8HD4

Full-length crystal structure of mycobacterium tuberculosis FadD23 in complex with AMPC16


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.68 Å
  • R-Value Free: 0.252 
  • R-Value Work: 0.214 
  • R-Value Observed: 0.216 

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Ligand Structure Quality Assessment 


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Literature

The Key Roles of Mycobacterium tuberculosis FadD23 C-terminal Domain in Catalytic Mechanisms.

Yan, M.Cao, L.Zhao, L.Zhou, W.Liu, X.Zhang, W.Rao, Z.

(2023) Front Microbiol 14: 1090534-1090534

  • DOI: https://doi.org/10.3389/fmicb.2023.1090534
  • Primary Citation of Related Structures:  
    8HCZ, 8HD4, 8HDF

  • PubMed Abstract: 

    Sulfolipid-1 (SL-1) is located in the Mycobacterium tuberculosis ( M. tb ) cell wall, and is essential for pathogen virulence and intracellular growth. Multiple proteins (e.g., Pks2, FadD23, PapA1, and MmpL8) in the SL-1 synthesis pathway can be treated as drug targets, but, to date, their structures have not been solved. The crystal structures of FadD23 bound to ATP or hexadecanoyl adenylate was determined in this study. We have also investigated long-chain saturated fatty acids as biological substrates of FadD23 through structural, biological, and chemical analyses. The mutation at the active site of FadD23 greatly influences enzymatic activity. Meanwhile, the FadD23 N-terminal domain alone cannot bind palmitic acid without C-terminal domain facilitation since it is almost inactive after removing the C-terminal domain. FadD23 is the first protein in the SL-1 synthesis pathway whose structure has been solved. These results reveal the importance of the C-terminal domain in the catalytic mechanism.


  • Organizational Affiliation

    State Key Laboratory of Medicinal Chemical Biology, Frontiers Science Center for Cell Responses, College of Life Sciences, Nankai University, Tianjin, China.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Long-chain-fatty-acid--AMP ligase FadD23605Mycobacterium tuberculosis H37RvMutation(s): 0 
Gene Names: fadD23Rv3826
EC: 6.2.1.57
UniProt
Find proteins for P9WQ47 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv))
Explore P9WQ47 
Go to UniProtKB:  P9WQ47
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP9WQ47
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
1TF (Subject of Investigation/LOI)
Query on 1TF

Download Ideal Coordinates CCD File 
B [auth A]palmitoyl adenylate
C26 H44 N5 O8 P
CMRDSXPYXCUXMI-VJUOEERUSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.68 Å
  • R-Value Free: 0.252 
  • R-Value Work: 0.214 
  • R-Value Observed: 0.216 
  • Space Group: P 61 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 73.582α = 90
b = 73.582β = 90
c = 462.593γ = 120
Software Package:
Software NamePurpose
XSCALEdata scaling
PHENIXrefinement
PDB_EXTRACTdata extraction
XDSdata reduction
PHENIXphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Natural Science Foundation of China (NSFC)China--

Revision History  (Full details and data files)

  • Version 1.0: 2023-02-15
    Type: Initial release
  • Version 1.1: 2023-03-22
    Changes: Database references