3i7v
From Proteopedia
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| - | {{STRUCTURE_3i7v| PDB=3i7v | SCENE= }} | ||
| - | ===Crystal structure of AP4A hydrolase complexed with AP4A (ATP) (aq_158) from Aquifex aeolicus Vf5=== | ||
| - | {{ABSTRACT_PUBMED_20124691}} | ||
| - | == | + | ==Crystal structure of AP4A hydrolase complexed with AP4A (ATP) (aq_158) from Aquifex aeolicus Vf5== |
| - | [[3i7v]] is a 2 chain structure with sequence from [ | + | <StructureSection load='3i7v' size='340' side='right'caption='[[3i7v]], [[Resolution|resolution]] 1.95Å' scene=''> |
| + | == Structural highlights == | ||
| + | <table><tr><td colspan='2'>[[3i7v]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Aquifex_aeolicus_VF5 Aquifex aeolicus VF5]. This structure supersedes the now removed PDB entry [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=2pq1 2pq1]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3I7V OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3I7V FirstGlance]. <br> | ||
| + | </td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.95Å</td></tr> | ||
| + | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ATP:ADENOSINE-5-TRIPHOSPHATE'>ATP</scene>, <scene name='pdbligand=B4P:BIS(ADENOSINE)-5-TETRAPHOSPHATE'>B4P</scene>, <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene></td></tr> | ||
| + | <tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=3i7v FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3i7v OCA], [https://pdbe.org/3i7v PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3i7v RCSB], [https://www.ebi.ac.uk/pdbsum/3i7v PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3i7v ProSAT]</span></td></tr> | ||
| + | </table> | ||
| + | == Function == | ||
| + | [https://www.uniprot.org/uniprot/O66548_AQUAE O66548_AQUAE] | ||
| + | == Evolutionary Conservation == | ||
| + | [[Image:Consurf_key_small.gif|200px|right]] | ||
| + | Check<jmol> | ||
| + | <jmolCheckbox> | ||
| + | <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/i7/3i7v_consurf.spt"</scriptWhenChecked> | ||
| + | <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked> | ||
| + | <text>to colour the structure by Evolutionary Conservation</text> | ||
| + | </jmolCheckbox> | ||
| + | </jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=3i7v ConSurf]. | ||
| + | <div style="clear:both"></div> | ||
| + | <div style="background-color:#fffaf0;"> | ||
| + | == Publication Abstract from PubMed == | ||
| + | Asymmetric diadenosine tetraphosphate (Ap(4)A) hydrolases degrade the metabolite Ap(4)A back into ATP and AMP. The three-dimensional crystal structure of Ap(4)A hydrolase (16 kDa) from Aquifex aeolicus has been determined in free and ATP-bound forms at 1.8 and 1.95 A resolution, respectively. The overall three-dimensional crystal structure of the enzyme shows an alphabetaalpha-sandwich architecture with a characteristic loop adjacent to the catalytic site of the protein molecule. The ATP molecule is bound in the primary active site and the adenine moiety of the nucleotide binds in a ring-stacking arrangement equivalent to that observed in the X-ray structure of Ap(4)A hydrolase from Caenorhabditis elegans. Binding of ATP in the active site induces local conformational changes which may have important implications in the mechanism of substrate recognition in this class of enzymes. Furthermore, two invariant water molecules have been identified and their possible structural and/or functional roles are discussed. In addition, modelling of the substrate molecule at the primary active site of the enzyme suggests a possible path for entry and/or exit of the substrate and/or product molecule. | ||
| - | + | Free and ATP-bound structures of Ap4A hydrolase from Aquifex aeolicus V5.,Jeyakanthan J, Kanaujia SP, Nishida Y, Nakagawa N, Praveen S, Shinkai A, Kuramitsu S, Yokoyama S, Sekar K Acta Crystallogr D Biol Crystallogr. 2010 Feb;66(Pt 2):116-24. Epub 2010, Jan 22. PMID:20124691<ref>PMID:20124691</ref> | |
| - | <ref | + | |
| - | [[Category: Aquifex aeolicus | + | From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> |
| - | [[Category: Jeyakanthan | + | </div> |
| - | [[Category: Kanaujia | + | <div class="pdbe-citations 3i7v" style="background-color:#fffaf0;"></div> |
| - | [[Category: Kuramitsu | + | == References == |
| - | [[Category: Nakagawa | + | <references/> |
| - | + | __TOC__ | |
| - | [[Category: Sekar | + | </StructureSection> |
| - | [[Category: Shinkai | + | [[Category: Aquifex aeolicus VF5]] |
| - | [[Category: Yokoyama | + | [[Category: Large Structures]] |
| - | + | [[Category: Jeyakanthan J]] | |
| - | + | [[Category: Kanaujia SP]] | |
| - | + | [[Category: Kuramitsu S]] | |
| - | + | [[Category: Nakagawa N]] | |
| - | + | [[Category: Sekar K]] | |
| - | + | [[Category: Shinkai A]] | |
| - | + | [[Category: Yokoyama S]] | |
| - | + | ||
| - | + | ||
Current revision
Crystal structure of AP4A hydrolase complexed with AP4A (ATP) (aq_158) from Aquifex aeolicus Vf5
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