3Q9B

Crystal Structure of APAH complexed with M344


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.25 Å
  • R-Value Free: 0.202 
  • R-Value Work: 0.171 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Structure of prokaryotic polyamine deacetylase reveals evolutionary functional relationships with eukaryotic histone deacetylases .

Lombardi, P.M.Angell, H.D.Whittington, D.A.Flynn, E.F.Rajashankar, K.R.Christianson, D.W.

(2011) Biochemistry 50: 1808-1817

  • DOI: 10.1021/bi101859k
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Polyamines are a ubiquitous class of polycationic small molecules that can influence gene expression by binding to nucleic acids. Reversible polyamine acetylation regulates nucleic acid binding and is required for normal cell cycle progression and pr ...

    Polyamines are a ubiquitous class of polycationic small molecules that can influence gene expression by binding to nucleic acids. Reversible polyamine acetylation regulates nucleic acid binding and is required for normal cell cycle progression and proliferation. Here, we report the structures of Mycoplana ramosa acetylpolyamine amidohydrolase (APAH) complexed with a transition state analogue and a hydroxamate inhibitor and an inactive mutant complexed with two acetylpolyamine substrates. The structure of APAH is the first of a histone deacetylase-like oligomer and reveals that an 18-residue insert in the L2 loop promotes dimerization and the formation of an 18 Å long "L"-shaped active site tunnel at the dimer interface, accessible only to narrow and flexible substrates. The importance of dimerization for polyamine deacetylase function leads to the suggestion that a comparable dimeric or double-domain histone deacetylase could catalyze polyamine deacetylation reactions in eukaryotes.


    Organizational Affiliation

    Roy and Diana Vagelos Laboratories, Department of Chemistry, University of Pennsylvania, 231 South 34th Street, Philadelphia, Pennsylvania 19104-6323, United States.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Acetylpolyamine amidohydrolase
A, B, C, D, E, F, G, H, I, J, K, L
341Mycoplana ramosaMutation(s): 0 
Gene Names: aphA (aph)
EC: 3.5.1.-
Find proteins for Q48935 (Mycoplana ramosa)
Go to UniProtKB:  Q48935
Small Molecules
Ligands 5 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
K
Query on K

Download SDF File 
Download CCD File 
A, B, C, D, E, F, G, H, I, J, K, L
POTASSIUM ION
K
NPYPAHLBTDXSSS-UHFFFAOYSA-N
 Ligand Interaction
ZN
Query on ZN

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Download CCD File 
A, B, C, D, E, F, G, H, I, J, K, L
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
NA
Query on NA

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Download CCD File 
A, B, C, D, E, F, G, H, I, J, K, L
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
 Ligand Interaction
DMS
Query on DMS

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Download CCD File 
A, B, C, D, E, F, G, H, I, J, K, L
DIMETHYL SULFOXIDE
C2 H6 O S
IAZDPXIOMUYVGZ-UHFFFAOYSA-N
 Ligand Interaction
B3N
Query on B3N

Download SDF File 
Download CCD File 
A, B, C, D, E, F, G, H, I, J, K, L
4-(dimethylamino)-N-[7-(hydroxyamino)-7-oxoheptyl]benzamide
M344
C16 H25 N3 O3
MXWDSZWTBOCWBK-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.25 Å
  • R-Value Free: 0.202 
  • R-Value Work: 0.171 
  • Space Group: P 1
Unit Cell:
Length (Å)Angle (°)
a = 118.657α = 98.09
b = 119.734β = 95.15
c = 119.526γ = 115.33
Software Package:
Software NamePurpose
CNSrefinement
PDB_EXTRACTdata extraction
HKL-2000data reduction
CNSphasing
HKL-2000data scaling
APS-24IDCdata collection

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2011-03-02
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Version format compliance