4CFP

Crystal structure of MltC in complex with tetrasaccharide at 2.15 A resolution


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.15 Å
  • R-Value Free: 0.268 
  • R-Value Work: 0.191 
  • R-Value Observed: 0.195 

wwPDB Validation   3D Report Full Report


This is version 2.0 of the entry. See complete history


Literature

Structure and Cell Wall Cleavage by Modular Lytic Transglycosylase Mltc of Escherichia Coli.

Artola-Recolons, C.Lee, M.Bernardo-Garcia, N.Blazquez, B.Hesek, D.Bartual, S.G.Mahasenan, K.V.Lastochkin, E.Pi, H.Boggess, B.Meindl, K.Uson, I.Fisher, J.F.Mobashery, S.Hermoso, J.A.

(2014) ACS Chem Biol 9: 2058

  • DOI: 10.1021/cb500439c
  • Primary Citation of Related Structures:  
    4C5F, 4CFO, 4CFP, 4CHX

  • PubMed Abstract: 
  • The lytic transglycosylases are essential bacterial enzymes that catalyze the nonhydrolytic cleavage of the glycan strands of the bacterial cell wall. We describe here the structural and catalytic properties of MltC, one of the seven lytic transglycosylases found in the genome of the Gram-negative bacterium Escherichia coli ...

    The lytic transglycosylases are essential bacterial enzymes that catalyze the nonhydrolytic cleavage of the glycan strands of the bacterial cell wall. We describe here the structural and catalytic properties of MltC, one of the seven lytic transglycosylases found in the genome of the Gram-negative bacterium Escherichia coli. The 2.3 Å resolution X-ray structure of a soluble construct of MltC shows a unique, compared to known lytic transglycosylase structures, two-domain structure characterized by an expansive active site of 53 Å length extending through an interface between the domains. The structures of three complexes of MltC with cell wall analogues suggest the positioning of the peptidoglycan in the active site both as a substrate and as a product. One complex is suggested to correspond to an intermediate in the course of sequential and exolytic cleavage of the peptidoglycan. Moreover, MltC partitioned its reactive oxocarbenium-like intermediate between trapping by the C6-hydroxyl of the muramyl moiety (lytic transglycosylase activity, the major path) and by water (muramidase activity). Genomic analysis identifies the presence of an MltC homologue in no less than 791 bacterial genomes. While the role of MltC in cell wall assembly and maturation remains uncertain, we propose a functional role for this enzyme as befits the uniqueness of its two-domain structure.


    Organizational Affiliation

    Department of Crystallography and Structural Biology, Inst. Química-Física "Rocasolano", CSIC , Serrano 119, 28006 Madrid, Spain.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
MEMBRANE-BOUND LYTIC MUREIN TRANSGLYCOSYLASE CA, B341Escherichia coliMutation(s): 1 
EC: 4.2.2
UniProt
Find proteins for P0C066 (Escherichia coli (strain K12))
Explore P0C066 
Go to UniProtKB:  P0C066
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0C066
Protein Feature View
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  • Reference Sequence
Oligosaccharides

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Entity ID: 2
MoleculeChainsChain Length2D DiagramGlycosylation3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-N-acetyl-beta-muramic acid-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-methyl 2-acetamido-3-O-[(1R)-1-carboxyethyl]-2-deoxy-beta-D-glucopyranosideC, D 4N/A Oligosaccharides Interaction
Glycosylation Resources
GlyTouCan:  G12322WX
GlyCosmos:  G12322WX
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
P6G
Query on P6G

Download Ideal Coordinates CCD File 
E [auth A]HEXAETHYLENE GLYCOL
C12 H26 O7
IIRDTKBZINWQAW-UHFFFAOYSA-N
 Ligand Interaction
CIT
Query on CIT

Download Ideal Coordinates CCD File 
F [auth B]CITRIC ACID
C6 H8 O7
KRKNYBCHXYNGOX-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.15 Å
  • R-Value Free: 0.268 
  • R-Value Work: 0.191 
  • R-Value Observed: 0.195 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 49.51α = 90
b = 114.33β = 93.28
c = 61.771γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
MOLREPphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2014-07-23
    Type: Initial release
  • Version 1.1: 2014-10-01
    Changes: Database references
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Atomic model, Data collection, Derived calculations, Other, Structure summary