2e28: Difference between revisions

From Proteopedia
Jump to navigation Jump to search
← Older edit
No edit summary
No edit summary
 
(11 intermediate revisions by the same user not shown)
Line 1: Line 1:
{{Seed}}
[[Image:2e28.png|left|200px]]


<!--
==Crystal structure analysis of pyruvate kinase from Bacillus stearothermophilus==
The line below this paragraph, containing "STRUCTURE_2e28", creates the "Structure Box" on the page.
<StructureSection load='2e28' size='340' side='right'caption='[[2e28]], [[Resolution|resolution]] 2.40&Aring;' scene=''>
You may change the PDB parameter (which sets the PDB file loaded into the applet)
== Structural highlights ==
or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
<table><tr><td colspan='2'>[[2e28]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Geobacillus_stearothermophilus Geobacillus stearothermophilus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2E28 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2E28 FirstGlance]. <br>
or leave the SCENE parameter empty for the default display.
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.4&#8491;</td></tr>
-->
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
{{STRUCTURE_2e28|  PDB=2e28  |  SCENE=  }}
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=2e28 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2e28 OCA], [https://pdbe.org/2e28 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2e28 RCSB], [https://www.ebi.ac.uk/pdbsum/2e28 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2e28 ProSAT]</span></td></tr>
</table>
== Function ==
[https://www.uniprot.org/uniprot/KPYK_GEOSE KPYK_GEOSE]
== 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/e2/2e28_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=2e28 ConSurf].
<div style="clear:both"></div>
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
The pyruvate kinase (PK) from a moderate thermophile, Geobacillus stearothermophilus, is an allosteric enzyme activated by AMP and ribose 5-phosphate but not fructose 1, 6-bisphosphate (FBP), which is a common activator of PKs. It has an extra C-terminal sequence (ECTS), which contains a highly conserved phosphoenolpyruvate (PEP) binding motif, but its function and structure remain unclear. To elucidate the structural characteristics of the effector-binding site and the ECTS, the crystal structure of the C9S/C268S mutant of the enzyme was determined at 2.4 A resolution. The crystal belonged to space group P6(2)22, with unit cell parameters a, b = 145.97 A, c = 118.03 A. The enzyme was a homotetramer and its overall domain structure was similar to the previously solved structures except that the ECTS formed a new domain (C' domain). The structure of the C' domain closely resembled that of the PEP binding domain of maize pyruvate phosphate dikinase. A sulphate ion was found in a pocket in the effector-binding C domain. This site corresponds to the 6-phosphate group-binding site in yeast PK bound FBP and seems to be the effector-binding site. Through comparison of the structure of the putative effector-binding site to that of the FBP binding site of the yeast enzyme, the structural basis of the effector specificity of the G. stearothermophilus PK is discussed.


===Crystal structure analysis of pyruvate kinase from Bacillus stearothermophilus===
Crystal structure of pyruvate kinase from Geobacillus stearothermophilus.,Suzuki K, Ito S, Shimizu-Ibuka A, Sakai H J Biochem. 2008 Sep;144(3):305-12. Epub 2008 May 28. PMID:18511452<ref>PMID:18511452</ref>


From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
</div>
<div class="pdbe-citations 2e28" style="background-color:#fffaf0;"></div>


<!--
==See Also==
The line below this paragraph, {{ABSTRACT_PUBMED_18511452}}, adds the Publication Abstract to the page
*[[Pyruvate kinase 3D structures|Pyruvate kinase 3D structures]]
(as it appears on PubMed at http://www.pubmed.gov), where 18511452 is the PubMed ID number.
== References ==
-->
<references/>
{{ABSTRACT_PUBMED_18511452}}
__TOC__
 
</StructureSection>
==About this Structure==
2E28 is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Geobacillus_stearothermophilus Geobacillus stearothermophilus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2E28 OCA].
 
==Reference==
Crystal structure of pyruvate kinase from Geobacillus stearothermophilus., Suzuki K, Ito S, Shimizu-Ibuka A, Sakai H, J Biochem. 2008 Sep;144(3):305-12. Epub 2008 May 28. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/18511452 18511452]
[[Category: Geobacillus stearothermophilus]]
[[Category: Geobacillus stearothermophilus]]
[[Category: Pyruvate kinase]]
[[Category: Large Structures]]
[[Category: Single protein]]
[[Category: Suzuki K]]
[[Category: Suzuki, K.]]
[[Category: Allosteric]]
[[Category: Pyruvate kinase]]
[[Category: Transferase]]
 
''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Nov  5 10:42:11 2008''

Latest revision as of 11:33, 25 October 2023

Crystal structure analysis of pyruvate kinase from Bacillus stearothermophilusCrystal structure analysis of pyruvate kinase from Bacillus stearothermophilus

Structural highlights

2e28 is a 1 chain structure with sequence from Geobacillus stearothermophilus. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:X-ray diffraction, Resolution 2.4Å
Ligands:
Resources:FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

KPYK_GEOSE

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 pyruvate kinase (PK) from a moderate thermophile, Geobacillus stearothermophilus, is an allosteric enzyme activated by AMP and ribose 5-phosphate but not fructose 1, 6-bisphosphate (FBP), which is a common activator of PKs. It has an extra C-terminal sequence (ECTS), which contains a highly conserved phosphoenolpyruvate (PEP) binding motif, but its function and structure remain unclear. To elucidate the structural characteristics of the effector-binding site and the ECTS, the crystal structure of the C9S/C268S mutant of the enzyme was determined at 2.4 A resolution. The crystal belonged to space group P6(2)22, with unit cell parameters a, b = 145.97 A, c = 118.03 A. The enzyme was a homotetramer and its overall domain structure was similar to the previously solved structures except that the ECTS formed a new domain (C' domain). The structure of the C' domain closely resembled that of the PEP binding domain of maize pyruvate phosphate dikinase. A sulphate ion was found in a pocket in the effector-binding C domain. This site corresponds to the 6-phosphate group-binding site in yeast PK bound FBP and seems to be the effector-binding site. Through comparison of the structure of the putative effector-binding site to that of the FBP binding site of the yeast enzyme, the structural basis of the effector specificity of the G. stearothermophilus PK is discussed.

Crystal structure of pyruvate kinase from Geobacillus stearothermophilus.,Suzuki K, Ito S, Shimizu-Ibuka A, Sakai H J Biochem. 2008 Sep;144(3):305-12. Epub 2008 May 28. PMID:18511452[1]

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

See Also

References

  1. ↑ Suzuki K, Ito S, Shimizu-Ibuka A, Sakai H. Crystal structure of pyruvate kinase from Geobacillus stearothermophilus. J Biochem. 2008 Sep;144(3):305-12. Epub 2008 May 28. PMID:18511452 doi:10.1093/jb/mvn069

2e28, resolution 2.40Å

Drag the structure with the mouse to rotate

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

OCA
Retrieved from "https://proteopedia.openfox.io/wiki/index.php?title=2e28&oldid=3924348"