6LVU | pdb_00006lvu

Crystal structure of apo acyl carrier protein from Thermotoga maritima


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.29 Å
  • R-Value Free: 
    0.284 (Depositor), 0.287 (DCC) 
  • R-Value Work: 
    0.222 (Depositor), 0.223 (DCC) 
  • R-Value Observed: 
    0.228 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 6LVU

This is version 1.2 of the entry. See complete history

Literature

Structural Characterization of an ACP fromThermotoga maritima: Insights into Hyperthermal Adaptation.

Lee, Y.Jang, A.Jeong, M.C.Park, N.Park, J.Lee, W.C.Cheong, C.Kim, Y.

(2020) Int J Mol Sci 21

  • DOI: https://doi.org/10.3390/ijms21072600
  • Primary Citation Related Structures: 
    6LVT, 6LVU

  • PubMed Abstract: 

    Thermotoga maritima , a deep-branching hyperthermophilic bacterium, expresses an extraordinarily stable Thermotoga maritima acyl carrier protein ( Tm -ACP) that functions as a carrier in the fatty acid synthesis system at near-boiling aqueous environments. Here, to understand the hyperthermal adaptation of Tm -ACP, we investigated the structure and dynamics of Tm -ACP by nuclear magnetic resonance (NMR) spectroscopy. The melting temperature of Tm -ACP (101.4 °C) far exceeds that of other ACPs, owing to extensive ionic interactions and tight hydrophobic packing. The D59 residue, which replaces Pro/Ser of other ACPs, mediates ionic clustering between helices III and IV. This creates a wide pocket entrance to facilitate the accommodation of long acyl chains required for hyperthermal adaptation of the T. maritima cell membrane. Tm -ACP is revealed to be the first ACP that harbor an amide proton hyperprotected against hydrogen/deuterium exchange for I15. The hydrophobic interactions mediated by I15 appear to be the key driving forces of the global folding process of Tm -ACP. Our findings provide insights into the structural basis of the hyperthermal adaptation of ACP, which might have allowed T. maritima to survive in hot ancient oceans.


  • Organizational Affiliation
    • Department of Bioscience and Biotechnology, Konkuk University, Seoul 05029, Korea.

Macromolecule Content 

  • Total Structure Weight: 18.4 kDa 
  • Atom Count: 1,236 
  • Modeled Residue Count: 156 
  • Deposited Residue Count: 162 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Acyl carrier protein
A, B
81Thermotoga maritima MSB8Mutation(s): 0 
Gene Names: acpP
UniProt
Find proteins for Q9WZD0 (Thermotoga maritima (strain ATCC 43589 / DSM 3109 / JCM 10099 / NBRC 100826 / MSB8))
Explore Q9WZD0 
Go to UniProtKB:  Q9WZD0
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9WZD0
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
ZN

Query on ZN



Download:Ideal Coordinates CCD File
C [auth A]
D [auth A]
E [auth A]
F [auth A]
G [auth B]
C [auth A],
D [auth A],
E [auth A],
F [auth A],
G [auth B],
H [auth B],
I [auth B],
J [auth B],
K [auth B]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.29 Å
  • R-Value Free:  0.284 (Depositor), 0.287 (DCC) 
  • R-Value Work:  0.222 (Depositor), 0.223 (DCC) 
  • R-Value Observed: 0.228 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 23.834α = 90
b = 61.955β = 90
c = 95.724γ = 90
Software Package:
Software NamePurpose
SCALEPACKdata scaling
PHASERphasing
PHENIXrefinement
PDB_EXTRACTdata extraction
HKL-2000data reduction

Structure Validation

View Full Validation Report



Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Research Foundation (NRF, Korea)Korea, Republic OfS201903S00006

Revision History  (Full details and data files)

  • Version 1.0: 2020-04-22
    Type: Initial release
  • Version 1.1: 2020-04-29
    Changes: Database references
  • Version 1.2: 2023-11-29
    Changes: Data collection, Database references, Derived calculations, Refinement description