2bi3: Difference between revisions
No edit summary |
No edit summary |
||
| (18 intermediate revisions by the same user not shown) | |||
| Line 1: | Line 1: | ||
== | ==Radiation damage of the Schiff base in phosphoserine aminotransferase (structure D)== | ||
The X-ray susceptibility of the lysine-pyridoxal-5'-phosphate Schiff base | <StructureSection load='2bi3' size='340' side='right'caption='[[2bi3]], [[Resolution|resolution]] 1.69Å' scene=''> | ||
== Structural highlights == | |||
<table><tr><td colspan='2'>[[2bi3]] 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=2BI3 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2BI3 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]] 1.69Å</td></tr> | |||
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=1PE:PENTAETHYLENE+GLYCOL'>1PE</scene>, <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=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=2bi3 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2bi3 OCA], [https://pdbe.org/2bi3 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2bi3 RCSB], [https://www.ebi.ac.uk/pdbsum/2bi3 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2bi3 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/2bi3_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=2bi3 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. | |||
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> | |||
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | |||
</div> | |||
<div class="pdbe-citations 2bi3" style="background-color:#fffaf0;"></div> | |||
==See Also== | |||
*[[Phosphoserine aminotransferase|Phosphoserine aminotransferase]] | |||
== References == | |||
<references/> | |||
__TOC__ | |||
</StructureSection> | |||
[[Category: Alkalihalobacillus alcalophilus]] | |||
[[Category: Large Structures]] | |||
[[Category: Dubnovitsky AP]] | |||
[[Category: Papageorgiou AC]] | |||
[[Category: Popov AN]] | |||
[[Category: Ravelli RBG]] | |||