2G6G

Crystal structure of MltA from Neisseria gonorrhoeae


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.2 Å
  • R-Value Free: 0.259 
  • R-Value Work: 0.213 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Crystal Structures of the Lytic Transglycosylase MltA from N.gonorrhoeae and E.coli: Insights into Interdomain Movements and Substrate Binding.

Powell, A.J.Liu, Z.J.Nicholas, R.A.Davies, C.

(2006) J.Mol.Biol. 359: 122-136

  • DOI: 10.1016/j.jmb.2006.03.023
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • MltA is a lytic transglycosylase of Gram-negative bacteria that cleaves the beta-1,4 glycosidic linkages between N-acetylmuramic acid (MurNAc) and N-acetylglucosamine (GlcNAc) in peptidoglycan. We have determined the crystal structures of MltA from N ...

    MltA is a lytic transglycosylase of Gram-negative bacteria that cleaves the beta-1,4 glycosidic linkages between N-acetylmuramic acid (MurNAc) and N-acetylglucosamine (GlcNAc) in peptidoglycan. We have determined the crystal structures of MltA from Neisseria gonorrhoeae and Escherichia coli (NgMltA and EcMltA), which have only 21.5% sequence identity. Both proteins have two main domains separated by a deep groove. Domain 1 shows structural similarity with the so-called double-psi barrel family of proteins. Comparison of the two structures reveals substantial differences in the relative positions of domains 1 and 2 such that the active site groove in NgMltA is much wider and appears more able to accommodate peptidoglycan substrate than EcMltA, suggesting that domain closure occurs after substrate binding. Docking of a peptidoglycan molecule into the structure of NgMltA reveals a number of conserved residues that are likely involved in substrate binding, including a potential binding pocket for the peptidyl moieties. This structure supports the assignment of Asp405 as the acid catalyst responsible for cleavage of the glycosidic bond. In EcMltA, the equivalent residue is Asp328, which has been identified previously. The structures also suggest a catalytic role for Asp393 (Asp317 in EcMltA) in activating the C6 hydroxyl group during formation of the 1,6-anhydro linkage. Finally, in comparison to EcMltA, NgMltA contains a unique third domain that is an insertion within domain 2. The domain is beta in structure and may mediate protein-protein interactions that are specific to peptidoglycan metabolism in N.gonorrhoeae.


    Organizational Affiliation

    Department of Biochemistry & Molecular Biology, Medical University of South Carolina, Charleston, 29425, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
GNA33
A
422Neisseria gonorrhoeae (strain ATCC 700825 / FA 1090)Mutation(s): 0 
Find proteins for Q5F581 (Neisseria gonorrhoeae (strain ATCC 700825 / FA 1090))
Go to UniProtKB:  Q5F581
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download SDF File 
Download CCD File 
A
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
GOL
Query on GOL

Download SDF File 
Download CCD File 
A
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
MSE
Query on MSE
A
L-PEPTIDE LINKINGC5 H11 N O2 SeMET
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.2 Å
  • R-Value Free: 0.259 
  • R-Value Work: 0.213 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 48.060α = 90.00
b = 87.260β = 90.00
c = 111.950γ = 90.00
Software Package:
Software NamePurpose
REFMACrefinement
SOLVEphasing
SCALEPACKdata scaling
MAR345data collection

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2006-05-02
    Type: Initial release
  • Version 1.1: 2008-05-01
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Advisory, Refinement description, Version format compliance
  • Version 1.3: 2017-10-18
    Type: Refinement description