4KAV | pdb_00004kav

Crystal Structure of the soluble domain of Lipooligosaccharide phosphoethanolamine transferase A from Neisseria meningitidis


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.43 Å
  • R-Value Free: 
    0.157 (Depositor), 0.158 (DCC) 
  • R-Value Work: 
    0.116 (Depositor), 0.118 (DCC) 
  • R-Value Observed: 
    0.118 (Depositor) 

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Ligand Structure Quality Assessment 


This is version 1.3 of the entry. See complete history

Literature

The Structure of the Neisserial Lipooligosaccharide Phosphoethanolamine Transferase A (LptA) Required for Resistance to Polymyxin.

Wanty, C.Anandan, A.Piek, S.Walshe, J.Ganguly, J.Carlson, R.W.Stubbs, K.A.Kahler, C.M.Vrielink, A.

(2013) J Mol Biology 425: 3389-3402

  • DOI: https://doi.org/10.1016/j.jmb.2013.06.029
  • Primary Citation Related Structures: 
    4KAV, 4KAY

  • PubMed Abstract: 

    Gram-negative bacteria possess an outer membrane envelope consisting of an outer leaflet of lipopolysaccharides, also called endotoxins, which protect the pathogen from antimicrobial peptides and have multifaceted roles in virulence. Lipopolysaccharide consists of a glycan moiety attached to lipid A, embedded in the outer membrane. Modification of the lipid A headgroups by phosphoethanolamine (PEA) or 4-amino-arabinose residues increases resistance to the cationic cyclic polypeptide antibiotic, polymyxin. Lipid A PEA transferases are members of the YhjW/YjdB/YijP superfamily and usually consist of a transmembrane domain anchoring the enzyme to the periplasmic face of the cytoplasmic membrane attached to a soluble catalytic domain. The crystal structure of the soluble domain of the protein of the lipid A PEA transferase from Neisseria meningitidis has been determined crystallographically and refined to 1.4Å resolution. The structure reveals a core hydrolase fold similar to that of alkaline phosphatase. Loop regions in the structure differ, presumably to enable interaction with the membrane-localized substrates and to provide substrate specificity. A phosphorylated form of the putative nucleophile, Thr280, is observed. Metal ions present in the active site are coordinated to Thr280 and to residues conserved among the family of transferases. The structure reveals the protein components needed for the transferase chemistry; however, substrate-binding regions are not evident and are likely to reside in the transmembrane domain of the protein.


  • Organizational Affiliation
    • School of Chemistry and Biochemistry, University of Western Australia, 35 Stirling Highway, Crawley, WA 6009, Australia.

Macromolecule Content 

  • Total Structure Weight: 38.77 kDa 
  • Atom Count: 3,392 
  • Modeled Residue Count: 334 
  • Deposited Residue Count: 335 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
YhbX/YhjW/YijP/YjdB family protein335Neisseria meningitidis MC58Mutation(s): 0 
Gene Names: lptaNMB1638
EC: 3.1.3.27
UniProt
Find proteins for Q7DD94 (Neisseria meningitidis serogroup B (strain ATCC BAA-335 / MC58))
Explore Q7DD94 
Go to UniProtKB:  Q7DD94
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ7DD94
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 6 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
DDQ

Query on DDQ



Download:Ideal Coordinates CCD File
H [auth A]DECYLAMINE-N,N-DIMETHYL-N-OXIDE
C12 H27 N O
ZRKZFNZPJKEWPC-UHFFFAOYSA-N
PO4

Query on PO4



Download:Ideal Coordinates CCD File
D [auth A]PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
ZN

Query on ZN



Download:Ideal Coordinates CCD File
B [auth A]ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
CU

Query on CU



Download:Ideal Coordinates CCD File
C [auth A]COPPER (II) ION
Cu
JPVYNHNXODAKFH-UHFFFAOYSA-N
MG

Query on MG



Download:Ideal Coordinates CCD File
F [auth A]MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
NA

Query on NA



Download:Ideal Coordinates CCD File
E [auth A],
G [auth A]
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
Modified Residues  2 Unique
IDChains TypeFormula2D DiagramParent
MSE
Query on MSE
A
L-PEPTIDE LINKINGC5 H11 N O2 SeMET
TPO
Query on TPO
A
L-PEPTIDE LINKINGC4 H10 N O6 PTHR

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.43 Å
  • R-Value Free:  0.157 (Depositor), 0.158 (DCC) 
  • R-Value Work:  0.116 (Depositor), 0.118 (DCC) 
  • R-Value Observed: 0.118 (Depositor) 
Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 43.696α = 70.26
b = 44.923β = 69.36
c = 50.179γ = 61.13
Software Package:
Software NamePurpose
Blu-Icedata collection
SHELXSphasing
PHENIXrefinement
XDSdata reduction
SCALAdata scaling

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2013-07-24
    Type: Initial release
  • Version 1.1: 2013-10-23
    Changes: Database references
  • Version 1.2: 2017-11-15
    Changes: Refinement description
  • Version 1.3: 2024-11-06
    Changes: Data collection, Database references, Derived calculations, Structure summary