8HQ9

Crystal structure of the MlaD domain of the MlaD protein from Escherichia coli (Form II)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.70 Å
  • R-Value Free: 0.261 
  • R-Value Work: 0.204 
  • R-Value Observed: 0.207 

Starting Model: experimental
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This is version 1.2 of the entry. See complete history


Literature

The Structural Features of MlaD Illuminate its Unique Ligand-Transporting Mechanism and Ancestry.

Dutta, A.Kanaujia, S.P.

(2024) Protein J 43: 298-315

  • DOI: https://doi.org/10.1007/s10930-023-10179-5
  • Primary Citation of Related Structures:  
    8HPZ, 8HQ9, 8HQA

  • PubMed Abstract: 

    The membrane-associated solute-binding protein (SBP) MlaD of the maintenance of lipid asymmetry (Mla) system has been reported to help the transport of phospholipids (PLs) between the outer and inner membranes of Gram-negative bacteria. Despite the availability of structural information, the molecular mechanism underlying the transport of PLs and the ancestry of the protein MlaD remain unclear. In this study, we report the crystal structures of the periplasmic region of MlaD from Escherichia coli (EcMlaD) at a resolution range of 2.3-3.2 Å. The EcMlaD protomer consists of two distinct regions, viz. N-terminal β-barrel fold consisting of seven strands (referred to as MlaD domain) and C-terminal α-helical domain (HD). The protein EcMlaD oligomerizes to give rise to a homo-hexameric ring with a central channel that is hydrophobic and continuous with a variable diameter. Interestingly, the structural analysis revealed that the HD, instead of the MlaD domain, plays a critical role in determining the oligomeric state of the protein. Based on the analysis of available structural information, we propose a working mechanism of PL transport, viz. "asymmetric protomer movement (APM)". Wherein half of the EcMlaD hexamer would rise in the periplasmic side along with an outward movement of pore loops, resulting in the change of the central channel geometry. Furthermore, this study highlights that, unlike typical SBPs, EcMlaD possesses a fold similar to EF/AMT-type beta(6)-barrel and a unique ancestry. Altogether, the findings firmly establish EcMlaD to be a non-canonical SBP with a unique ligand-transport mechanism.


  • Organizational Affiliation

    Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati, Guwahati, Assam, 781039, India.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Intermembrane phospholipid transport system binding protein MlaD
A, B, C, D, E
A, B, C, D, E, F
162Escherichia coli K-12Mutation(s): 0 
Gene Names: mlaDyrbDb3193JW3160
UniProt
Find proteins for P64604 (Escherichia coli (strain K12))
Explore P64604 
Go to UniProtKB:  P64604
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP64604
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.70 Å
  • R-Value Free: 0.261 
  • R-Value Work: 0.204 
  • R-Value Observed: 0.207 
  • Space Group: P 21 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 60.42α = 90
b = 106.95β = 90
c = 117.12γ = 90
Software Package:
Software NamePurpose
HKL-3000data collection
MOSFLMdata reduction
Aimlessdata scaling
PHASERphasing
REFMACrefinement
Cootmodel building
PDB_EXTRACTdata extraction

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Science and Engineering Research Board (SERB)IndiaECR/2018/000013

Revision History  (Full details and data files)

  • Version 1.0: 2024-01-10
    Type: Initial release
  • Version 1.1: 2024-02-21
    Changes: Database references
  • Version 1.2: 2024-05-15
    Changes: Database references