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[[Image:1kdn.jpg|left|200px]]


{{Structure
==STRUCTURE OF NUCLEOSIDE DIPHOSPHATE KINASE==
|PDB= 1kdn |SIZE=350|CAPTION= <scene name='initialview01'>1kdn</scene>, resolution 2.0&Aring;
<StructureSection load='1kdn' size='340' side='right'caption='[[1kdn]], [[Resolution|resolution]] 2.00&Aring;' scene=''>
|SITE=  
== Structural highlights ==
|LIGAND= <scene name='pdbligand=ADP:ADENOSINE-5&#39;-DIPHOSPHATE'>ADP</scene>, <scene name='pdbligand=AF3:ALUMINUM+FLUORIDE'>AF3</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>
<table><tr><td colspan='2'>[[1kdn]] is a 3 chain structure with sequence from [https://en.wikipedia.org/wiki/Dictyostelium_discoideum Dictyostelium discoideum]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1KDN OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1KDN FirstGlance]. <br>
|ACTIVITY= <span class='plainlinks'>[http://en.wikipedia.org/wiki/Nucleoside-diphosphate_kinase Nucleoside-diphosphate kinase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.7.4.6 2.7.4.6] </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&#8491;</td></tr>
|GENE=
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ADP:ADENOSINE-5-DIPHOSPHATE'>ADP</scene>, <scene name='pdbligand=AF3:ALUMINUM+FLUORIDE'>AF3</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</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=1kdn FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1kdn OCA], [https://pdbe.org/1kdn PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1kdn RCSB], [https://www.ebi.ac.uk/pdbsum/1kdn PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1kdn ProSAT]</span></td></tr>
|RELATEDENTRY=
</table>
|RESOURCES=<span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1kdn FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1kdn OCA], [http://www.ebi.ac.uk/pdbsum/1kdn PDBsum], [http://www.rcsb.org/pdb/explore.do?structureId=1kdn RCSB]</span>
== Function ==
}}
[https://www.uniprot.org/uniprot/NDKC_DICDI NDKC_DICDI]
== 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/kd/1kdn_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=1kdn ConSurf].
<div style="clear:both"></div>


'''STRUCTURE OF NUCLEOSIDE DIPHOSPHATE KINASE'''
==See Also==
 
*[[Nucleoside diphosphate kinase 3D structures|Nucleoside diphosphate kinase 3D structures]]
 
__TOC__
==Overview==
</StructureSection>
Nucleoside diphosphate kinase reversibly transfers the gamma-phosphate of ATP onto its active site histidine. We have investigated the transition state of histidine phosphorylation with the high-resolution crystal structures of the enzyme from Dictyostelium discoideum with MgADP and either aluminium or beryllium fluoride. The bound aluminium fluoride species is the neutral species AlF3 and not the more common AlF4-. AlF3 forms a trigonal bipyramid that makes it an accurate analog of the transition state of the gamma-phosphate of ATP undergoing transfer to the catalytic histidine. Its axial ligands are a histidine nitrogen and a beta-phosphate oxygen. Beryllium fluoride also binds at the same position and with the same ligands but in a tetrahedral geometry resembling the Michaelis complex rather than the transition state. The two x-ray structures show explicit enzyme-substrate interactions that discriminate between the ground and the transition states of the reaction. They also illustrate the partially dissociative geometry of the transition state of phosphoryl transfer and demonstrate the potential applications of metallofluorides for the study of kinase mechanisms.
 
==About this Structure==
1KDN is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Dictyostelium_discoideum Dictyostelium discoideum]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1KDN OCA].
 
==Reference==
AlF3 mimics the transition state of protein phosphorylation in the crystal structure of nucleoside diphosphate kinase and MgADP., Xu YW, Morera S, Janin J, Cherfils J, Proc Natl Acad Sci U S A. 1997 Apr 15;94(8):3579-83. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/9108019 9108019]
[[Category: Dictyostelium discoideum]]
[[Category: Dictyostelium discoideum]]
[[Category: Nucleoside-diphosphate kinase]]
[[Category: Large Structures]]
[[Category: Single protein]]
[[Category: Cherfils J]]
[[Category: Cherfils, J.]]
[[Category: Janin J]]
[[Category: Janin, J.]]
[[Category: Morera S]]
[[Category: Morera, S.]]
[[Category: Xu YW]]
[[Category: Xu, Y W.]]
[[Category: atp-binding]]
[[Category: kinase]]
[[Category: phosphotransferase]]
[[Category: transferase]]
 
''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sun Mar 30 21:47:01 2008''

Latest revision as of 10:46, 7 February 2024

STRUCTURE OF NUCLEOSIDE DIPHOSPHATE KINASESTRUCTURE OF NUCLEOSIDE DIPHOSPHATE KINASE

Structural highlights

1kdn is a 3 chain structure with sequence from Dictyostelium discoideum. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:X-ray diffraction, Resolution 2Å
Ligands:, ,
Resources:FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

NDKC_DICDI

Evolutionary Conservation

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

See Also

1kdn, resolution 2.00Å

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