2bi1

From Proteopedia

(Difference between revisions)

Revision as of 11:21, 22 May 2024

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

Structural highlights

2bi1 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.

References

↑ 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
↑ 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

1 Structural highlights
2 Function
3 Evolutionary Conservation
4 Publication Abstract from PubMed
5 See Also
6 References

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/2bi1"

@@ Line 3: / Line 3: @@
 <StructureSection load='2bi1' size='340' side='right'caption='[[2bi1]], [[Resolution|resolution]] 1.69&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[2bi1]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Atcc_27647 Atcc 27647]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2BI1 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2BI1 FirstGlance]. <br>
+<table><tr><td colspan='2'>[[2bi1]] 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=2BI1 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2BI1 FirstGlance]. <br>
-</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>
+</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='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[1w23|1w23]], [[2bhx|2bhx]], [[2bi2|2bi2]], [[2bi3|2bi3]], [[2bi5|2bi5]], [[2bi9|2bi9]], [[2bia|2bia]], [[2bie|2bie]], [[2big|2big]]</div></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='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/Phosphoserine_transaminase Phosphoserine transaminase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.6.1.52 2.6.1.52] </span></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=2bi1 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2bi1 OCA], [https://pdbe.org/2bi1 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2bi1 RCSB], [https://www.ebi.ac.uk/pdbsum/2bi1 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2bi1 ProSAT]</span></td></tr>
 </table>
 == Function ==
-[[https://www.uniprot.org/uniprot/SERC_BACAO SERC_BACAO]] Catalyzes the reversible conversion of 3-phosphohydroxypyruvate to phosphoserine and of 3-hydroxy-2-oxo-4-phosphonooxybutanoate to phosphohydroxythreonine.<ref>PMID:14646107</ref>
+[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]]
@@ Line 37: / Line 36: @@
 __TOC__
 </StructureSection>
-[[Category: Atcc 27647]]
+[[Category: Alkalihalobacillus alcalophilus]]
 [[Category: Large Structures]]
-[[Category: Phosphoserine transaminase]]
+[[Category: Dubnovitsky AP]]
-[[Category: Dubnovitsky, A P]]
+[[Category: Papageorgiou AC]]
-[[Category: Papageorgiou, A C]]
+[[Category: Popov AN]]
-[[Category: Popov, A N]]
+[[Category: Ravelli RBG]]
-[[Category: Ravelli, R B.G]]
-[[Category: Aminotransferase]]
-[[Category: Pyridoxal-5'-phosphate]]
-[[Category: Radiation damage]]
-[[Category: Transferase]]

2bi1

From Proteopedia

Revision as of 11:21, 22 May 2024

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

Structural highlights

Function

Evolutionary Conservation

Publication Abstract from PubMed

See Also

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

Views

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