1be4: Difference between revisions

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-[[Image:1be4.gif|left|200px]]<br />
-<applet load="1be4" size="450" color="white" frame="true" align="right" spinBox="true"
-caption="1be4, resolution 2.4&Aring;" />
-'''NUCLEOSIDE DIPHOSPHATE KINASE ISOFORM B FROM BOVINE RETINA'''<br />
-==Overview==
+==NUCLEOSIDE DIPHOSPHATE KINASE ISOFORM B FROM BOVINE RETINA==
-The biochemical and structural properties of bovine retinal nucleoside, diphosphate kinase were investigated. The enzyme showed two polypeptides, of approximately 17.5 and 18.5 kDa on SDS-PAGE, while isoelectric focusing, revealed seven to eight proteins with a pI range of 7.4-8.2. Sedimentation, equilibrium yielded a molecular mass of 96 +/- 2 kDa for the enzyme., Carbohydrate analysis revealed that both polypeptides contained Gal, Man, GlcNAc, Fuc, and GalNac saccharides. Like other nucleoside diphosphate, kinases, the retinal enzyme showed substantial differences in the Km, values for various di- and triphosphate nucleotides. Immunogold labeling, of bovine retina revealed that the enzyme is localized on both the, membranes and in the cytoplasm. Screening of a retinal cDNA library, yielded full-length clones encoding two distinct isoforms (NBR-A and, NBR-B). Both isoforms were overexpressed in Escherichia coli and their, biochemical properties compared with retinal NDP-kinase. The structures of, NBR-A and NBR-B were determined by X-ray crystallography in the presence, of guanine nucleotide(s). Both isoforms are hexameric, and the fold of the, monomer is similar to other nucleoside diphosphate kinase structures. The, NBR-A active site contained both a cGMP and a GDP molecule each bound at, half occupancy while the NBR-B active site contained only cGMP.
+<StructureSection load='1be4' size='340' side='right'caption='[[1be4]], [[Resolution|resolution]] 2.40&Aring;' scene=''>
+== Structural highlights ==
+<table><tr><td colspan='2'>[[1be4]] is a 3 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=1BE4 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1BE4 FirstGlance]. <br>
+</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=PCG:CYCLIC+GUANOSINE+MONOPHOSPHATE'>PCG</scene></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=1be4 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1be4 OCA], [https://pdbe.org/1be4 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1be4 RCSB], [https://www.ebi.ac.uk/pdbsum/1be4 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1be4 ProSAT]</span></td></tr>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/NDKA2_BOVIN NDKA2_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/be/1be4_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=1be4 ConSurf].
+<div style="clear:both"></div>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+The biochemical and structural properties of bovine retinal nucleoside diphosphate kinase were investigated. The enzyme showed two polypeptides of approximately 17.5 and 18.5 kDa on SDS-PAGE, while isoelectric focusing revealed seven to eight proteins with a pI range of 7.4-8.2. Sedimentation equilibrium yielded a molecular mass of 96 +/- 2 kDa for the enzyme. Carbohydrate analysis revealed that both polypeptides contained Gal, Man, GlcNAc, Fuc, and GalNac saccharides. Like other nucleoside diphosphate kinases, the retinal enzyme showed substantial differences in the Km values for various di- and triphosphate nucleotides. Immunogold labeling of bovine retina revealed that the enzyme is localized on both the membranes and in the cytoplasm. Screening of a retinal cDNA library yielded full-length clones encoding two distinct isoforms (NBR-A and NBR-B). Both isoforms were overexpressed in Escherichia coli and their biochemical properties compared with retinal NDP-kinase. The structures of NBR-A and NBR-B were determined by X-ray crystallography in the presence of guanine nucleotide(s). Both isoforms are hexameric, and the fold of the monomer is similar to other nucleoside diphosphate kinase structures. The NBR-A active site contained both a cGMP and a GDP molecule each bound at half occupancy while the NBR-B active site contained only cGMP.
-==About this Structure==
+Nucleoside diphosphate kinase from bovine retina: purification, subcellular localization, molecular cloning, and three-dimensional structure.,Abdulaev NG, Karaschuk GN, Ladner JE, Kakuev DL, Yakhyaev AV, Tordova M, Gaidarov IO, Popov VI, Fujiwara JH, Chinchilla D, Eisenstein E, Gilliland GL, Ridge KD Biochemistry. 1998 Oct 6;37(40):13958-67. PMID:9760230<ref>PMID:9760230</ref>
-BE4 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 PCG 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] Structure known Active Site: NUL. Full crystallographic information is available from [http://ispc.weizmann.ac.il/oca-bin/ocashort?id=1BE4 OCA].
-==Reference==
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-Nucleoside diphosphate kinase from bovine retina: purification, subcellular localization, molecular cloning, and three-dimensional structure., Abdulaev NG, Karaschuk GN, Ladner JE, Kakuev DL, Yakhyaev AV, Tordova M, Gaidarov IO, Popov VI, Fujiwara JH, Chinchilla D, Eisenstein E, Gilliland GL, Ridge KD, Biochemistry. 1998 Oct 6;37(40):13958-67. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=9760230 9760230]
+</div>
+<div class="pdbe-citations 1be4" style="background-color:#fffaf0;"></div>
+== References ==
+<references/>
+__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: PCG]]
-[[Category: phosphotransferase]]
-''Page seeded by [http://ispc.weizmann.ac.il/oca OCA ] on Mon Nov  5 14:54:23 2007''