5ZY8

Crystal structure of C terminal truncated HadBC (3R-Hydroxyacyl-ACP Dehydratase) complex from Mycobacterium tuberculosis


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.90 Å
  • R-Value Free: 0.228 
  • R-Value Work: 0.186 
  • R-Value Observed: 0.188 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

The C-terminal end of mycobacterial HadBC regulates AcpM interaction during the FAS-II pathway: a structural perspective.

Singh, B.K.Biswas, R.Bhattacharyya, S.Basak, A.Das, A.K.

(2022) FEBS J 

  • DOI: https://doi.org/10.1111/febs.16405
  • Primary Citation of Related Structures:  
    5ZY8

  • PubMed Abstract: 

    Comprehending the molecular strategies employed by Mycobacterium tuberculosis (Mtb) in FAS-II regulation is of paramount significance for curbing tuberculosis progression. Mtb employs two sets of dehydratases, namely HadAB and HadBC (β-hydroxyacyl acyl carrier protein dehydratase), for the regulation of the fatty acid synthase (FAS-II) pathway. We utilized a sequence similarity network to discern the basis for the presence of two copies of the dehydratase gene in Mtb. This analysis groups HadC and HadA in different clusters, which could be attributed to the variability in their physiological role with respect to the acyl chain uptake. Our study reveals structural details pertaining to the crystal structure of the last remaining enzyme of the FAS-II pathway. It also provides insights into the highly flexible hot-dog helix and substrate regulatory loop. Additionally, mutational studies assisted in establishing the role of the C-terminal end in HadC of HadBC in the regulation of acyl carrier protein from Mtb-mediated interactions. Complemented with surface plasmon resonance and molecular dynamics simulation studies, the present study provides the first evidence of the molecular mechanisms involved in the differential binding affinity of the acyl carrier protein from Mtb towards both mtbHadAB and mtbHadBC.


  • Organizational Affiliation

    School of Biosciences, Indian Institute of Technology Kharagpur, India.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
UPF0336 protein Rv0637
A, C
158Mycobacterium tuberculosis H37RvMutation(s): 0 
Gene Names: Rv0637MTCY20H10.18
UniProt
Find proteins for P9WFJ9 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv))
Explore P9WFJ9 
Go to UniProtKB:  P9WFJ9
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP9WFJ9
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
3-hydroxyacyl-ACP dehydratase
B, D
142Mycobacterium tuberculosis H37RvMutation(s): 0 
Gene Names: LH57_03445
UniProt
Find proteins for I6WYY7 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv))
Explore I6WYY7 
Go to UniProtKB:  I6WYY7
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupI6WYY7
Sequence Annotations
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.90 Å
  • R-Value Free: 0.228 
  • R-Value Work: 0.186 
  • R-Value Observed: 0.188 
  • Space Group: P 31 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 119.417α = 90
b = 119.417β = 90
c = 99.177γ = 120
Software Package:
Software NamePurpose
XDSdata reduction
SCALAdata scaling
MOLREPphasing
PHENIXrefinement
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
IndiaBT/PR12404/BRB/10/1362/2014

Revision History  (Full details and data files)

  • Version 1.0: 2019-06-12
    Type: Initial release
  • Version 1.1: 2022-03-09
    Changes: Database references
  • Version 1.2: 2023-11-22
    Changes: Data collection, Refinement description