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[[Image:1kp4.jpg|left|200px]]


{{Structure
==CALCIUM-BOUND FORM OF PROKARYOTIC PHOSPHOLIPASE A2==
|PDB= 1kp4 |SIZE=350|CAPTION= <scene name='initialview01'>1kp4</scene>, resolution 1.60&Aring;
<StructureSection load='1kp4' size='340' side='right'caption='[[1kp4]], [[Resolution|resolution]] 1.60&Aring;' scene=''>
|SITE=  
== Structural highlights ==
|LIGAND= <scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>
<table><tr><td colspan='2'>[[1kp4]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Streptomyces_violaceoruber Streptomyces violaceoruber]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1KP4 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1KP4 FirstGlance]. <br>
|ACTIVITY= <span class='plainlinks'>[http://en.wikipedia.org/wiki/Phospholipase_A(2) Phospholipase A(2)], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.1.1.4 3.1.1.4] </span>
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.6&#8491;</td></tr>
|GENE=  
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene></td></tr>
|DOMAIN=
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1kp4 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1kp4 OCA], [https://pdbe.org/1kp4 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1kp4 RCSB], [https://www.ebi.ac.uk/pdbsum/1kp4 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1kp4 ProSAT]</span></td></tr>
|RELATEDENTRY=[[1faz|1FAZ]], [[1it4|1IT4]], [[1it5|1IT5]]
</table>
|RESOURCES=<span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1kp4 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1kp4 OCA], [http://www.ebi.ac.uk/pdbsum/1kp4 PDBsum], [http://www.rcsb.org/pdb/explore.do?structureId=1kp4 RCSB]</span>
== Function ==
}}
[https://www.uniprot.org/uniprot/Q6UV28_STRVN Q6UV28_STRVN]
== 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/kp/1kp4_consurf.spt"</scriptWhenChecked>
    <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview03.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=1kp4 ConSurf].
<div style="clear:both"></div>
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
In this study, the x-ray crystal structures of the calcium-free and calcium-bound forms of phospholipase A(2) (PLA(2)), produced extracellularly by Streptomyces violaceoruber, were determined by using the multiple isomorphous replacement and molecular replacement methods, respectively. The former and latter structures were refined to an R-factor of 18.8% at a 1.4-A resolution and an R-factor of 15.0% at a 1.6-A resolution, respectively. The overall structure of the prokaryotic PLA(2) exhibits a novel folding topology that demonstrates that it is completely distinct from those of eukaryotic PLA(2)s, which have been already determined by x-ray and NMR analyses. Furthermore, the coordination geometry of the calcium(II) ion apparently deviated from that of eukaryotic PLA(2)s. Regardless of the evolutionary divergence, the catalytic mechanism including the calcium(II) ion on secreted PLA(2) seems to be conserved between prokaryotic and eukaryotic cells. Demonstrating that the overall structure determined by x-ray analysis is almost the same as that determined by NMR analysis is useful to discuss the catalytic mechanism at the molecular level of the bacterial PLA(2).


'''CALCIUM-BOUND FORM OF PROKARYOTIC PHOSPHOLIPASE A2'''
The crystal structure of prokaryotic phospholipase A2.,Matoba Y, Katsube Y, Sugiyama M J Biol Chem. 2002 May 31;277(22):20059-69. Epub 2002 Mar 15. PMID:11897785<ref>PMID:11897785</ref>


From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
</div>
<div class="pdbe-citations 1kp4" style="background-color:#fffaf0;"></div>


