2A3L

X-Ray Structure of Adenosine 5'-Monophosphate Deaminase from Arabidopsis Thaliana in Complex with Coformycin 5'-Phosphate

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.34 Å
  • R-Value Free: 0.323 
  • R-Value Work: 0.237 

wwPDB Validation 3D Report Full Report


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

Literature

Membrane association, mechanism of action, and structure of Arabidopsis embryonic factor 1 (FAC1).

Han, B.W., Bingman, C.A., Mahnke, D.K., Bannen, R.M., Bednarek, S.Y., Sabina, R.L., Phillips, G.N.

(2006) J.Biol.Chem. 281: 14939-14947

  • DOI: 10.1074/jbc.M513009200

  • PubMed Abstract: 

    • Embryonic factor 1 (FAC1) is one of the earliest expressed plant genes and encodes an AMP deaminase (AMPD), which is also an identified herbicide target. This report identifies an N-terminal transmembrane domain in Arabidopsis FAC1, explores subcellu ...

    Embryonic factor 1 (FAC1) is one of the earliest expressed plant genes and encodes an AMP deaminase (AMPD), which is also an identified herbicide target. This report identifies an N-terminal transmembrane domain in Arabidopsis FAC1, explores subcellular fractionation, and presents a 3.3-A globular catalytic domain x-ray crystal structure with a bound herbicide-based transition state inhibitor that provides the first glimpse of a complete AMPD active site. FAC1 contains an (alpha/beta)(8)-barrel characterized by loops in place of strands 5 and 6 that places it in a small subset of the amidohydrolase superfamily with imperfect folds. Unlike tetrameric animal orthologs, FAC1 is a dimer and each subunit contains an exposed Walker A motif that may be involved in the dramatic combined K(m) (25-80-fold lower) and V(max) (5-6-fold higher) activation by ATP. Normal mode analysis predicts a hinge motion that flattens basic surfaces on each monomer that flank the dimer interface, which suggests a reversible association between the FAC1 globular catalytic domain and intracellular membranes, with N-terminal transmembrane and disordered linker regions serving as the anchor and attachment to the globular catalytic domain, respectively.

    Related Citations: 
    • Crystallization and preliminary X-ray crystallographic analysis of adenosine 5'-monophosphate deaminase (AMPD) from Arabidopsis thaliana in complex with coformycin 5'-phosphate
      Han, B.W.,Bingham, C.A.,Mahnke, D.K.,Sabina, R.L.,Phillips Jr., G.N.
      (2005) Acta Crystallogr.,Sect.F 61: 740

    Organizational Affiliation: 

    Department of Biochemistry, University of Wisconsin, Madison, WI 53706, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
AMP deaminase
A
701Arabidopsis thalianaMutation(s): 1 
Gene Names: AMPD (FAC1)
EC: 3.5.4.6
Find proteins for O80452 (Arabidopsis thaliana)
Go to UniProtKB:  O80452
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
PO4
Query on PO4
Download SDF File 
Download CCD File 
A
PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
 Ligand Interaction
ZN
Query on ZN
Download SDF File 
Download CCD File 
A
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
CF5
Query on CF5
Download SDF File 
Download CCD File 
A
COFORMYCIN 5'-PHOSPHATE
C11 H17 N4 O8 P
LWLMFZVGOXTQAI-LODYRLCVSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.34 Å
  • R-Value Free: 0.323 
  • R-Value Work: 0.237 
  • Space Group: P 62 2 2
Unit Cell:
Length (Å)Angle (°)
a = 131.325α = 90.00
b = 131.325β = 90.00
c = 208.254γ = 120.00
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
PDB_EXTRACTdata extraction
CNSrefinement
REFMACrefinement
MOLREPphasing

Structure Validation

View Full Validation Report or Ramachandran Plots


View more in-depth experimental data

Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2005-07-19
    Type: Initial release
  • Version 1.1: 2008-04-30
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Derived calculations, Version format compliance
  • Version 1.3: 2017-10-11
    Type: Refinement description
  • Version 1.4: 2019-07-24
    Type: Data collection, Refinement description