2bie: Difference between revisions

← Older edit

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

OCA

@@ Line 1: / Line 1: @@
-[[Image:2bie.png|left|200px]]
-{{STRUCTURE_2bie|  PDB=2bie  |  SCENE=  }}
+==Radiation damage of the Schiff base in phosphoserine aminotransferase (structure H)==
+<StructureSection load='2bie' size='340' side='right'caption='[[2bie]], [[Resolution|resolution]] 1.30&Aring;' scene=''>
+== Structural highlights ==
+<table><tr><td colspan='2'>[[2bie]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Alkalihalobacillus_alcalophilus Alkalihalobacillus alcalophilus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2BIE OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2BIE 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]] 1.3&#8491;</td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=PEG:DI(HYDROXYETHYL)ETHER'>PEG</scene>, <scene name='pdbligand=PGE:TRIETHYLENE+GLYCOL'>PGE</scene>, <scene name='pdbligand=PLP:PYRIDOXAL-5-PHOSPHATE'>PLP</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=2bie FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2bie OCA], [https://pdbe.org/2bie PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2bie RCSB], [https://www.ebi.ac.uk/pdbsum/2bie PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2bie ProSAT]</span></td></tr>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/SERC_ALKAL SERC_ALKAL] Catalyzes the reversible conversion of 3-phosphohydroxypyruvate to phosphoserine and of 3-hydroxy-2-oxo-4-phosphonooxybutanoate to phosphohydroxythreonine.<ref>PMID:14646107</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/bi/2bie_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=2bie ConSurf].
+<div style="clear:both"></div>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+The X-ray susceptibility of the lysine-pyridoxal-5'-phosphate Schiff base in Bacillus alcalophilus phosphoserine aminotransferase has been investigated using crystallographic data collected at 100 K to 1.3 A resolution, complemented by on-line spectroscopic studies. X-rays induce deprotonation of the internal aldimine, changes in the Schiff base conformation, displacement of the cofactor molecule, and disruption of the Schiff base linkage between pyridoxal-5'-phosphate and the Lys residue. Analysis of the "undamaged" structure reveals a significant chemical strain on the internal aldimine bond that leads to a pronounced geometrical distortion of the cofactor. However, upon crystal exposure to the X-rays, the strain and distortion are relaxed and eventually diminished when the total absorbed dose has exceeded 4.7 x 10(6) Ggamma. Our data provide new insights into the enzymatic activation of pyridoxal-5'-phosphate and suggest that special care should be taken while using macromolecular crystallography to study details in strained active sites.
-===RADIATION DAMAGE OF THE SCHIFF BASE IN PHOSPHOSERINE AMINOTRANSFERASE (STRUCTURE H)===
+Strain relief at the active site of phosphoserine aminotransferase induced by radiation damage.,Dubnovitsky AP, Ravelli RB, Popov AN, Papageorgiou AC Protein Sci. 2005 Jun;14(6):1498-507. Epub 2005 May 9. PMID:15883191<ref>PMID:15883191</ref>
-{{ABSTRACT_PUBMED_15883191}}
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
+</div>
-==About this Structure==
+<div class="pdbe-citations 2bie" style="background-color:#fffaf0;"></div>
-[[2bie]] is a 2 chain structure of [[Phosphoserine aminotransferase]] with sequence from [http://en.wikipedia.org/wiki/Bacillus_alcalophilus Bacillus alcalophilus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2BIE OCA].
 ==See Also==
 *[[Phosphoserine aminotransferase|Phosphoserine aminotransferase]]
+== References ==
-==Reference==
+<references/>
-<ref group="xtra">PMID:015883191</ref><references group="xtra"/>
+__TOC__
-[[Category: Bacillus alcalophilus]]
+</StructureSection>
-[[Category: Phosphoserine transaminase]]
+[[Category: Alkalihalobacillus alcalophilus]]
-[[Category: Dubnovitsky, A P.]]
+[[Category: Large Structures]]
-[[Category: Papageorgiou, A C.]]
+[[Category: Dubnovitsky AP]]
-[[Category: Popov, A N.]]
+[[Category: Papageorgiou AC]]
-[[Category: Ravelli, R B.G.]]
+[[Category: Popov AN]]
-[[Category: Aminotransferase]]
+[[Category: Ravelli RBG]]
-[[Category: Pyridoxal-5'-phosphate]]
-[[Category: Radiation damage]]
-[[Category: Transferase]]