2big

From Proteopedia

(Difference between revisions)

Revision as of 09:44, 5 May 2021

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

Structural highlights

2big is a 2 chain structure with sequence from Atcc 27647. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Ligands:	, , , ,
Related:	1w23, 2bhx, 2bi1, 2bi2, 2bi3, 2bi5, 2bi9, 2bia, 2bie
Activity:	Phosphoserine transaminase, with EC number 2.6.1.52
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

[SERC_BACAO] 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/2big"

@@ Line 3: / Line 3: @@
 <StructureSection load='2big' size='340' side='right'caption='[[2big]], [[Resolution|resolution]] 1.30&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[2big]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Atcc_27647 Atcc 27647]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2BIG OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2BIG FirstGlance]. <br>
+<table><tr><td colspan='2'>[[2big]] 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=2BIG OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2BIG FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><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>
+</td></tr><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='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[1w23|1w23]], [[2bhx|2bhx]], [[2bi1|2bi1]], [[2bi2|2bi2]], [[2bi3|2bi3]], [[2bi5|2bi5]], [[2bi9|2bi9]], [[2bia|2bia]], [[2bie|2bie]]</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]], [[2bi1|2bi1]], [[2bi2|2bi2]], [[2bi3|2bi3]], [[2bi5|2bi5]], [[2bi9|2bi9]], [[2bia|2bia]], [[2bie|2bie]]</div></td></tr>
-<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[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] </span></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'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2big FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2big OCA], [http://pdbe.org/2big PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2big RCSB], [http://www.ebi.ac.uk/pdbsum/2big PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=2big ProSAT]</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=2big FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2big OCA], [https://pdbe.org/2big PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2big RCSB], [https://www.ebi.ac.uk/pdbsum/2big PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2big ProSAT]</span></td></tr>
 </table>
 == Function ==
-[[http://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_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>
 == Evolutionary Conservation ==
 [[Image:Consurf_key_small.gif|200px|right]]

2big

From Proteopedia

Revision as of 09:44, 5 May 2021

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

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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