2bie

From Proteopedia

(Difference between revisions)
Jump to: navigation, search
Current revision (08:24, 9 April 2025) (edit) (undo)
 
(15 intermediate revisions not shown.)
Line 1: Line 1:
-
[[Image:2bie.gif|left|200px]]
 
-
{{Structure
+
==Radiation damage of the Schiff base in phosphoserine aminotransferase (structure H)==
-
|PDB= 2bie |SIZE=350|CAPTION= <scene name='initialview01'>2bie</scene>, resolution 1.30&Aring;
+
<StructureSection load='2bie' size='340' side='right'caption='[[2bie]], [[Resolution|resolution]] 1.30&Aring;' scene=''>
-
|SITE= <scene name='pdbsite=AC1:Peg+Binding+Site+For+Chain+B'>AC1</scene>
+
== Structural highlights ==
-
|LIGAND= <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=PLP:PYRIDOXAL-5&#39;-PHOSPHATE'>PLP</scene>, <scene name='pdbligand=PGE:TRIETHYLENE+GLYCOL'>PGE</scene> and <scene name='pdbligand=PEG:DI(HYDROXYETHYL)ETHER'>PEG</scene>
+
<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>
-
|ACTIVITY= [http://en.wikipedia.org/wiki/Phosphoserine_transaminase Phosphoserine transaminase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.6.1.52 2.6.1.52]
+
</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>
-
|GENE=
+
<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>
-
'''RADIATION DAMAGE OF THE SCHIFF BASE IN PHOSPHOSERINE AMINOTRANSFERASE (STRUCTURE H)'''
+
== 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 ==
-
==Overview==
+
[[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/initialview03.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.
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.
-
==About this Structure==
+
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>
-
2BIE is a [[Single protein]] structure of 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].
+
-
==Reference==
+
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-
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:[http://www.ncbi.nlm.nih.gov/pubmed/15883191 15883191]
+
</div>
-
[[Category: Bacillus alcalophilus]]
+
<div class="pdbe-citations 2bie" style="background-color:#fffaf0;"></div>
-
[[Category: Phosphoserine transaminase]]
+
-
[[Category: Single protein]]
+
-
[[Category: Dubnovitsky, A P.]]
+
-
[[Category: Papageorgiou, A C.]]
+
-
[[Category: Popov, A N.]]
+
-
[[Category: Ravelli, R B.G.]]
+
-
[[Category: CL]]
+
-
[[Category: MG]]
+
-
[[Category: PEG]]
+
-
[[Category: PGE]]
+
-
[[Category: PLP]]
+
-
[[Category: aminotransferase]]
+
-
[[Category: pyridoxal-5'-phosphate]]
+
-
[[Category: radiation damage]]
+
-
[[Category: transferase]]
+
-
''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sun Mar 23 14:45:13 2008''
+
==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]]

Current revision

Radiation damage of the Schiff base in phosphoserine aminotransferase (structure H)

PDB ID 2bie

Drag the structure with the mouse to rotate

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/2bie"
Personal tools