==Overview==
==See Also==
In this study, the x-ray crystal structures of the calcium-free and calcium-bound forms of phospholipase A(2) (PLA(2)), produced extracellularly by Streptomyces violaceoruber, were determined by using the multiple isomorphous replacement and molecular replacement methods, respectively. The former and latter structures were refined to an R-factor of 18.8% at a 1.4-A resolution and an R-factor of 15.0% at a 1.6-A resolution, respectively. The overall structure of the prokaryotic PLA(2) exhibits a novel folding topology that demonstrates that it is completely distinct from those of eukaryotic PLA(2)s, which have been already determined by x-ray and NMR analyses. Furthermore, the coordination geometry of the calcium(II) ion apparently deviated from that of eukaryotic PLA(2)s. Regardless of the evolutionary divergence, the catalytic mechanism including the calcium(II) ion on secreted PLA(2) seems to be conserved between prokaryotic and eukaryotic cells. Demonstrating that the overall structure determined by x-ray analysis is almost the same as that determined by NMR analysis is useful to discuss the catalytic mechanism at the molecular level of the bacterial PLA(2).
*[[Phospholipase A2 3D structures|Phospholipase A2 3D structures]]
 
== References ==
==About this Structure==
<references/>
1KP4 is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Streptomyces_violaceoruber Streptomyces violaceoruber]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1KP4 OCA].
__TOC__
 
</StructureSection>
==Reference==
[[Category: Large Structures]]
The crystal structure of prokaryotic phospholipase A2., Matoba Y, Katsube Y, Sugiyama M, J Biol Chem. 2002 May 31;277(22):20059-69. Epub 2002 Mar 15. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/11897785 11897785]
[[Category: Phospholipase A(2)]]
[[Category: Single protein]]
[[Category: Streptomyces violaceoruber]]
[[Category: Streptomyces violaceoruber]]
[[Category: Katsube, Y.]]
[[Category: Katsube Y]]
[[Category: Matoba, Y.]]
[[Category: Matoba Y]]
[[Category: Sugiyama, M.]]
[[Category: Sugiyama M]]
[[Category: calcium ion]]
[[Category: phospholipase a2]]
[[Category: prokaryote]]
 
''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sun Mar 30 21:51:36 2008''

Latest revision as of 10:29, 23 October 2024

CALCIUM-BOUND FORM OF PROKARYOTIC PHOSPHOLIPASE A2CALCIUM-BOUND FORM OF PROKARYOTIC PHOSPHOLIPASE A2

Structural highlights

1kp4 is a 1 chain structure with sequence from Streptomyces violaceoruber. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:X-ray diffraction, Resolution 1.6Å
Ligands:
Resources:FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

Q6UV28_STRVN

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

In this study, the x-ray crystal structures of the calcium-free and calcium-bound forms of phospholipase A(2) (PLA(2)), produced extracellularly by Streptomyces violaceoruber, were determined by using the multiple isomorphous replacement and molecular replacement methods, respectively. The former and latter structures were refined to an R-factor of 18.8% at a 1.4-A resolution and an R-factor of 15.0% at a 1.6-A resolution, respectively. The overall structure of the prokaryotic PLA(2) exhibits a novel folding topology that demonstrates that it is completely distinct from those of eukaryotic PLA(2)s, which have been already determined by x-ray and NMR analyses. Furthermore, the coordination geometry of the calcium(II) ion apparently deviated from that of eukaryotic PLA(2)s. Regardless of the evolutionary divergence, the catalytic mechanism including the calcium(II) ion on secreted PLA(2) seems to be conserved between prokaryotic and eukaryotic cells. Demonstrating that the overall structure determined by x-ray analysis is almost the same as that determined by NMR analysis is useful to discuss the catalytic mechanism at the molecular level of the bacterial PLA(2).

The crystal structure of prokaryotic phospholipase A2.,Matoba Y, Katsube Y, Sugiyama M J Biol Chem. 2002 May 31;277(22):20059-69. Epub 2002 Mar 15. PMID:11897785[1]

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

See Also

References

  1. ↑ Matoba Y, Katsube Y, Sugiyama M. The crystal structure of prokaryotic phospholipase A2. J Biol Chem. 2002 May 31;277(22):20059-69. Epub 2002 Mar 15. PMID:11897785 doi:10.1074/jbc.M200263200

1kp4, resolution 1.60Å

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