3Q9F

Crystal Structure of APAH complexed with CAPS

Summary for 3Q9F

• Entry DOI: 10.2210/pdb3q9f/pdb
• Related: 3Q9B 3Q9C 3Q9E
• Descriptor: Acetylpolyamine amidohydrolase, 3-CYCLOHEXYL-1-PROPYLSULFONIC ACID, PHOSPHATE ION, ... (7 entities in total)
• Functional Keywords: hdac, polyamine, arginase fold, deacetylase, hydrolase
• Biological source: Mycoplana ramosa (Mycoplana bullata)
• Total number of polymer chains: 12
• Total formula weight: 442078.11

Authors

Lombardi, P.M.,Christianson, D.W. (deposition date: 2011-01-07, release date: 2011-03-02, Last modification date: 2024-04-03)

Primary citation

Lombardi, P.M.,Angell, H.D.,Whittington, D.A.,Flynn, E.F.,Rajashankar, K.R.,Christianson, D.W.
Structure of prokaryotic polyamine deacetylase reveals evolutionary functional relationships with eukaryotic histone deacetylases .
Biochemistry, 50:1808-1817, 2011

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 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.

PubMed: 21268586
DOI: 10.1021/bi101859k

Experimental method

X-RAY DIFFRACTION (2.35 Å)