3adk
From Proteopedia
(New page: 200px<br /><applet load="3adk" size="450" color="white" frame="true" align="right" spinBox="true" caption="3adk, resolution 2.1Å" /> '''REFINED STRUCTURE OF ...) |
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| - | [[Image:3adk.gif|left|200px]]<br /><applet load="3adk" size=" | + | [[Image:3adk.gif|left|200px]]<br /><applet load="3adk" size="350" color="white" frame="true" align="right" spinBox="true" |
caption="3adk, resolution 2.1Å" /> | caption="3adk, resolution 2.1Å" /> | ||
'''REFINED STRUCTURE OF PORCINE CYTOSOLIC ADENYLATE KINASE AT 2.1 ANGSTROMS RESOLUTION'''<br /> | '''REFINED STRUCTURE OF PORCINE CYTOSOLIC ADENYLATE KINASE AT 2.1 ANGSTROMS RESOLUTION'''<br /> | ||
==Overview== | ==Overview== | ||
| - | The crystal structure of porcine cytosolic adenylate kinase has been | + | 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. |
==About this Structure== | ==About this Structure== | ||
| - | 3ADK is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Sus_scrofa Sus scrofa] with SO4 and ACE as [http://en.wikipedia.org/wiki/ligands ligands]. This structure | + | 3ADK is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Sus_scrofa Sus scrofa] with <scene name='pdbligand=SO4:'>SO4</scene> and <scene name='pdbligand=ACE:'>ACE</scene> as [http://en.wikipedia.org/wiki/ligands ligands]. This structure supersedes the now removed PDB entries 2ADK and 1ADK. Active as [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] Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3ADK OCA]. |
==Reference== | ==Reference== | ||
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[[Category: Single protein]] | [[Category: Single protein]] | ||
[[Category: Sus scrofa]] | [[Category: Sus scrofa]] | ||
| - | [[Category: Schulz, G | + | [[Category: Schulz, G E.]] |
[[Category: ACE]] | [[Category: ACE]] | ||
[[Category: SO4]] | [[Category: SO4]] | ||
[[Category: transferase(phosphotransferase)]] | [[Category: transferase(phosphotransferase)]] | ||
| - | ''Page seeded by [http:// | + | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Feb 21 19:02:39 2008'' |
Revision as of 17:02, 21 February 2008
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REFINED STRUCTURE OF PORCINE CYTOSOLIC ADENYLATE KINASE AT 2.1 ANGSTROMS RESOLUTION
Overview
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.
About this Structure
3ADK is a Single protein structure of sequence from Sus scrofa with and as ligands. This structure supersedes the now removed PDB entries 2ADK and 1ADK. Active as Adenylate kinase, with EC number 2.7.4.3 Full crystallographic information is available from OCA.
Reference
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
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