2BLN

N-terminal formyltransferase domain of ArnA in complex with N-5- formyltetrahydrofolate and UMP


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.2 Å
  • R-Value Free: 0.158 
  • R-Value Work: 0.135 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Structure and Function of Both Domains of Arna, a Dual Function Decarboxylase and a Formyltransferase, Involved in 4-Amino-4-Deoxy-L-Arabinose Biosynthesis.

Williams, G.J.Breazeale, S.D.Raetz, C.R.H.Naismith, J.H.

(2005) J.Biol.Chem. 280: 23000

  • DOI: 10.1074/jbc.M501534200
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Modification of the lipid A moiety of lipopolysaccharide by the addition of the sugar 4-amino-4-deoxy-L-arabinose (L-Ara4N) is a strategy adopted by pathogenic Gram-negative bacteria to evade cationic antimicrobial peptides produced by the innate imm ...

    Modification of the lipid A moiety of lipopolysaccharide by the addition of the sugar 4-amino-4-deoxy-L-arabinose (L-Ara4N) is a strategy adopted by pathogenic Gram-negative bacteria to evade cationic antimicrobial peptides produced by the innate immune system. L-Ara4N biosynthesis is therefore a potential anti-infective target, because inhibiting its synthesis would render certain pathogens more sensitive to the immune system. The bifunctional enzyme ArnA, which is required for L-Ara4N biosynthesis, catalyzes the NAD(+)-dependent oxidative decarboxylation of UDP-glucuronic acid to generate a UDP-4'-keto-pentose sugar and also catalyzes transfer of a formyl group from N-10-formyltetrahydrofolate to the 4'-amine of UDP-L-Ara4N. We now report the crystal structure of the N-terminal formyltransferase domain in a complex with uridine monophosphate and N-5-formyltetrahydrofolate. Using this structure, we identify the active site of formyltransfer in ArnA, including the key catalytic residues Asn(102), His(104), and Asp(140). Additionally, we have shown that residues Ser(433) and Glu(434) of the decarboxylase domain are required for the oxidative decarboxylation of UDP-GlcUA. An E434Q mutant is inactive, suggesting that chemical rather than steric properties of this residue are crucial in the decarboxylation reaction. Our data suggest that the decarboxylase domain catalyzes both hydride abstraction (oxidation) from the C-4' position and the subsequent decarboxylation.


    Organizational Affiliation

    Centre for Biomolecular Science, The University of St. Andrews, UK.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
PROTEIN YFBG
A, B
305Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: arnA (pmrI, yfbG)
Find proteins for P77398 (Escherichia coli (strain K12))
Go to UniProtKB:  P77398
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
FON
Query on FON

Download SDF File 
Download CCD File 
A, B
N-{[4-({[(6R)-2-amino-5-formyl-4-oxo-1,4,5,6,7,8-hexahydropteridin-6-yl]methyl}amino)phenyl]carbonyl}-L-glutamic acid
[6R]-5-FORMYL-5,6,7,8-TETRAHYDROFOLATE; 6R-FOLINIC ACID
C20 H23 N7 O7
VVIAGPKUTFNRDU-OLZOCXBDSA-N
 Ligand Interaction
ACT
Query on ACT

Download SDF File 
Download CCD File 
A, B
ACETATE ION
C2 H3 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-M
 Ligand Interaction
U5P
Query on U5P

Download SDF File 
Download CCD File 
A, B
URIDINE-5'-MONOPHOSPHATE
C9 H13 N2 O9 P
DJJCXFVJDGTHFX-XVFCMESISA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.2 Å
  • R-Value Free: 0.158 
  • R-Value Work: 0.135 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 67.176α = 90.00
b = 89.957β = 90.00
c = 97.885γ = 90.00
Software Package:
Software NamePurpose
MOSFLMdata reduction
SCALAdata scaling
SOLVEphasing
REFMACrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2005-04-08
    Type: Initial release
  • Version 1.1: 2011-05-08
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance