5W7L

Structure of Campylobacter concisus PglC I57M/Q175M variant

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.74 Å
  • R-Value Free: 0.281 
  • R-Value Work: 0.259 
  • R-Value Observed: 0.260 

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Ligand Structure Quality Assessment 


This is version 1.4 of the entry. See complete history. 


Literature

Membrane association of monotopic phosphoglycosyl transferase underpins function.

Ray, L.C., Das, D., Entova, S., Lukose, V., Lynch, A.J., Imperiali, B., Allen, K.N.

(2018) Nat Chem Biol 14: 538-541

  • DOI: 10.1038/s41589-018-0054-z
  • Primary Citation of Related Structures:  
    5W7L

  • PubMed Abstract: 

    • Polyprenol phosphate phosphoglycosyl transferases (PGTs) catalyze the first membrane-committed step in assembly of essential glycoconjugates. Currently there is no structure-function information to describe how monotopic PGTs coordinate the reaction between membrane-embedded and soluble substrates ...

    Polyprenol phosphate phosphoglycosyl transferases (PGTs) catalyze the first membrane-committed step in assembly of essential glycoconjugates. Currently there is no structure-function information to describe how monotopic PGTs coordinate the reaction between membrane-embedded and soluble substrates. We describe the structure and mode of membrane association of PglC, a PGT from Campylobacter concisus. The structure reveals a unique architecture, provides mechanistic insight and identifies ligand-binding determinants for PglC and the monotopic PGT superfamily.

    Organizational Affiliation: 

    Department of Chemistry, Boston University, Boston, MA, USA. drkallen@bu.edu.



Macromolecules
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(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
N,N'-diacetylbacilliosaminyl-1-phosphate transferaseA, B205Campylobacter concisus 13826Mutation(s): 2 
Gene Names: pglC, CCC13826_0450
EC: 2.7.8.36
Membrane Entity: Yes 
UniProt
Find proteins for A7ZET4 (Campylobacter concisus (strain 13826))
Explore A7ZET4 
Go to UniProtKB:  A7ZET4
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA7ZET4
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
PEF
Query on PEF
Download Ideal Coordinates CCD File 
E [auth A],
F [auth A],
I [auth B],
J [auth B]		DI-PALMITOYL-3-SN-PHOSPHATIDYLETHANOLAMINE
C37 H74 N O8 P
SLKDGVPOSSLUAI-PGUFJCEWSA-N		 Ligand Interaction
PG4
Query on PG4
Download Ideal Coordinates CCD File 
G [auth A]TETRAETHYLENE GLYCOL
C8 H18 O5
UWHCKJMYHZGTIT-UHFFFAOYSA-N		 Ligand Interaction
PO4
Query on PO4
Download Ideal Coordinates CCD File 
D [auth A]PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K		 Ligand Interaction
MG
Query on MG
Download Ideal Coordinates CCD File 
C [auth A],
H [auth B]		MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N		 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.74 Å
  • R-Value Free: 0.281 
  • R-Value Work: 0.259 
  • R-Value Observed: 0.260 
  • Space Group: P 32 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 70.802α = 90
b = 70.802β = 90
c = 188.442γ = 120
Software Package:
Software NamePurpose
PHENIXrefinement
PDB_EXTRACTdata extraction
XDSdata reduction
Aimlessdata scaling
SHELXDphasing
PHENIXmodel building

Structure Validation

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Ligand Structure Quality Assessment 


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Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
National Science Foundation (NSF, United States)United StatesMCB1614608
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesGM-039334

Revision History  (Full details and data files)

  • Version 1.0: 2018-05-23
    Type: Initial release
  • Version 1.1: 2018-05-30
    Changes: Data collection, Database references
  • Version 1.2: 2018-11-07
    Changes: Data collection, Database references
  • Version 1.3: 2019-02-20
    Changes: Author supporting evidence, Data collection
  • Version 1.4: 2019-11-27
    Changes: Author supporting evidence