5XHQ

Apolipoprotein N-acyl Transferase


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.59 Å
  • R-Value Free: 0.288 
  • R-Value Work: 0.233 
  • R-Value Observed: 0.235 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 1.6 of the entry. See complete history


Literature

Crystal structure of E. coli apolipoprotein N-acyl transferase

Lu, G.Xu, Y.Zhang, K.Xiong, Y.Li, H.Cui, L.Wang, X.Lou, J.Zhai, Y.Sun, F.Zhang, X.C.

(2017) Nat Commun 8: 15948-15948

  • DOI: https://doi.org/10.1038/ncomms15948
  • Primary Citation of Related Structures:  
    5XHQ

  • PubMed Abstract: 

    In Gram-negative bacteria, lipid modification of proteins is catalysed in a three-step pathway. Apolipoprotein N-acyl transferase (Lnt) catalyses the third step in this pathway, whereby it transfers an acyl chain from a phospholipid to the amine group of the N-terminal cysteine residue of the apolipoprotein. Here, we report the 2.6-Å crystal structure of Escherichia coli Lnt. This enzyme contains an exo-membrane nitrilase domain fused to a transmembrane (TM) domain. The TM domain of Lnt contains eight TM helices which form a membrane-embedded cavity with a lateral opening and a periplasmic exit. The nitrilase domain is located on the periplasmic side of the membrane, with its catalytic cavity connected to the periplasmic exit of the TM domain. An amphipathic lid loop from the nitrilase domain interacts with the periplasmic lipid leaflet, forming an interfacial entrance from the lipid bilayer to the catalytic centre for both the lipid donor and acceptor substrates.


  • Organizational Affiliation

    National Laboratory of Macromolecules, Institute of Biophysics, CAS Center for Excellence in Biomacromolecules, Chinese Academy of Sciences, 15 Datun Road, Beijing 100101, China.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Apolipoprotein N-acyltransferase
A, B
516Escherichia coli K-12Mutation(s): 3 
Gene Names: lntcutEb0657JW0654
EC: 2.3.1 (PDB Primary Data), 2.3.1.269 (UniProt)
Membrane Entity: Yes 
UniProt
Find proteins for P23930 (Escherichia coli (strain K12))
Explore P23930 
Go to UniProtKB:  P23930
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP23930
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
HTG
Query on HTG

Download Ideal Coordinates CCD File 
C [auth A]
D [auth A]
F [auth B]
G [auth B]
H [auth B]
C [auth A],
D [auth A],
F [auth B],
G [auth B],
H [auth B],
I [auth B]
heptyl 1-thio-beta-D-glucopyranoside
C13 H26 O5 S
HPEGNLMTTNTJSP-LBELIVKGSA-N
PEG
Query on PEG

Download Ideal Coordinates CCD File 
E [auth A],
J [auth B]
DI(HYDROXYETHYL)ETHER
C4 H10 O3
MTHSVFCYNBDYFN-UHFFFAOYSA-N
GOL
Query on GOL

Download Ideal Coordinates CCD File 
K [auth B],
L [auth B]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.59 Å
  • R-Value Free: 0.288 
  • R-Value Work: 0.233 
  • R-Value Observed: 0.235 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 90.869α = 90
b = 134.094β = 90
c = 135.159γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
the Ministry of Science and Technology (China)China2014CB910104 to XCZ
the Chinese Academy of SciencesChinaXDB080203 to XCZ and FS
National Natural Science Foundation of ChinaChina31470745 to XCZ

Revision History  (Full details and data files)

  • Version 1.0: 2017-07-26
    Type: Initial release
  • Version 1.1: 2017-08-16
    Changes: Database references
  • Version 1.2: 2017-08-30
    Changes: Data collection
  • Version 1.3: 2017-11-01
    Changes: Database references
  • Version 1.4: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Derived calculations, Structure summary
  • Version 1.5: 2023-11-22
    Changes: Data collection, Database references, Refinement description, Structure summary
  • Version 1.6: 2024-10-23
    Changes: Structure summary