3i7u
From Proteopedia
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| - | + | ==Crystal structure of AP4A hydrolase (aq_158) from Aquifex aeolicus VF5== | |
| - | + | <StructureSection load='3i7u' size='340' side='right' caption='[[3i7u]], [[Resolution|resolution]] 1.80Å' scene=''> | |
| - | + | == Structural highlights == | |
| + | <table><tr><td colspan='2'>[[3i7u]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Aquifex_aeolicus Aquifex aeolicus]. This structure supersedes the now removed PDB entry [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=2pbt 2pbt]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3I7U OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3I7U FirstGlance]. <br> | ||
| + | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=PEG:DI(HYDROXYETHYL)ETHER'>PEG</scene>, <scene name='pdbligand=PG4:TETRAETHYLENE+GLYCOL'>PG4</scene>, <scene name='pdbligand=PGE:TRIETHYLENE+GLYCOL'>PGE</scene>, <scene name='pdbligand=TRS:2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL'>TRS</scene></td></tr> | ||
| + | <tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[3i7v|3i7v]]</td></tr> | ||
| + | <tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">apfA, aq_158 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=63363 Aquifex aeolicus])</td></tr> | ||
| + | <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=3i7u FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3i7u OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3i7u RCSB], [http://www.ebi.ac.uk/pdbsum/3i7u PDBsum]</span></td></tr> | ||
| + | </table> | ||
| + | == 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/i7/3i7u_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/chain_selection.php?pdb_ID=2ata 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> | |
| - | + | ||
| - | == | + | From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> |
| - | < | + | </div> |
| + | == References == | ||
| + | <references/> | ||
| + | __TOC__ | ||
| + | </StructureSection> | ||
[[Category: Aquifex aeolicus]] | [[Category: Aquifex aeolicus]] | ||
| - | [[Category: Jeyakanthan, J | + | [[Category: Jeyakanthan, J]] |
| - | [[Category: Kanaujia, S P | + | [[Category: Kanaujia, S P]] |
| - | [[Category: Kuramitsu, S | + | [[Category: Kuramitsu, S]] |
| - | [[Category: Nakagawa, N | + | [[Category: Nakagawa, N]] |
| - | [[Category: | + | [[Category: Structural genomic]] |
| - | [[Category: Sekar, K | + | [[Category: Sekar, K]] |
| - | [[Category: Shinkai, A | + | [[Category: Shinkai, A]] |
| - | [[Category: Yokoyama, S | + | [[Category: Yokoyama, S]] |
[[Category: Ap4a]] | [[Category: Ap4a]] | ||
[[Category: Diadenosine polyphosphate]] | [[Category: Diadenosine polyphosphate]] | ||
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[[Category: Nppsfa]] | [[Category: Nppsfa]] | ||
[[Category: Nudix protein]] | [[Category: Nudix protein]] | ||
| - | [[Category: Riken structural genomics/proteomics initiative]] | ||
[[Category: Rsgi]] | [[Category: Rsgi]] | ||
| - | [[Category: Structural genomic]] | ||
Revision as of 06:23, 18 December 2014
Crystal structure of AP4A hydrolase (aq_158) from Aquifex aeolicus VF5
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