8HKB

TPA bound-form of Periplasmic terephthalate binding protein (TBP) from Ideonella sakaiensis mutant K184D


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.40 Å
  • R-Value Free: 0.181 
  • R-Value Work: 0.153 
  • R-Value Observed: 0.154 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


Literature

Molecular mechanism underlying high-affinity terephthalate binding and conformational change of TBP from Ideonella sakaiensis.

Lee, S.H.Seo, H.Hong, H.Kim, M.Kim, K.J.

(2023) Int J Biol Macromol 243: 125252-125252

  • DOI: https://doi.org/10.1016/j.ijbiomac.2023.125252
  • Primary Citation of Related Structures:  
    8HK9, 8HKA, 8HKB

  • PubMed Abstract: 

    Ideonella sakaiensis is the bacterium that can survive by degrading polyethylene terephthalate (PET) plastic, and terephthalic acid (TPA) binding protein (IsTBP) is an essential periplasmic protein for uptake of TPA into the cytosol for complete degradation of PET. Here, we demonstrated that IsTBP has remarkably high specificity for TPA among 33 monophenolic compounds and two 1,6-dicarboxylic acids tested. Structural comparisons with 6-carboxylic acid binding protein (RpAdpC) and TBP from Comamonas sp. E6 (CsTphC) revealed the key structural features that contribute to high TPA specificity and affinity of IsTBP. We also elucidated the molecular mechanism underlying the conformational change upon TPA binding. In addition, we developed the IsTBP variant with enhanced TPA sensitivity, which can be expanded for the use of TBP as a biosensor for PET degradation.


  • Organizational Affiliation

    School of Life Sciences, BK21 FOUR KNU Creative BioResearch Group, KNU Institute for Microorganisms, Kyungpook National University, Daegu 41566, Republic of Korea.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Periplasmic terephthalate binding protein (TBP)305Piscinibacter sakaiensisMutation(s): 1 
UniProt
Find proteins for A0A0K8P8D2 (Piscinibacter sakaiensis)
Explore A0A0K8P8D2 
Go to UniProtKB:  A0A0K8P8D2
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A0K8P8D2
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
UB7
Query on UB7

Download Ideal Coordinates CCD File 
B [auth A]terephthalic acid
C8 H6 O4
KKEYFWRCBNTPAC-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.40 Å
  • R-Value Free: 0.181 
  • R-Value Work: 0.153 
  • R-Value Observed: 0.154 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 40.054α = 90
b = 59.302β = 104.27
c = 54.298γ = 90
Software Package:
Software NamePurpose
HKL-2000data scaling
REFMACrefinement
HKL-2000data reduction
MOLREPphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Other governmentKorea, Republic Of--

Revision History  (Full details and data files)

  • Version 1.0: 2023-06-21
    Type: Initial release
  • Version 1.1: 2023-06-28
    Changes: Database references
  • Version 1.2: 2024-05-22
    Changes: Data collection