2bi2: Difference between revisions

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Revision as of 17:02, 20 March 2008

File:2bi2.gif

, resolution 1.69Å

Sites:

Ligands:

, , , and

Activity:

Phosphoserine transaminase, with EC number 2.6.1.52

Coordinates:

save as pdb, mmCIF, xml

RADIATION DAMAGE OF THE SCHIFF BASE IN PHOSPHOSERINE AMINOTRANSFERASE (STRUCTURE C)

OverviewOverview

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 StructureAbout this Structure

2BI2 is a Single protein structure of sequence from Bacillus alcalophilus. Full crystallographic information is available from OCA.

ReferenceReference

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

Page seeded by OCA on Thu Mar 20 16:02:13 2008

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

OCA

@@ Line 1: / Line 1: @@
-[[Image:2bi2.gif|left|200px]]<br /><applet load="2bi2" size="350" color="white" frame="true" align="right" spinBox="true"
+[[Image:2bi2.gif|left|200px]]
-caption="2bi2, resolution 1.69&Aring;" />
-'''RADIATION DAMAGE OF THE SCHIFF BASE IN PHOSPHOSERINE AMINOTRANSFERASE (STRUCTURE C)'''<br />
+ {{Structure
+|PDB= 2bi2 |SIZE=350|CAPTION= <scene name='initialview01'>2bi2</scene>, resolution 1.69&Aring;
+|SITE= <scene name='pdbsite=AC1:Peg+Binding+Site+For+Chain+A'>AC1</scene>
+|LIGAND= <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=PLP:PYRIDOXAL-5'-PHOSPHATE'>PLP</scene>, <scene name='pdbligand=1PE:PENTAETHYLENE+GLYCOL'>1PE</scene> and <scene name='pdbligand=PEG:DI(HYDROXYETHYL)ETHER'>PEG</scene>
+|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]
+|GENE=
+}}
+'''RADIATION DAMAGE OF THE SCHIFF BASE IN PHOSPHOSERINE AMINOTRANSFERASE (STRUCTURE C)'''
 ==Overview==
@@ Line 7: / Line 16: @@
 ==About this Structure==
-BI2 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 <scene name='pdbligand=MG:'>MG</scene>, <scene name='pdbligand=CL:'>CL</scene>, <scene name='pdbligand=PLP:'>PLP</scene>, <scene name='pdbligand=1PE:'>1PE</scene> and <scene name='pdbligand=PEG:'>PEG</scene> 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] Known structural/functional Site: <scene name='pdbsite=AC1:Peg+Binding+Site+For+Chain+A'>AC1</scene>. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2BI2 OCA].
+BI2 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=2BI2 OCA].
 ==Reference==
-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]
+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]
 [[Category: Bacillus alcalophilus]]
 [[Category: Phosphoserine transaminase]]
@@ Line 28: / Line 37: @@
 [[Category: transferase]]
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Feb 21 16:38:02 2008''
+''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Mar 20 16:02:13 2008''