1pp2: Difference between revisions

From Proteopedia
Jump to navigation Jump to search
← Older edit
No edit summary
No edit summary
 
(13 intermediate revisions by the same user not shown)
Line 1: Line 1:
[[Image:1pp2.gif|left|200px]]


{{Structure
==THE REFINED CRYSTAL STRUCTURE OF DIMERIC PHOSPHOLIPASE A2 AT 2.5 ANGSTROMS. ACCESS TO A SHIELDED CATALYTIC CENTER==
|PDB= 1pp2 |SIZE=350|CAPTION= <scene name='initialview01'>1pp2</scene>, resolution 2.5&Aring;
<StructureSection load='1pp2' size='340' side='right'caption='[[1pp2]], [[Resolution|resolution]] 2.50&Aring;' scene=''>
|SITE=  
== Structural highlights ==
|LIGAND=  
<table><tr><td colspan='2'>[[1pp2]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Crotalus_atrox Crotalus atrox]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1PP2 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1PP2 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]] 2.5&#8491;</td></tr>
|GENE=
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1pp2 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1pp2 OCA], [https://pdbe.org/1pp2 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1pp2 RCSB], [https://www.ebi.ac.uk/pdbsum/1pp2 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1pp2 ProSAT]</span></td></tr>
|DOMAIN=
</table>
|RELATEDENTRY=
== Function ==
|RESOURCES=<span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1pp2 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1pp2 OCA], [http://www.ebi.ac.uk/pdbsum/1pp2 PDBsum], [http://www.rcsb.org/pdb/explore.do?structureId=1pp2 RCSB]</span>
[https://www.uniprot.org/uniprot/PA2A_CROAT PA2A_CROAT] PLA2 catalyzes the calcium-dependent hydrolysis of the 2-acyl groups in 3-sn-phosphoglycerides.
}}
== 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/pp/1pp2_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=1pp2 ConSurf].
<div style="clear:both"></div>
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
The 2.5-A crystal structure of the calcium-free form of the dimeric venom phospholipase A2 from the Western Diamondback rattlesnake Crotalus atrox, has been refined to an R-factor of 17.8% (I greater than 2 sigma) and acceptable stereochemistry. The molecule is a nearly perfect 2-fold symmetric dimer in which most of the catalytic residues of both subunits face an internal cavity. The restricted access to the putative catalytic sites is especially puzzling as the optimal substrates for this and most other phospholipase A2 are phospholipids condensed in micellar or lamellar aggregates. We point out that substrate access to the internal cavity may be aided by calcium binding which can alter the intersubunit contacts that shield the catalytic network. We also suggest that a system of hydrogen-bonded moieties exists on the surface of the dimer that links the amino terminus to the catalytic system, through an invariant Gln 4 side chain and the backbone of the active center residue, Tyr 73. This hydrogen-bonded network is on a highly accessible surface of the dimer and would appear to contribute to the enzyme's (as opposed to the proenzyme's) special capacity to attack aggregated rather than monomeric substrate.


'''THE REFINED CRYSTAL STRUCTURE OF DIMERIC PHOSPHOLIPASE A2 AT 2.5 ANGSTROMS. ACCESS TO A SHIELDED CATALYTIC CENTER'''
The refined crystal structure of dimeric phospholipase A2 at 2.5 A. Access to a shielded catalytic center.,Brunie S, Bolin J, Gewirth D, Sigler PB J Biol Chem. 1985 Aug 15;260(17):9742-9. PMID:4019493<ref>PMID:4019493</ref>


From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
</div>
<div class="pdbe-citations 1pp2" style="background-color:#fffaf0;"></div>


