1MDX

Crystal structure of ArnB transferase with pyridoxal 5' phosphate


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.96 Å
  • R-Value Free: 0.241 
  • R-Value Work: 0.198 
  • R-Value Observed: 0.206 

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

  • DOI: 10.1016/s0969-2126(02)00879-1
  • Primary Citation of Related Structures:  
    1MDZ, 1MDX, 1MDO

  • 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:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
ArnB aminotransferaseA393Salmonella enterica subsp. enterica serovar TyphimuriumMutation(s): 0 
EC: 2.6.1.87
Find proteins for Q8ZNF3 (Salmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720))
Explore Q8ZNF3 
Go to UniProtKB:  Q8ZNF3
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
PLP
Query on PLP

Download CCD File 
A
PYRIDOXAL-5'-PHOSPHATE
C8 H10 N O6 P
NGVDGCNFYWLIFO-UHFFFAOYSA-N
 Ligand Interaction
AKG
Query on AKG

Download CCD File 
A
2-OXOGLUTARIC ACID
C5 H6 O5
KPGXRSRHYNQIFN-UHFFFAOYSA-N
 Ligand Interaction
GOL
Query on GOL

Download CCD File 
A
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.96 Å
  • R-Value Free: 0.241 
  • R-Value Work: 0.198 
  • R-Value Observed: 0.206 
  • Space Group: P 43 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 91.152α = 90
b = 91.152β = 90
c = 128.683γ = 90
Software Package:
Software NamePurpose
MOSFLMdata reduction
SCALAdata scaling
REFMACrefinement
CCP4data scaling

Structure Validation

View Full Validation Report



Entry History 

Revision History 

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