1MDZ

Crystal structure of ArnB aminotransferase with cycloserine and pyridoxal 5' phosphate


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.07 Å
  • R-Value Free: 0.250 
  • R-Value Work: 0.212 

wwPDB Validation 3D Report Full Report


This is version 1.5 of the entry. See complete history

Literature

Structural studies of Salmonella typhimurium ArnB (PmrH) aminotransferase: A 4-amino-4-deoxy-L-arabinose lipopolysaccharide modifying enzyme

Noland, B.W.Newman, J.M.Hendle, J.Badger, J.Christopher, J.A.Tresser, J.Buchanan, M.D.Wright, T.Rutter, M.E.Sanderson, W.E.Muller-Dieckmann, H.-J.Gajiwala, K.Buchanan, S.G.

(2002) Structure 10: 1569-1580

  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Lipid A modification with 4-amino-4-deoxy-L-arabinose confers on certain pathogenic bacteria, such as Salmonella, resistance to cationic antimicrobial peptides, including those derived from the innate immune system. ArnB catalysis of amino group tran ...

    Lipid A modification with 4-amino-4-deoxy-L-arabinose confers on certain pathogenic bacteria, such as Salmonella, resistance to cationic antimicrobial peptides, including those derived from the innate immune system. ArnB catalysis of amino group transfer from glutamic acid to the 4"-position of a UDP-linked ketopyranose molecule to form UDP-4-amino-4-deoxy-L-arabinose represents a key step in the lipid A modification pathway. Structural and functional studies of the ArnB aminotransferase were undertaken by combining X-ray crystallography with biochemical analyses. High-resolution crystal structures were solved for two native forms and one covalently inhibited form of S. typhimurium ArnB. These structures permitted identification of key residues involved in substrate binding and catalysis, including a rarely observed nonprolyl cis peptide bond in the active site.


    Related Citations: 
    • Structural analysis of a set of proteins resulting from a bacterial genomics project
      Badger, J.,Sauder, J.M.,Adams, J.M.,Antonysamy, S.,Bain, K.,Bergseid, M.G.,Buchanan, S.G.,Buchanan, M.D.,Batiyenko, Y.,Christopher, J.A.,Emtage, S.,Eroshkina, A.,Feil, I.,Furlong, E.B.,Gajiwala, K.S.,Gao, X.,He, D.,Hendle, J.,Huber, A.,Hoda, K.,Kearins, P.,Kissinger, C.,Laubert, B.,Lewis, H.A.,Lin, J.,Loomis, K.,Lorimer, D.,Louie, G.,Maletic, M.,Marsh, C.D.,Miller, I.,Molinari, J.,Muller-Dieckmann, H.J.,Newman, J.M.,Noland, B.W.,Pagarigan, B.,Park, F.,Peat, T.S.,Post, K.W.,Radojicic, S.,Ramos, A.,Romero, R.,Rutter, M.E.,Sanderson, W.E.,Schwinn, K.D.,Tresser, J.,Winhoven, J.,Wright, T.A.,Wu, L.,Xu, J.,Harris, T.J.R.
      (2005) Proteins 60: 787


    Organizational Affiliation

    Structural Genomix, San Diego, CA 92121, USA. brian.noland@stromix.com




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
ArnB aminotransferase
A
393Salmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720)Mutation(s): 0 
Gene Names: arnB (pbgP, pbgP1, pmrH)
EC: 2.6.1.87
Find proteins for Q8ZNF3 (Salmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720))
Go to UniProtKB:  Q8ZNF3
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
DCS
Query on DCS

Download SDF File 
Download CCD File 
A
D-[3-HYDROXY-2-METHYL-5-PHOSPHONOOXYMETHYL-PYRIDIN-4-YLMETHYL]-N,O-CYCLOSERYLAMIDE
D-PYRIDOXYL-N,O-CYCLOSERYLAMIDE-5-MONOPHOSPHATE
C11 H16 N3 O7 P
NNRZSZJOQKAGTO-SECBINFHSA-N
 Ligand Interaction
PLP
Query on PLP

Download SDF File 
Download CCD File 
A
PYRIDOXAL-5'-PHOSPHATE
VITAMIN B6 Phosphate
C8 H10 N O6 P
NGVDGCNFYWLIFO-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.07 Å
  • R-Value Free: 0.250 
  • R-Value Work: 0.212 
  • Space Group: P 43 21 2
Unit Cell:
Length (Å)Angle (°)
a = 90.904α = 90.00
b = 90.904β = 90.00
c = 127.710γ = 90.00
Software Package:
Software NamePurpose
REFMACrefinement
CCP4data scaling
SCALAdata scaling
MOSFLMdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Revision History 

  • Version 1.0: 2002-12-11
    Type: Initial release
  • Version 1.1: 2008-04-28
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Derived calculations, Version format compliance
  • Version 1.3: 2018-10-03
    Type: Advisory, Data collection
  • Version 1.4: 2018-10-10
    Type: Data collection, Source and taxonomy, Structure summary
  • Version 1.5: 2018-12-26
    Type: Data collection, Structure summary