6i06: Difference between revisions

Latest revision as of 11:43, 24 January 2024

Crystal structure of psychrophilic phosphoglycerate kinase from Pseudomonas TACII18

Structural highlights

6i06 is a 1 chain structure with sequence from Pseudomonas. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	X-ray diffraction, Resolution 2Å
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

Q9RBS3_9PSED

Publication Abstract from PubMed

Crystal structures of phosphoglycerate kinase (PGK) from the psychrophile Pseudomonas sp. TACII 18 have been determined at high resolution by X-ray crystallography methods and compared with mesophilic, thermophilic and hyperthermophilic counterparts. PGK is a two-domain enzyme undergoing large domain movements to catalyze the production of ATP from 1,3-biphosphoglycerate and ADP. Whereas the conformational dynamics sustaining the catalytic mechanism of this hinge-bending enzyme now seems rather clear, the determinants which underlie high catalytic efficiency at low temperatures of this psychrophilic PGK were unknown. The comparison of the three-dimensional structures shows that multiple (global and local) specific adaptations have been brought about by this enzyme. Together, these reside in an overall increased flexibility of the cold-adapted PGK thereby allowing a better accessibility to the active site, but also a potentially more disordered transition state of the psychrophilic enzyme, due to the destabilization of some catalytic residues.

Structural determinants increasing flexibility confer cold adaptation in psychrophilic phosphoglycerate kinase.,Mandelman D, Ballut L, Wolff DA, Feller G, Gerday C, Haser R, Aghajari N Extremophiles. 2019 May 30. pii: 10.1007/s00792-019-01102-x. doi:, 10.1007/s00792-019-01102-x. PMID:31147836^[1]

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

References

↑ Mandelman D, Ballut L, Wolff DA, Feller G, Gerday C, Haser R, Aghajari N. Structural determinants increasing flexibility confer cold adaptation in psychrophilic phosphoglycerate kinase. Extremophiles. 2019 May 30. pii: 10.1007/s00792-019-01102-x. doi:, 10.1007/s00792-019-01102-x. PMID:31147836 doi:https://dx.doi.org/10.1007/s00792-019-01102-x

Proteopedia Page Contributors and Editors (what is this?)

OCA

[1] Mandelman D, Ballut L, Wolff DA, Feller G, Gerday C, Haser R, Aghajari N. Structural determinants increasing flexibility confer cold adaptation in psychrophilic phosphoglycerate kinase. Extremophiles. 2019 May 30. pii: 10.1007/s00792-019-01102-x. doi:, 10.1007/s00792-019-01102-x. PMID:31147836 doi:https://dx.doi.org/10.1007/s00792-019-01102-x

[1]

@@ Line 3: / Line 3: @@
 <StructureSection load='6i06' size='340' side='right'caption='[[6i06]], [[Resolution|resolution]] 2.00&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[6i06]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/"chlorobacterium"_guillebeau_1890,_nom._rejic._opin._6_(not_"chlorobacterium"_lauterborn_1916) "chlorobacterium" guillebeau 1890, nom. rejic. opin. 6 (not "chlorobacterium" lauterborn 1916)]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6I06 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6I06 FirstGlance]. <br>
+<table><tr><td colspan='2'>[[6i06]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Pseudomonas Pseudomonas]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6I06 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6I06 FirstGlance]. <br>
-</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[6hxe|6hxe]]</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]] 2&#8491;</td></tr>
-<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">pgk ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=286 "Chlorobacterium" Guillebeau 1890, nom. rejic. Opin. 6 (not "Chlorobacterium" Lauterborn 1916)])</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=6i06 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6i06 OCA], [https://pdbe.org/6i06 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6i06 RCSB], [https://www.ebi.ac.uk/pdbsum/6i06 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6i06 ProSAT]</span></td></tr>
-<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Phosphoglycerate_kinase Phosphoglycerate kinase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.7.2.3 2.7.2.3] </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=6i06 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6i06 OCA], [http://pdbe.org/6i06 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6i06 RCSB], [http://www.ebi.ac.uk/pdbsum/6i06 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6i06 ProSAT]</span></td></tr>
 </table>
+== Function ==
+[https://www.uniprot.org/uniprot/Q9RBS3_9PSED Q9RBS3_9PSED]
 <div style="background-color:#fffaf0;">
 == Publication Abstract from PubMed ==
@@ Line 18: / Line 18: @@
 </div>
 <div class="pdbe-citations 6i06" style="background-color:#fffaf0;"></div>
+==See Also==
+*[[Phosphoglycerate kinase 3D structures|Phosphoglycerate kinase 3D structures]]
 == References ==
 <references/>
@@ Line 23: / Line 26: @@
 </StructureSection>
 [[Category: Large Structures]]
-[[Category: Phosphoglycerate kinase]]
+[[Category: Pseudomonas]]
-[[Category: Aghajari, N]]
+[[Category: Aghajari N]]
-[[Category: Haser, R]]
+[[Category: Haser R]]
-[[Category: Mandelman, D]]
+[[Category: Mandelman D]]
-[[Category: Glycolysis]]
-[[Category: Hinge binding]]
-[[Category: Kinase]]
-[[Category: Transferase]]

6i06: Difference between revisions

Latest revision as of 11:43, 24 January 2024

Crystal structure of psychrophilic phosphoglycerate kinase from Pseudomonas TACII18

Structural highlights

Function

Publication Abstract from PubMed

See Also

References

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