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 
  • R-Value Observed: 0.237 

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Ligand Structure Quality Assessment 


This is version 1.5 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
  • Primary Citation of Related Structures:  
    2A3L

  • 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 subcellular fractionation, and presents a 3 ...

    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 Struct Biol Cryst Commun 61: 740

    Organizational Affiliation

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



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
AMP deaminaseA701Arabidopsis thalianaMutation(s): 1 
Gene Names: At2g38280AMPDFAC1F16M14.21
EC: 3.5.4.6
UniProt
Find proteins for O80452 (Arabidopsis thaliana)
Explore O80452 
Go to UniProtKB:  O80452
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO80452
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CF5
Query on CF5

Download Ideal Coordinates CCD File 
D [auth A]COFORMYCIN 5'-PHOSPHATE
C11 H17 N4 O8 P
LWLMFZVGOXTQAI-LODYRLCVSA-N
 Ligand Interaction
PO4
Query on PO4

Download Ideal Coordinates CCD File 
C [auth A]PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
 Ligand Interaction
ZN
Query on ZN

Download Ideal Coordinates CCD File 
B [auth A]ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-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 
  • R-Value Observed: 0.237 
  • Space Group: P 62 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 131.325α = 90
b = 131.325β = 90
c = 208.254γ = 120
Software Package:
Software NamePurpose
CNSrefinement
SCALEPACKdata scaling
MOLREPphasing
REFMACrefinement
PDB_EXTRACTdata extraction
DENZOdata reduction

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2005-07-19
    Type: Initial release
  • Version 1.1: 2008-04-30
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Derived calculations, Version format compliance
  • Version 1.3: 2017-10-11
    Changes: Refinement description
  • Version 1.4: 2019-07-24
    Changes: Data collection, Refinement description
  • Version 1.5: 2021-10-20
    Changes: Database references, Derived calculations