1dvr: Difference between revisions

From Proteopedia
Jump to navigation Jump to search
← Older edit
No edit summary
No edit summary
 
(15 intermediate revisions by the same user not shown)
Line 1: Line 1:
[[Image:1dvr.jpg|left|200px]]


{{Structure
==STRUCTURE OF A MUTANT ADENYLATE KINASE LIGATED WITH AN ATP-ANALOGUE SHOWING DOMAIN CLOSURE OVER ATP==
|PDB= 1dvr |SIZE=350|CAPTION= <scene name='initialview01'>1dvr</scene>, resolution 2.36&Aring;
<StructureSection load='1dvr' size='340' side='right'caption='[[1dvr]], [[Resolution|resolution]] 2.36&Aring;' scene=''>
|SITE=  
== Structural highlights ==
|LIGAND= <scene name='pdbligand=ATF:PHOSPHODIFLUOROMETHYLPHOSPHONIC+ACID-ADENYLATE+ESTER'>ATF</scene>
<table><tr><td colspan='2'>[[1dvr]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Saccharomyces_cerevisiae Saccharomyces cerevisiae]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1DVR OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1DVR FirstGlance]. <br>
|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>
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.36&#8491;</td></tr>
|GENE=  
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ATF:PHOSPHODIFLUOROMETHYLPHOSPHONIC+ACID-ADENYLATE+ESTER'>ATF</scene></td></tr>
|DOMAIN=
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1dvr FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1dvr OCA], [https://pdbe.org/1dvr PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1dvr RCSB], [https://www.ebi.ac.uk/pdbsum/1dvr PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1dvr ProSAT]</span></td></tr>
|RELATEDENTRY=
</table>
|RESOURCES=<span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1dvr FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1dvr OCA], [http://www.ebi.ac.uk/pdbsum/1dvr PDBsum], [http://www.rcsb.org/pdb/explore.do?structureId=1dvr RCSB]</span>
== Function ==
}}
[https://www.uniprot.org/uniprot/KAD2_YEAST KAD2_YEAST] Catalyzes the reversible transfer of the terminal phosphate group between ATP and AMP. Plays an important role in cellular energy homeostasis and in adenine nucleotide metabolism. Adenylate kinase activity is critical for regulation of the phosphate utilization and the AMP de novo biosynthesis pathways.[HAMAP-Rule:MF_03168]<ref>PMID:18433446</ref> <ref>PMID:2848829</ref> <ref>PMID:2850178</ref>
== 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/dv/1dvr_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=1dvr ConSurf].
<div style="clear:both"></div>


'''STRUCTURE OF A MUTANT ADENYLATE KINASE LIGATED WITH AN ATP-ANALOGUE SHOWING DOMAIN CLOSURE OVER ATP'''
==See Also==
 
*[[Adenylate kinase 3D structures|Adenylate kinase 3D structures]]
 
== References ==
==Overview==
<references/>
Structural studies on unligated and ligated adenylate kinases have shown that two domains, LID and NMPbind, close over the bound substrates, ATP and AMP, respectively. These motions can be, but need not be independent from each other. Up to now, the known structures display only the states "both domains open", "both closed" and "NMP bind closed". In spite of numerous cocrystallization attempts with ATP, a crystalline state "LID closed" has not yet been produced. These experiences suggested that LID closure depends on a bound AMP molecule, in contrast to enzyme kinetic studies indicating a random-bi-bi mechanism. Using an inactive mutant of yeast adenylate kinase together with the ATP analogue AMPPCF2P, however, we have now crystallized an adenylate kinase in the LID closed state. The structure was established at 2.36 A resolution; it indicates that the domain motions occur largely independent from each other in agreement with the kinetic studies. As a side-result, we report the protein environment of the fluorine atoms of the bound ATP analogue.
__TOC__
 
</StructureSection>
==About this Structure==
[[Category: Large Structures]]
1DVR is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Saccharomyces_cerevisiae Saccharomyces cerevisiae]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1DVR OCA].
 
==Reference==
Structure of a mutant adenylate kinase ligated with an ATP-analogue showing domain closure over ATP., Schlauderer GJ, Proba K, Schulz GE, J Mol Biol. 1996 Feb 23;256(2):223-7. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/8594191 8594191]
[[Category: Adenylate kinase]]
[[Category: Saccharomyces cerevisiae]]
[[Category: Saccharomyces cerevisiae]]
[[Category: Single protein]]
[[Category: Schlauderer GJ]]
[[Category: Schlauderer, G J.]]
[[Category: Schulz GE]]
[[Category: Schulz, G E.]]
[[Category: myokinase]]
[[Category: nucleoside monophosphate kinase]]
 
''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sun Mar 30 19:49:44 2008''

Latest revision as of 09:59, 7 February 2024

STRUCTURE OF A MUTANT ADENYLATE KINASE LIGATED WITH AN ATP-ANALOGUE SHOWING DOMAIN CLOSURE OVER ATPSTRUCTURE OF A MUTANT ADENYLATE KINASE LIGATED WITH AN ATP-ANALOGUE SHOWING DOMAIN CLOSURE OVER ATP

Structural highlights

1dvr is a 2 chain structure with sequence from Saccharomyces cerevisiae. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:X-ray diffraction, Resolution 2.36Å
Ligands:
Resources:FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

KAD2_YEAST Catalyzes the reversible transfer of the terminal phosphate group between ATP and AMP. Plays an important role in cellular energy homeostasis and in adenine nucleotide metabolism. Adenylate kinase activity is critical for regulation of the phosphate utilization and the AMP de novo biosynthesis pathways.[HAMAP-Rule:MF_03168][1] [2] [3]

Evolutionary Conservation

Check, as determined by ConSurfDB. You may read the explanation of the method and the full data available from ConSurf.

See Also

References

  1. ↑ Gauthier S, Coulpier F, Jourdren L, Merle M, Beck S, Konrad M, Daignan-Fornier B, Pinson B. Co-regulation of yeast purine and phosphate pathways in response to adenylic nucleotide variations. Mol Microbiol. 2008 Jun;68(6):1583-94. doi: 10.1111/j.1365-2958.2008.06261.x., Epub 2008 Apr 21. PMID:18433446 doi:http://dx.doi.org/10.1111/j.1365-2958.2008.06261.x
  2. ↑ Konrad M. Analysis and in vivo disruption of the gene coding for adenylate kinase (ADK1) in the yeast Saccharomyces cerevisiae. J Biol Chem. 1988 Dec 25;263(36):19468-74. PMID:2848829
  3. ↑ Bandlow W, Strobel G, Zoglowek C, Oechsner U, Magdolen V. Yeast adenylate kinase is active simultaneously in mitochondria and cytoplasm and is required for non-fermentative growth. Eur J Biochem. 1988 Dec 15;178(2):451-7. PMID:2850178

1dvr, resolution 2.36Å

Drag the structure with the mouse to rotate

Proteopedia Page Contributors and Editors (what is this?)Proteopedia Page Contributors and Editors (what is this?)

OCA
Retrieved from "https://proteopedia.openfox.io/wiki/index.php?title=1dvr&oldid=4042356"