==Overview==
==See Also==
The 2.5-A crystal structure of the calcium-free form of the dimeric venom phospholipase A2 from the Western Diamondback rattlesnake Crotalus atrox, has been refined to an R-factor of 17.8% (I greater than 2 sigma) and acceptable stereochemistry. The molecule is a nearly perfect 2-fold symmetric dimer in which most of the catalytic residues of both subunits face an internal cavity. The restricted access to the putative catalytic sites is especially puzzling as the optimal substrates for this and most other phospholipase A2 are phospholipids condensed in micellar or lamellar aggregates. We point out that substrate access to the internal cavity may be aided by calcium binding which can alter the intersubunit contacts that shield the catalytic network. We also suggest that a system of hydrogen-bonded moieties exists on the surface of the dimer that links the amino terminus to the catalytic system, through an invariant Gln 4 side chain and the backbone of the active center residue, Tyr 73. This hydrogen-bonded network is on a highly accessible surface of the dimer and would appear to contribute to the enzyme's (as opposed to the proenzyme's) special capacity to attack aggregated rather than monomeric substrate.
*[[Phospholipase A2 3D structures|Phospholipase A2 3D structures]]
 
== References ==
==About this Structure==
<references/>
1PP2 is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Crotalus_atrox Crotalus atrox]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1PP2 OCA].
__TOC__
 
</StructureSection>
==Reference==
The refined crystal structure of dimeric phospholipase A2 at 2.5 A. Access to a shielded catalytic center., Brunie S, Bolin J, Gewirth D, Sigler PB, J Biol Chem. 1985 Aug 15;260(17):9742-9. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/4019493 4019493]
[[Category: Crotalus atrox]]
[[Category: Crotalus atrox]]
[[Category: Phospholipase A(2)]]
[[Category: Large Structures]]
[[Category: Single protein]]
[[Category: Brunie S]]
[[Category: Brunie, S.]]
[[Category: Sigler PB]]
[[Category: Sigler, P B.]]
[[Category: hydrolase]]
 
''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sun Mar 30 23:02:37 2008''

Latest revision as of 08:33, 5 June 2024

THE REFINED CRYSTAL STRUCTURE OF DIMERIC PHOSPHOLIPASE A2 AT 2.5 ANGSTROMS. ACCESS TO A SHIELDED CATALYTIC CENTERTHE REFINED CRYSTAL STRUCTURE OF DIMERIC PHOSPHOLIPASE A2 AT 2.5 ANGSTROMS. ACCESS TO A SHIELDED CATALYTIC CENTER

Structural highlights

1pp2 is a 2 chain structure with sequence from Crotalus atrox. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:X-ray diffraction, Resolution 2.5Å
Resources:FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

PA2A_CROAT PLA2 catalyzes the calcium-dependent hydrolysis of the 2-acyl groups in 3-sn-phosphoglycerides.

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 2.5-A crystal structure of the calcium-free form of the dimeric venom phospholipase A2 from the Western Diamondback rattlesnake Crotalus atrox, has been refined to an R-factor of 17.8% (I greater than 2 sigma) and acceptable stereochemistry. The molecule is a nearly perfect 2-fold symmetric dimer in which most of the catalytic residues of both subunits face an internal cavity. The restricted access to the putative catalytic sites is especially puzzling as the optimal substrates for this and most other phospholipase A2 are phospholipids condensed in micellar or lamellar aggregates. We point out that substrate access to the internal cavity may be aided by calcium binding which can alter the intersubunit contacts that shield the catalytic network. We also suggest that a system of hydrogen-bonded moieties exists on the surface of the dimer that links the amino terminus to the catalytic system, through an invariant Gln 4 side chain and the backbone of the active center residue, Tyr 73. This hydrogen-bonded network is on a highly accessible surface of the dimer and would appear to contribute to the enzyme's (as opposed to the proenzyme's) special capacity to attack aggregated rather than monomeric substrate.

The refined crystal structure of dimeric phospholipase A2 at 2.5 A. Access to a shielded catalytic center.,Brunie S, Bolin J, Gewirth D, Sigler PB J Biol Chem. 1985 Aug 15;260(17):9742-9. PMID:4019493[1]

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

See Also

References

  1. ↑ Brunie S, Bolin J, Gewirth D, Sigler PB. The refined crystal structure of dimeric phospholipase A2 at 2.5 A. Access to a shielded catalytic center. J Biol Chem. 1985 Aug 15;260(17):9742-9. PMID:4019493

1pp2, resolution 2.50Å

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=1pp2&oldid=4200184"