5AA4

Crystal structure of MltF from Pseudomonas aeruginosa in complex with cell-wall tetrapeptide


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free: 0.239 
  • R-Value Work: 0.185 
  • R-Value Observed: 0.188 

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Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


Literature

Activation by Allostery in Cell-Wall Remodeling by a Modular Membrane-Bound Lytic Transglycosylase from Pseudomonas aeruginosa.

Dominguez-Gil, T.Lee, M.Acebron-Avalos, I.Mahasenan, K.V.Hesek, D.Dik, D.A.Byun, B.Lastochkin, E.Fisher, J.F.Mobashery, S.Hermoso, J.A.

(2016) Structure 24: 1729-1741

  • DOI: https://doi.org/10.1016/j.str.2016.07.019
  • Primary Citation of Related Structures:  
    5A5X, 5AA1, 5AA2, 5AA3, 5AA4

  • PubMed Abstract: 

    Bacteria grow and divide without loss of cellular integrity. This accomplishment is notable, as a key component of their cell envelope is a surrounding glycopeptide polymer. In Gram-negative bacteria this polymer-the peptidoglycan-grows by the difference between concurrent synthesis and degradation. The regulation of the enzymatic ensemble for these activities is poorly understood. We report herein the structural basis for the control of one such enzyme, the lytic transglycosylase MltF of Pseudomonas aeruginosa. Its structure comprises two modules: an ABC-transporter-like regulatory module and a catalytic module. Occupancy of the regulatory module by peptidoglycan-derived muropeptides effects a dramatic and long-distance (40 Å) conformational change, occurring over the entire protein structure, to open its active site for catalysis. This discovery of the molecular basis for the allosteric control of MltF catalysis is foundational to further study of MltF within the complex enzymatic orchestration of the dynamic peptidoglycan.


  • Organizational Affiliation

    Departamento de Cristalografía y Biología Estructural, Instituto de Química-Física "Rocasolano", CSIC, Serrano 119, 28006 Madrid, Spain.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
MEMBRANE-BOUND LYTIC MUREIN TRANSGLYCOSYLASE F
A, C
451Pseudomonas aeruginosa BWHPSA013Mutation(s): 0 
EC: 4.2.2
UniProt
Find proteins for A0A1I9GEN8 (Pseudomonas aeruginosa BWHPSA013)
Explore A0A1I9GEN8 
Go to UniProtKB:  A0A1I9GEN8
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A1I9GEN8
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
MEMBRANE-BOUND LYTIC MUREIN TRANSGLYCOSYLASE F
B, D
451Pseudomonas aeruginosa BWHPSA013Mutation(s): 0 
EC: 4.2.2
UniProt
Find proteins for A0A1I9GEN9 (Pseudomonas aeruginosa BWHPSA013)
Explore A0A1I9GEN9 
Go to UniProtKB:  A0A1I9GEN9
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A1I9GEN9
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
6X4
Query on 6X4

Download Ideal Coordinates CCD File 
E [auth A][6-[[(2~{R})-1-azanyl-1-oxidanylidene-propan-2-yl]amino]-6-oxidanylidene-5-[[(4~{R})-5-oxidanyl-5-oxidanylidene-4-[[(2~{S})-2-[[(2~{R})-2-oxidanylpropanoyl]amino]propanoyl]amino]pentanoyl]amino]hexyl]azanium
C20 H37 N6 O8
NEROIIRQSNQGCX-XVIXHAIJSA-O
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free: 0.239 
  • R-Value Work: 0.185 
  • R-Value Observed: 0.188 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 66.116α = 90
b = 136.774β = 92.34
c = 138.098γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2016-10-12
    Type: Initial release
  • Version 1.1: 2017-03-22
    Changes: Database references
  • Version 1.2: 2024-01-10
    Changes: Data collection, Database references, Derived calculations, Other, Refinement description