6PI8

Crystal structure of Marinobacter subterrani acetylpolyamine amidohydrolase (msAPAH) complexed with acetate


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.635 Å
  • R-Value Free: 0.194 
  • R-Value Work: 0.168 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Structure and Function of the Acetylpolyamine Amidohydrolase from the Deep Earth HalophileMarinobacter subterrani.

Osko, J.D.Roose, B.W.Shinsky, S.A.Christianson, D.W.

(2019) Biochemistry 58: 3755-3766

  • DOI: 10.1021/acs.biochem.9b00582
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Polyamines are small organic cations that are essential for cellular function in all kingdoms of life. Polyamine metabolism is regulated by enzyme-catalyzed acetylation-deacetylation cycles in a fashion similar to the epigenetic regulation of histone ...

    Polyamines are small organic cations that are essential for cellular function in all kingdoms of life. Polyamine metabolism is regulated by enzyme-catalyzed acetylation-deacetylation cycles in a fashion similar to the epigenetic regulation of histone function in eukaryotes. Bacterial polyamine deacetylases are particularly intriguing, because these enzymes share the fold and function of eukaryotic histone deacetylases. Recently, acetylpolyamine amidohydrolase from the deep earth halophile Marinobacter subterrani (msAPAH) was described. This Zn 2+ -dependent deacetylase shares 53% amino acid sequence identity with the acetylpolyamine amidohydrolase from Mycoplana ramosa (mrAPAH) and 22% amino acid sequence identity with the catalytic domain of histone deacetylase 10 from Danio rerio (zebrafish; zHDAC10), the eukaryotic polyamine deacetylase. The X-ray crystal structure of msAPAH, determined in complexes with seven different inhibitors as well as the acetate coproduct, shows how the chemical strategy of Zn 2+ -dependent amide hydrolysis and the catalytic specificity for cationic polyamine substrates is conserved in a subterranean halophile. Structural comparisons with mrAPAH reveal that an array of aspartate and glutamate residues unique to msAPAH enable the binding of one or more Mg 2+ ions in the active site and elsewhere on the protein surface. Notwithstanding these differences, activity assays with a panel of acetylpolyamine and acetyllysine substrates confirm that msAPAH is a broad-specificity polyamine deacetylase, much like mrAPAH. The broad substrate specificity contrasts with the narrow substrate specificity of zHDAC10, which is highly specific for N 8 -acetylspermidine hydrolysis. Notably, quaternary structural features govern the substrate specificity of msAPAH and mrAPAH, whereas tertiary structural features govern the substrate specificity of zHDAC10.


    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
348Marinobacter subterraniMutation(s): 0 
Find proteins for A0A0J7JFD7 (Marinobacter subterrani)
Go to UniProtKB:  A0A0J7JFD7
Small Molecules
Ligands 5 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
K
Query on K

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Download CCD File 
A, B
POTASSIUM ION
K
NPYPAHLBTDXSSS-UHFFFAOYSA-N
 Ligand Interaction
ZN
Query on ZN

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A, B
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
ACT
Query on ACT

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A, B
ACETATE ION
C2 H3 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-M
 Ligand Interaction
EDO
Query on EDO

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Download CCD File 
A, B
1,2-ETHANEDIOL
ETHYLENE GLYCOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
 Ligand Interaction
MG
Query on MG

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Download CCD File 
A, B
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.635 Å
  • R-Value Free: 0.194 
  • R-Value Work: 0.168 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 52.371α = 90.00
b = 121.060β = 109.53
c = 66.556γ = 90.00
Software Package:
Software NamePurpose
Aimlessdata scaling
MOSFLMdata reduction
PHENIXrefinement
PHASERphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Human Genome Research Institute (NIH/NHGRI)United StatesGM49758

Revision History 

  • Version 1.0: 2019-09-18
    Type: Initial release
  • Version 1.1: 2019-09-25
    Type: Data collection, Database references
  • Version 1.2: 2019-12-18
    Type: Author supporting evidence