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[[Image:2bi3.gif|left|200px]]<br />
<applet load="2bi3" size="450" color="white" frame="true" align="right" spinBox="true"
caption="2bi3, resolution 1.69&Aring;" />
'''RADIATION DAMAGE OF THE SCHIFF BASE IN PHOSPHOSERINE AMINOTRANSFERASE (STRUCTURE D)'''<br />


==Overview==
==Radiation damage of the Schiff base in phosphoserine aminotransferase (structure D)==
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.
<StructureSection load='2bi3' size='340' side='right'caption='[[2bi3]], [[Resolution|resolution]] 1.69&Aring;' 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]] 1.69&#8491;</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.


==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>
2BI3 is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Bacillus_alcalophilus Bacillus alcalophilus] with MG, CL, PLP, 1PE and PEG as [http://en.wikipedia.org/wiki/ligands ligands]. Active as [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] Structure known Active Site: AC1. Full crystallographic information is available from [http://ispc.weizmann.ac.il/oca-bin/ocashort?id=2BI3 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://ispc.weizmann.ac.il//pmbin/getpm?pmid=15883191 15883191]
</div>
[[Category: Bacillus alcalophilus]]
<div class="pdbe-citations 2bi3" 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: 1PE]]
[[Category: CL]]
[[Category: MG]]
[[Category: PEG]]
[[Category: PLP]]
[[Category: aminotransferase]]
[[Category: pyridoxal-5'-phosphate]]
[[Category: radiation damage]]
[[Category: transferase]]


''Page seeded by [http://ispc.weizmann.ac.il/oca OCA ] on Mon Nov  5 15:21:29 2007''
==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]]

Latest revision as of 14:21, 22 May 2024

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

Structural highlights

2bi3 is a 2 chain structure with sequence from Alkalihalobacillus alcalophilus. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:X-ray diffraction, Resolution 1.69Å
Ligands:, , , ,
Resources:FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

SERC_ALKAL Catalyzes the reversible conversion of 3-phosphohydroxypyruvate to phosphoserine and of 3-hydroxy-2-oxo-4-phosphonooxybutanoate to phosphohydroxythreonine.[1]

Evolutionary Conservation

Check, as determined by ConSurfDB. You may read the explanation of the method and the full data available from ConSurf.

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[2]

From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.

See Also

References

  1. ↑ Dubnovitsky AP, Kapetaniou EG, Papageorgiou AC. Expression, purification, crystallization and preliminary crystallographic analysis of phosphoserine aminotransferase from Bacillus alcalophilus. Acta Crystallogr D Biol Crystallogr. 2003 Dec;59(Pt 12):2319-21. Epub 2003 Nov, 27. PMID:14646107
  2. ↑ Dubnovitsky AP, Ravelli RB, Popov AN, Papageorgiou AC. Strain relief at the active site of phosphoserine aminotransferase induced by radiation damage. Protein Sci. 2005 Jun;14(6):1498-507. Epub 2005 May 9. PMID:15883191 doi:http://dx.doi.org/10.1110/ps.051397905

2bi3, resolution 1.69Å

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