Avenue, New York, NY 10016, USA. Electronic address: Da-Neng.Wang@med.nyu.edu.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Riboflavin transporter RibU AE181Thermotoga maritima MSB8Mutation(s): 0 
Gene Names: ribUTM_1455
Find proteins for Q9X1G6 (Thermotoga maritima (strain ATCC 43589 / MSB8 / DSM 3109 / JCM 10099))
Explore Q9X1G6 
Go to UniProtKB:  Q9X1G6
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
RBF
Query on RBF

Download Ideal Coordinates CCD File 
A, E
RIBOFLAVIN
C17 H20 N4 O6
AUNGANRZJHBGPY-SCRDCRAPSA-N
 Ligand Interaction
BNG
Query on BNG

Download Ideal Coordinates CCD File 
A, E
nonyl beta-D-glucopyranoside
C15 H30 O6
QFAPUKLCALRPLH-UXXRCYHCSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.40 Å
  • R-Value Free: 0.270 
  • R-Value Work: 0.249 
  • R-Value Observed: 0.250 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 65.769α = 90
b = 80.784β = 90
c = 118.028γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of Diabetes and Digestive and Kidney Disease (NIH/NIDDK)United StatesR01-DK099023
National Institutes of Health/National Institute of Diabetes and Digestive and Kidney Disease (NIH/NIDDK)United StatesR01-DK053973
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesR01-GM093825
National Institutes of Health/National Institute of Mental Health (NIH/NIMH)United StatesR01- MH083840
National Institutes of Health/National Institute on Drug Abuse (NIH/NIDA)United StatesR01-DA019676

Revision History  (Full details and data files)

  • Version 1.0: 2016-06-29
    Type: Initial release
  • Version 1.1: 2016-08-17
    Changes: Database references
  • Version 1.2: 2017-09-06
    Changes: Author supporting evidence, Database references, Derived calculations
  • Version 1.3: 2017-11-01
    Changes: Author supporting evidence
  • Version 1.4: 2019-11-27
    Changes: Author supporting evidence
  • Version 1.5: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Data collection, Derived calculations, Structure summary