3adk: Difference between revisions
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==REFINED STRUCTURE OF PORCINE CYTOSOLIC ADENYLATE KINASE AT 2.1 ANGSTROMS RESOLUTION== | |||
<StructureSection load='3adk' size='340' side='right'caption='[[3adk]], [[Resolution|resolution]] 2.10Å' scene=''> | |||
== Structural highlights == | |||
<table><tr><td colspan='2'>[[3adk]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Sus_scrofa Sus scrofa]. This structure supersedes the now removed PDB entries [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=2adk 2adk] and [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=1adk 1adk]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3ADK OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3ADK 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]] 2.1Å</td></tr> | |||
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ACE:ACETYL+GROUP'>ACE</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</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=3adk FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3adk OCA], [https://pdbe.org/3adk PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3adk RCSB], [https://www.ebi.ac.uk/pdbsum/3adk PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3adk ProSAT]</span></td></tr> | |||
</table> | |||
== Function == | |||
[https://www.uniprot.org/uniprot/KAD1_PIG KAD1_PIG] Catalyzes the reversible transfer of the terminal phosphate group between ATP and AMP. Small ubiquitous enzyme involved in energy metabolism and nucleotide synthesis that is essential for maintenance and cell growth. | |||
== 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/ad/3adk_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=3adk ConSurf]. | |||
<div style="clear:both"></div> | |||
<div style="background-color:#fffaf0;"> | |||
== Publication Abstract from PubMed == | |||
The crystal structure of porcine cytosolic adenylate kinase has been established at 2.1 A resolution using a restrained least-squares refinement method. Based on 11,251 independent reflections of better than 10 A resolution, a final R-factor of 19.3% was obtained with a model obeying standard geometry within 0.026 A in bond lengths and 3.3 degrees in bond angles. In comparison with the previous structure at 3 A resolution, there is a significant improvement. The high resolution structure has been used to rationalize the strictly conserved residues in the adenylate kinase family. Among these is the glycine-rich loop, which forms a giant anion hole accommodating a sulfate ion which mimics a phosphoryl group of a substrate. Such a structure seems to occur in a large group of mononucleotide binding proteins. Moreover, a conserved cis-proline has been detected in the active center. A structural comparison with the complex between adenylate kinase from yeast and a substrate-analog at medium resolution indicates that this kinase performs appreciable mechanical movements during a catalytic cycle. The reported structure presumably represents an open form of the enzyme, similar to that in solution in the absence of substrates. However, since there are large intermolecular contacts in the crystal, some deviation from the solution structure has to be expected. | |||
Refined structure of porcine cytosolic adenylate kinase at 2.1 A resolution.,Dreusicke D, Karplus PA, Schulz GE J Mol Biol. 1988 Jan 20;199(2):359-71. PMID:2832612<ref>PMID:2832612</ref> | |||
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | |||
</div> | |||
<div class="pdbe-citations 3adk" style="background-color:#fffaf0;"></div> | |||
==See Also== | ==See Also== | ||
*[[Adenylate kinase|Adenylate kinase]] | *[[Adenylate kinase 3D structures|Adenylate kinase 3D structures]] | ||
== References == | |||
== | <references/> | ||
< | __TOC__ | ||
[[Category: | </StructureSection> | ||
[[Category: Large Structures]] | |||
[[Category: Sus scrofa]] | [[Category: Sus scrofa]] | ||
[[Category: Schulz | [[Category: Schulz GE]] | ||
Latest revision as of 08:40, 5 June 2024
REFINED STRUCTURE OF PORCINE CYTOSOLIC ADENYLATE KINASE AT 2.1 ANGSTROMS RESOLUTIONREFINED STRUCTURE OF PORCINE CYTOSOLIC ADENYLATE KINASE AT 2.1 ANGSTROMS RESOLUTION
Structural highlights
FunctionKAD1_PIG Catalyzes the reversible transfer of the terminal phosphate group between ATP and AMP. Small ubiquitous enzyme involved in energy metabolism and nucleotide synthesis that is essential for maintenance and cell growth. Evolutionary Conservation Check, as determined by ConSurfDB. You may read the explanation of the method and the full data available from ConSurf. Publication Abstract from PubMedThe crystal structure of porcine cytosolic adenylate kinase has been established at 2.1 A resolution using a restrained least-squares refinement method. Based on 11,251 independent reflections of better than 10 A resolution, a final R-factor of 19.3% was obtained with a model obeying standard geometry within 0.026 A in bond lengths and 3.3 degrees in bond angles. In comparison with the previous structure at 3 A resolution, there is a significant improvement. The high resolution structure has been used to rationalize the strictly conserved residues in the adenylate kinase family. Among these is the glycine-rich loop, which forms a giant anion hole accommodating a sulfate ion which mimics a phosphoryl group of a substrate. Such a structure seems to occur in a large group of mononucleotide binding proteins. Moreover, a conserved cis-proline has been detected in the active center. A structural comparison with the complex between adenylate kinase from yeast and a substrate-analog at medium resolution indicates that this kinase performs appreciable mechanical movements during a catalytic cycle. The reported structure presumably represents an open form of the enzyme, similar to that in solution in the absence of substrates. However, since there are large intermolecular contacts in the crystal, some deviation from the solution structure has to be expected. Refined structure of porcine cytosolic adenylate kinase at 2.1 A resolution.,Dreusicke D, Karplus PA, Schulz GE J Mol Biol. 1988 Jan 20;199(2):359-71. PMID:2832612[1] From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine. See AlsoReferences |
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