3L7L | pdb_00003l7l

Structure of the Wall Teichoic Acid Polymerase TagF, H444N + CDPG (30 minute soak)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.95 Å
  • R-Value Free: 
    0.254 (Depositor), 0.250 (DCC) 
  • R-Value Work: 
    0.193 (Depositor), 0.186 (DCC) 
  • R-Value Observed: 
    0.196 (Depositor) 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 1.3 of the entry. See complete history

Literature

Structure of the bacterial teichoic acid polymerase TagF provides insights into membrane association and catalysis.

Lovering, A.L.Lin, L.Y.Sewell, E.W.Spreter, T.Brown, E.D.Strynadka, N.C.

(2010) Nat Struct Mol Biol 17: 582-589

  • DOI: https://doi.org/10.1038/nsmb.1819
  • Primary Citation Related Structures: 
    3L7I, 3L7J, 3L7K, 3L7L, 3L7M

  • PubMed Abstract: 

    Teichoic acid polymers are composed of polyol-phosphate units and form a major component of Gram-positive bacterial cell walls. These anionic compounds perform a multitude of important roles in bacteria and are synthesized by monotopic membrane proteins of the TagF polymerase family. We have determined the structure of Staphylococcus epidermidis TagF to 2.7-A resolution from a construct that includes both the membrane-targeting region and the glycerol-phosphate polymerase domains. TagF possesses a helical region for interaction with the lipid bilayer, placing the active site at a suitable distance for access to the membrane-bound substrate. Characterization of active-site residue variants and analysis of a CDP-glycerol substrate complex suggest a mechanism for polymer synthesis. With the importance of teichoic acid in Gram-positive physiology, this elucidation of the molecular details of TagF function provides a critical new target in the development of novel anti-infectives.


  • Organizational Affiliation
    • Department of Biochemistry and Molecular Biology, Vancouver, Canada.

Macromolecule Content 

  • Total Structure Weight: 349.9 kDa 
  • Atom Count: 13,868 
  • Modeled Residue Count: 1,633 
  • Deposited Residue Count: 2,916 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Teichoic acid biosynthesis protein F
A, B, C, D
729Staphylococcus epidermidis RP62AMutation(s): 1 
Gene Names: SERP1960tagF
EC: 2.7.8.12
Membrane Entity: Yes 
UniProt
Find proteins for Q5HLM5 (Staphylococcus epidermidis (strain ATCC 35984 / DSM 28319 / BCRC 17069 / CCUG 31568 / BM 3577 / RP62A))
Explore Q5HLM5 
Go to UniProtKB:  Q5HLM5
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ5HLM5
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
C2G

Query on C2G



Download:Ideal Coordinates CCD File
CA [auth D][CYTIDINE-5'-PHOSPHATE] GLYCERYLPHOSPHORIC ACID ESTER
C12 H21 N3 O13 P2
HHPOUCCVONEPRK-CNYIRLTGSA-N
SO4

Query on SO4



Download:Ideal Coordinates CCD File
E [auth A]
F [auth A]
O [auth B]
P [auth B]
V [auth C]
E [auth A],
F [auth A],
O [auth B],
P [auth B],
V [auth C],
W [auth C]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
EDO

Query on EDO



Download:Ideal Coordinates CCD File
GA [auth D]1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
CL

Query on CL



Download:Ideal Coordinates CCD File
AA [auth C]
BA [auth C]
DA [auth D]
EA [auth D]
FA [auth D]
AA [auth C],
BA [auth C],
DA [auth D],
EA [auth D],
FA [auth D],
G [auth A],
H [auth A],
I [auth A],
J [auth A],
K [auth A],
L [auth A],
M [auth A],
N [auth A],
Q [auth B],
R [auth B],
S [auth B],
T [auth B],
U [auth B],
X [auth C],
Y [auth C],
Z [auth C]
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.95 Å
  • R-Value Free:  0.254 (Depositor), 0.250 (DCC) 
  • R-Value Work:  0.193 (Depositor), 0.186 (DCC) 
  • R-Value Observed: 0.196 (Depositor) 
Space Group: P 41 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 222.88α = 90
b = 222.88β = 90
c = 100.75γ = 90
Software Package:
Software NamePurpose
MAR345dtbdata collection
SHELXSphasing
PHENIXrefinement
MOSFLMdata 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: 2010-04-28
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2021-10-13
    Changes: Database references, Derived calculations
  • Version 1.3: 2023-09-06
    Changes: Data collection, Refinement description