3q9b

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==Crystal Structure of APAH complexed with M344==
==Crystal Structure of APAH complexed with M344==
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<StructureSection load='3q9b' size='340' side='right' caption='[[3q9b]], [[Resolution|resolution]] 2.25&Aring;' scene=''>
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<StructureSection load='3q9b' size='340' side='right'caption='[[3q9b]], [[Resolution|resolution]] 2.25&Aring;' scene=''>
== Structural highlights ==
== Structural highlights ==
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<table><tr><td colspan='2'>[[3q9b]] is a 12 chain structure with sequence from [http://en.wikipedia.org/wiki/Mycoplana_ramosa Mycoplana ramosa]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3Q9B OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3Q9B FirstGlance]. <br>
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<table><tr><td colspan='2'>[[3q9b]] is a 12 chain structure with sequence from [https://en.wikipedia.org/wiki/Mycoplana_ramosa Mycoplana ramosa]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3Q9B OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3Q9B FirstGlance]. <br>
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</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=B3N:4-(DIMETHYLAMINO)-N-[7-(HYDROXYAMINO)-7-OXOHEPTYL]BENZAMIDE'>B3N</scene>, <scene name='pdbligand=DMS:DIMETHYL+SULFOXIDE'>DMS</scene>, <scene name='pdbligand=K:POTASSIUM+ION'>K</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
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</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.25&#8491;</td></tr>
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<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[3q9c|3q9c]], [[3q9e|3q9e]], [[3q9f|3q9f]]</td></tr>
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<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=B3N:4-(DIMETHYLAMINO)-N-[7-(HYDROXYAMINO)-7-OXOHEPTYL]BENZAMIDE'>B3N</scene>, <scene name='pdbligand=DMS:DIMETHYL+SULFOXIDE'>DMS</scene>, <scene name='pdbligand=K:POTASSIUM+ION'>K</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
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<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">aphA, aph ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=40837 Mycoplana ramosa])</td></tr>
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<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=3q9b FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3q9b OCA], [https://pdbe.org/3q9b PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3q9b RCSB], [https://www.ebi.ac.uk/pdbsum/3q9b PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3q9b ProSAT]</span></td></tr>
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<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3q9b FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3q9b OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3q9b RCSB], [http://www.ebi.ac.uk/pdbsum/3q9b PDBsum]</span></td></tr>
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</table>
</table>
== Function ==
== Function ==
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[[http://www.uniprot.org/uniprot/APHA_MYCRA APHA_MYCRA]] Acts on many types of acetylpolyamines. Has high affinity towards acetylputrescine, acetylcadaverine, acetylspermidine, and acetylspermine. Acts on L-Lys-(epsilon-acetyl)-coumarin, but has very low activity towards acetylated peptides.
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[https://www.uniprot.org/uniprot/APAH_MYCRA APAH_MYCRA] Involved in polyamine metabolism. Catalyzes the deacetylation of various acetylated polyamines such as N-acetylputrescine, N-acetylcadaverine, N(1)-acetylspermine, N(1)-acetylspermidine and N(8)-acetylspermidine (PubMed:8824626, PubMed:3207420). In vitro, is also able to deacetylate L-Lys(epsilon-acetyl)coumarin, but has very low activity towards the larger tetrapeptide N-acetyl-L-Arg-L-His-L-Lys(epsilon-acetyl)-L-Lys(epsilon-acetyl)coumarin (PubMed:21268586).<ref>PMID:21268586</ref> <ref>PMID:3207420</ref> <ref>PMID:8824626</ref>
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<div style="background-color:#fffaf0;">
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== Publication Abstract from PubMed ==
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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 A 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.
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Structure of Prokaryotic Polyamine Deacetylase Reveals Evolutionary Functional Relationships with Eukaryotic Histone Deacetylases .,Lombardi PM, Angell HD, Whittington DA, Flynn EF, Rajashankar KR, Christianson DW Biochemistry. 2011 Jan 26. PMID:21268586<ref>PMID:21268586</ref>
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From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
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</div>
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== References ==
== References ==
<references/>
<references/>
__TOC__
__TOC__
</StructureSection>
</StructureSection>
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[[Category: Large Structures]]
[[Category: Mycoplana ramosa]]
[[Category: Mycoplana ramosa]]
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[[Category: Christianson, D W]]
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[[Category: Christianson DW]]
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[[Category: Lombardi, P M]]
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[[Category: Lombardi PM]]
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[[Category: Arginase fold]]
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[[Category: Deacetylase]]
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[[Category: Hdac]]
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[[Category: Hydrolase-hydrolase inhibitor complex]]
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[[Category: Polyamine]]
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Current revision

Crystal Structure of APAH complexed with M344

PDB ID 3q9b

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