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==X-RAY STRUCTURE OF NM23 HUMAN NUCLEOSIDE DIPHOSPHATE KINASE B COMPLEXED WITH GDP AT 2 ANGSTROMS RESOLUTION==
==X-RAY STRUCTURE OF NM23 HUMAN NUCLEOSIDE DIPHOSPHATE KINASE B COMPLEXED WITH GDP AT 2 ANGSTROMS RESOLUTION==
<StructureSection load='1nue' size='340' side='right' caption='[[1nue]], [[Resolution|resolution]] 2.00&Aring;' scene=''>
<StructureSection load='1nue' size='340' side='right'caption='[[1nue]], [[Resolution|resolution]] 2.00&Aring;' scene=''>
== Structural highlights ==
== Structural highlights ==
<table><tr><td colspan='2'>[[1nue]] is a 6 chain structure with sequence from [http://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1NUE OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1NUE FirstGlance]. <br>
<table><tr><td colspan='2'>[[1nue]] is a 6 chain structure with sequence from [https://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1NUE OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1NUE FirstGlance]. <br>
</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=GDP:GUANOSINE-5-DIPHOSPHATE'>GDP</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></td></tr>
</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>
<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><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='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=GDP:GUANOSINE-5-DIPHOSPHATE'>GDP</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></td></tr>
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1nue FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1nue OCA], [http://pdbe.org/1nue PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1nue RCSB], [http://www.ebi.ac.uk/pdbsum/1nue PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1nue ProSAT]</span></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=1nue FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1nue OCA], [https://pdbe.org/1nue PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1nue RCSB], [https://www.ebi.ac.uk/pdbsum/1nue PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1nue ProSAT]</span></td></tr>
</table>
</table>
== Function ==
== Function ==
[[http://www.uniprot.org/uniprot/NDKB_HUMAN NDKB_HUMAN]] Major role in the synthesis of nucleoside triphosphates other than ATP. Negatively regulates Rho activity by interacting with AKAP13/LBC. Acts as a transcriptional activator of the MYC gene; binds DNA non-specifically (PubMed:8392752). Exhibits histidine protein kinase activity.<ref>PMID:15249197</ref> <ref>PMID:20946858</ref>
[https://www.uniprot.org/uniprot/NDKB_HUMAN NDKB_HUMAN] Major role in the synthesis of nucleoside triphosphates other than ATP. Negatively regulates Rho activity by interacting with AKAP13/LBC. Acts as a transcriptional activator of the MYC gene; binds DNA non-specifically (PubMed:8392752). Exhibits histidine protein kinase activity.<ref>PMID:15249197</ref> <ref>PMID:20946858</ref>  
== Evolutionary Conservation ==
== Evolutionary Conservation ==
[[Image:Consurf_key_small.gif|200px|right]]
[[Image:Consurf_key_small.gif|200px|right]]
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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=1nue ConSurf].
</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=1nue ConSurf].
<div style="clear:both"></div>
<div style="clear:both"></div>
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
BACKGROUND: Nucleoside diphosphate (NDP) kinases provide precursors for DNA and RNA synthesis. In mammals, these enzymes are also involved in cell regulations. Human NDP kinase B, product of the human nm23-H2 gene, is both an enzyme and a transcription factor. It activates transcription of the c-myc oncogene independently of its catalytic function, by binding to its promoter DNA. How do the two functions coexist? RESULTS: Recombinant human NDP kinase B was co-crystallized with GDP. The X-ray structure was solved at 2.0 A resolution by molecular replacement from the homologous Drosophila Awd protein. Both enzymes are homo-hexamers with a characteristic beta alpha beta beta alpha beta fold. GDP binds near the active site His118. The guanine base is in a surface cleft and interacts with the C terminus of another subunit. CONCLUSIONS: The beta alpha beta beta alpha beta fold, also present in the 'palm' domain of Escherichia coli DNA polymerase I and HIV reverse transcriptase, is both a mononucleotide- and a polynucleotide-binding fold. If NDP kinase B binds DNA in the same way as the polymerases, the enzyme must undergo a conformation change in order to carry out gene activation.


X-ray structure of human nucleoside diphosphate kinase B complexed with GDP at 2 A resolution.,Morera S, Lacombe ML, Xu Y, LeBras G, Janin J Structure. 1995 Dec 15;3(12):1307-14. PMID:8747457<ref>PMID:8747457</ref>
==See Also==
 
*[[Nucleoside diphosphate kinase 3D structures|Nucleoside diphosphate kinase 3D structures]]
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
</div>
<div class="pdbe-citations 1nue" style="background-color:#fffaf0;"></div>
== References ==
== References ==
<references/>
<references/>
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</StructureSection>
</StructureSection>
[[Category: Homo sapiens]]
[[Category: Homo sapiens]]
[[Category: Nucleoside-diphosphate kinase]]
[[Category: Large Structures]]
[[Category: Janin, J]]
[[Category: Janin J]]
[[Category: Lacombe, M L]]
[[Category: Lacombe M-L]]
[[Category: Lebras, G]]
[[Category: Lebras G]]
[[Category: Morera, S]]
[[Category: Morera S]]
[[Category: Yingwu, X]]
[[Category: Yingwu X]]
[[Category: Nucleoside diphosphate]]
[[Category: Nucleoside triphosphate]]
[[Category: Phosphotransferase]]

Latest revision as of 10:59, 14 February 2024

X-RAY STRUCTURE OF NM23 HUMAN NUCLEOSIDE DIPHOSPHATE KINASE B COMPLEXED WITH GDP AT 2 ANGSTROMS RESOLUTIONX-RAY STRUCTURE OF NM23 HUMAN NUCLEOSIDE DIPHOSPHATE KINASE B COMPLEXED WITH GDP AT 2 ANGSTROMS RESOLUTION

Structural highlights

1nue is a 6 chain structure with sequence from Homo sapiens. 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

NDKB_HUMAN Major role in the synthesis of nucleoside triphosphates other than ATP. Negatively regulates Rho activity by interacting with AKAP13/LBC. Acts as a transcriptional activator of the MYC gene; binds DNA non-specifically (PubMed:8392752). Exhibits histidine protein kinase activity.[1] [2]

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. ↑ Iwashita S, Fujii M, Mukai H, Ono Y, Miyamoto M. Lbc proto-oncogene product binds to and could be negatively regulated by metastasis suppressor nm23-H2. Biochem Biophys Res Commun. 2004 Aug 6;320(4):1063-8. PMID:15249197 doi:http://dx.doi.org/10.1016/j.bbrc.2004.06.067
  2. ↑ Wieland T, Hippe HJ, Ludwig K, Zhou XB, Korth M, Klumpp S. Reversible histidine phosphorylation in mammalian cells: a teeter-totter formed by nucleoside diphosphate kinase and protein histidine phosphatase 1. Methods Enzymol. 2010;471:379-402. doi: 10.1016/S0076-6879(10)71020-X. Epub 2010 , Mar 1. PMID:20946858 doi:http://dx.doi.org/10.1016/S0076-6879(10)71020-X

1nue, resolution 2.00Å

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