1bhn: Difference between revisions

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-[[Image:1bhn.gif|left|200px]]<br /><applet load="1bhn" size="350" color="white" frame="true" align="right" spinBox="true"
-caption="1bhn, resolution 2.4&Aring;" />
-'''NUCLEOSIDE DIPHOSPHATE KINASE ISOFORM A FROM BOVINE RETINA'''<br />
-==Overview==
+==NUCLEOSIDE DIPHOSPHATE KINASE ISOFORM A FROM BOVINE RETINA==
-The crystal structures of two isoforms of nucleoside diphosphate kinase from bovine retina overexpressed in Escherischia coli have been determined to 2.4 A resolution. Both the isoforms, NBR-A and NBR-B, are hexameric and the fold of the monomer is in agreement with NDP-kinase structures from other biological sources. Although the polypeptide chains of the two isoforms differ by only two residues, they crystallize in different space groups. NBR-A crystallizes in space group P212121 with an entire hexamer in the asymmetric unit, while NBR-B crystallizes in space group P43212 with a trimer in the asymmetric unit. The highly conserved nucleotide-binding site observed in other nucleoside diphosphate kinase structures is also observed here. Both NBR-A and NBR-B were crystallized in the presence of cGMP. The nucleotide is bound with the base in the anti conformation. The NBR-A active site contained both cGMP and GDP each bound at half occupancy. Presumably, NBR-A had retained GDP (or GTP) from the purification process. The NBR-B active site contained only cGMP.
+<StructureSection load='1bhn' size='340' side='right'caption='[[1bhn]], [[Resolution|resolution]] 2.40&Aring;' scene=''>
+== Structural highlights ==
-==About this Structure==
+<table><tr><td colspan='2'>[[1bhn]] is a 6 chain structure with sequence from [https://en.wikipedia.org/wiki/Bos_taurus Bos taurus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1BHN OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1BHN FirstGlance]. <br>
-BHN is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Bos_taurus Bos taurus] with <scene name='pdbligand=35G:'>35G</scene> as [http://en.wikipedia.org/wiki/ligand ligand]. Active as [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] Known structural/functional Sites: <scene name='pdbsite=A:C-Gmp+And+Gdp+Are+Found+(Each+w.+Half+Occupancy)+In+The+...'>A</scene>, <scene name='pdbsite=AND F:C-Gmp+And+Gdp+Are+Found+(Each+w.+Half+Occupancy)+In+The+...'>AND F</scene>, <scene name='pdbsite=B:C-Gmp+And+Gdp+Are+Found+(Each+w.+Half+Occupancy)+In+The+...'>B</scene>, <scene name='pdbsite=C:C-Gmp+And+Gdp+Are+Found+(Each+w.+Half+Occupancy)+In+The+...'>C</scene>, <scene name='pdbsite=D:C-Gmp+And+Gdp+Are+Found+(Each+w.+Half+Occupancy)+In+The+...'>D</scene> and <scene name='pdbsite=E:C-Gmp+And+Gdp+Are+Found+(Each+w.+Half+Occupancy)+In+The+...'>E</scene>. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1BHN OCA].
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.4&#8491;</td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=35G:GUANOSINE-3,5-MONOPHOSPHATE'>35G</scene>, <scene name='pdbligand=GDP:GUANOSINE-5-DIPHOSPHATE'>GDP</scene></td></tr>
-==Reference==
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1bhn FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1bhn OCA], [https://pdbe.org/1bhn PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1bhn RCSB], [https://www.ebi.ac.uk/pdbsum/1bhn PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1bhn ProSAT]</span></td></tr>
-The three-dimensional structures of two isoforms of nucleoside diphosphate kinase from bovine retina., Ladner JE, Abdulaev NG, Kakuev DL, Tordova M, Ridge KD, Gilliland GL, Acta Crystallogr D Biol Crystallogr. 1999 Jun;55(Pt 6):1127-35. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=10329774 10329774]
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/NDKA1_BOVIN NDKA1_BOVIN]
+== 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/bh/1bhn_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=1bhn ConSurf].
+<div style="clear:both"></div>
+__TOC__
+</StructureSection>
 [[Category: Bos taurus]]
-[[Category: Nucleoside-diphosphate kinase]]
+[[Category: Large Structures]]
-[[Category: Single protein]]
+[[Category: Abdulaev NG]]
-[[Category: Abdulaev, N G.]]
+[[Category: Eisenstein E]]
-[[Category: Eisenstein, E.]]
+[[Category: Fujiwara JH]]
-[[Category: Fujiwara, J H.]]
+[[Category: Gilliland GL]]
-[[Category: Gilliland, G L.]]
+[[Category: Kakuev DL]]
-[[Category: Kakuev, D L.]]
+[[Category: Karaschuk GN]]
-[[Category: Karaschuk, G N.]]
+[[Category: Ladner JE]]
-[[Category: Ladner, J E.]]
+[[Category: Ridge KD]]
-[[Category: Ridge, K D.]]
+[[Category: Tordova M]]
-[[Category: Tordova, M.]]
-[[Category: 35G]]
-[[Category: phosphotransferase]]
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Feb 21 11:55:22 2008''