2rh5

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[[Image:2rh5.jpg|left|200px]]
 
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{{Structure
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==Structure of Apo Adenylate Kinase from Aquifex Aeolicus==
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|PDB= 2rh5 |SIZE=350|CAPTION= <scene name='initialview01'>2rh5</scene>, resolution 2.480&Aring;
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<StructureSection load='2rh5' size='340' side='right'caption='[[2rh5]], [[Resolution|resolution]] 2.48&Aring;' scene=''>
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|SITE=
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== Structural highlights ==
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|LIGAND=
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<table><tr><td colspan='2'>[[2rh5]] is a 3 chain structure with sequence from [https://en.wikipedia.org/wiki/Aquifex_aeolicus Aquifex aeolicus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2RH5 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2RH5 FirstGlance]. <br>
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|ACTIVITY= <span class='plainlinks'>[http://en.wikipedia.org/wiki/Adenylate_kinase Adenylate kinase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.7.4.3 2.7.4.3] </span>
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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]] 2.48&#8491;</td></tr>
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|GENE= adk ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=63363 Aquifex aeolicus])
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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=2rh5 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2rh5 OCA], [https://pdbe.org/2rh5 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2rh5 RCSB], [https://www.ebi.ac.uk/pdbsum/2rh5 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2rh5 ProSAT]</span></td></tr>
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|DOMAIN=
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</table>
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|RELATEDENTRY=[[2rgx|2RGX]]
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== Function ==
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|RESOURCES=<span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2rh5 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2rh5 OCA], [http://www.ebi.ac.uk/pdbsum/2rh5 PDBsum], [http://www.rcsb.org/pdb/explore.do?structureId=2rh5 RCSB]</span>
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[https://www.uniprot.org/uniprot/KAD_AQUAE KAD_AQUAE] Catalyzes the reversible transfer of the terminal phosphate group between ATP and AMP. This small ubiquitous enzyme involved in the energy metabolism and nucleotide synthesis, is essential for maintenance and cell growth (By similarity).
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}}
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== Evolutionary Conservation ==
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[[Image:Consurf_key_small.gif|200px|right]]
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Check<jmol>
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<jmolCheckbox>
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<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/rh/2rh5_consurf.spt"</scriptWhenChecked>
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<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
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<text>to colour the structure by Evolutionary Conservation</text>
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</jmolCheckbox>
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</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=2rh5 ConSurf].
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<div style="clear:both"></div>
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'''Structure of Apo Adenylate Kinase from Aquifex Aeolicus'''
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==See Also==
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*[[Adenylate kinase 3D structures|Adenylate kinase 3D structures]]
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__TOC__
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==Overview==
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</StructureSection>
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The mechanisms by which enzymes achieve extraordinary rate acceleration and specificity have long been of key interest in biochemistry. It is generally recognized that substrate binding coupled to conformational changes of the substrate-enzyme complex aligns the reactive groups in an optimal environment for efficient chemistry. Although chemical mechanisms have been elucidated for many enzymes, the question of how enzymes achieve the catalytically competent state has only recently become approachable by experiment and computation. Here we show crystallographic evidence for conformational substates along the trajectory towards the catalytically competent 'closed' state in the ligand-free form of the enzyme adenylate kinase. Molecular dynamics simulations indicate that these partially closed conformations are sampled in nanoseconds, whereas nuclear magnetic resonance and single-molecule fluorescence resonance energy transfer reveal rare sampling of a fully closed conformation occurring on the microsecond-to-millisecond timescale. Thus, the larger-scale motions in substrate-free adenylate kinase are not random, but preferentially follow the pathways that create the configuration capable of proficient chemistry. Such preferred directionality, encoded in the fold, may contribute to catalysis in many enzymes.
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==About this Structure==
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2RH5 is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Aquifex_aeolicus Aquifex aeolicus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2RH5 OCA].
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==Reference==
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Intrinsic motions along an enzymatic reaction trajectory., Henzler-Wildman KA, Thai V, Lei M, Ott M, Wolf-Watz M, Fenn T, Pozharski E, Wilson MA, Petsko GA, Karplus M, Hubner CG, Kern D, Nature. 2007 Dec 6;450(7171):838-44. Epub 2007 Nov 18. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/18026086 18026086]
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[[Category: Adenylate kinase]]
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[[Category: Aquifex aeolicus]]
[[Category: Aquifex aeolicus]]
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[[Category: Single protein]]
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[[Category: Large Structures]]
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[[Category: Fenn, T]]
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[[Category: Fenn T]]
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[[Category: Kern, D.]]
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[[Category: Kern D]]
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[[Category: Petsko, G A.]]
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[[Category: Petsko GA]]
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[[Category: Pozharski, E.]]
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[[Category: Pozharski E]]
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[[Category: Thai, V.]]
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[[Category: Thai V]]
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[[Category: Wilson, M A.]]
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[[Category: Wilson MA]]
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[[Category: Wolf-Watz, M.]]
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[[Category: Wolf-Watz M]]
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[[Category: atp-binding]]
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[[Category: cytoplasm]]
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[[Category: kinase]]
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[[Category: nucleotide-binding]]
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[[Category: transferase(phosphotransferase)]]
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''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Mon Mar 31 05:00:20 2008''
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Current revision

Structure of Apo Adenylate Kinase from Aquifex Aeolicus

PDB ID 2rh5

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