1qmd

From Proteopedia

(Difference between revisions)
Jump to: navigation, search
Current revision (12:48, 13 December 2023) (edit) (undo)
 
(15 intermediate revisions not shown.)
Line 1: Line 1:
-
[[Image:1qmd.jpg|left|200px]]<br /><applet load="1qmd" size="350" color="white" frame="true" align="right" spinBox="true"
 
-
caption="1qmd, resolution 2.20&Aring;" />
 
-
'''CALCIUM BOUND CLOSED FORM ALPHA-TOXIN FROM CLOSTRIDIUM PERFRINGENS'''<br />
 
-
==Overview==
+
==calcium bound closed form alpha-toxin from Clostridium perfringens==
 +
<StructureSection load='1qmd' size='340' side='right'caption='[[1qmd]], [[Resolution|resolution]] 2.20&Aring;' scene=''>
 +
== Structural highlights ==
 +
<table><tr><td colspan='2'>[[1qmd]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Clostridium_perfringens Clostridium perfringens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1QMD OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1QMD FirstGlance]. <br>
 +
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.2&#8491;</td></tr>
 +
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></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=1qmd FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1qmd OCA], [https://pdbe.org/1qmd PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1qmd RCSB], [https://www.ebi.ac.uk/pdbsum/1qmd PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1qmd ProSAT]</span></td></tr>
 +
</table>
 +
== Function ==
 +
[https://www.uniprot.org/uniprot/PHLC_CLOP1 PHLC_CLOP1] Bacterial hemolysins are exotoxins that attack blood cell membranes and cause cell rupture. Constitutes an essential virulence factor in gas gangrene. Binds to eukaryotic membranes where it hydrolyzes both phosphatidylcholine and sphingomyelin. The diacylglycerol produced can activate both the arachidonic acid pathway, leading to modulation of the inflammatory response cascade and thrombosis, and protein kinase C, leading to activation of eukaryotic phospholipases and further membrane damage. Acts on human and mouse erythrocytes, but not on rabbit or horse erythrocytes.
 +
== 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/qm/1qmd_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=1qmd ConSurf].
 +
<div style="clear:both"></div>
 +
<div style="background-color:#fffaf0;">
 +
== Publication Abstract from PubMed ==
Alpha-toxin is the key determinant in gas-gangrene. The toxin, a phospholipase C, cleaves phosphatidylcholine in eukaryotic cell membranes. Calcium ions have been shown to be required for the specific binding of toxin to membranes prior to phospholipid cleavage. Reported X-ray crystallographic structures of the toxin show that the C-terminal domain has a fold that is analogous to the eukaryotic calcium and membrane-binding C2 domains. We report the binding sites for three calcium ions that have been identified, by crystallographic methods, in the C-terminal domain of the protein close to the postulated membrane-binding surface. The position of these ions at the tip of the domain, and their function (to facilitate membrane binding) is similar to that of calcium ions observed bound to C2 domains. Using the optical spectroscopic techniques of circular dichroism (CD) and fluorescence spectroscopy, pronounced changes to both near and far-UV CD and tryptophan emission fluorescence upon addition of calcium to the C-terminal domain of alpha-toxin have been observed. The changes in near-UV CD, fluorescence enhancement and a 2 nm blue-shift in the fluorescence emission spectrum are consistent with tryptophan residue(s) becoming more immobilised in a hydrophobic environment. Calcium binding appears to be low-affinity: Kd approximately 175-250 microM at pH 8 assuming a 1:1 stoichiometry. as measured by spectroscopic methods.
Alpha-toxin is the key determinant in gas-gangrene. The toxin, a phospholipase C, cleaves phosphatidylcholine in eukaryotic cell membranes. Calcium ions have been shown to be required for the specific binding of toxin to membranes prior to phospholipid cleavage. Reported X-ray crystallographic structures of the toxin show that the C-terminal domain has a fold that is analogous to the eukaryotic calcium and membrane-binding C2 domains. We report the binding sites for three calcium ions that have been identified, by crystallographic methods, in the C-terminal domain of the protein close to the postulated membrane-binding surface. The position of these ions at the tip of the domain, and their function (to facilitate membrane binding) is similar to that of calcium ions observed bound to C2 domains. Using the optical spectroscopic techniques of circular dichroism (CD) and fluorescence spectroscopy, pronounced changes to both near and far-UV CD and tryptophan emission fluorescence upon addition of calcium to the C-terminal domain of alpha-toxin have been observed. The changes in near-UV CD, fluorescence enhancement and a 2 nm blue-shift in the fluorescence emission spectrum are consistent with tryptophan residue(s) becoming more immobilised in a hydrophobic environment. Calcium binding appears to be low-affinity: Kd approximately 175-250 microM at pH 8 assuming a 1:1 stoichiometry. as measured by spectroscopic methods.
-
==About this Structure==
+
Characterisation of the calcium-binding C-terminal domain of Clostridium perfringens alpha-toxin.,Naylor CE, Jepson M, Crane DT, Titball RW, Miller J, Basak AK, Bolgiano B J Mol Biol. 1999 Dec 3;294(3):757-70. PMID:10610794<ref>PMID:10610794</ref>
-
1QMD is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Clostridium_perfringens Clostridium perfringens] with <scene name='pdbligand=ZN:'>ZN</scene> and <scene name='pdbligand=CA:'>CA</scene> as [http://en.wikipedia.org/wiki/ligands ligands]. Active as [http://en.wikipedia.org/wiki/Phospholipase_C Phospholipase C], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.1.4.3 3.1.4.3] Known structural/functional Sites: <scene name='pdbsite=CA1:C-Terminal+Ca+(Membrane+Interactions).+In'>CA1</scene>, <scene name='pdbsite=CA2:C-Terminal+Ca+(Membrane+Interactions).+In'>CA2</scene>, <scene name='pdbsite=CA3:C-Terminal+Ca+(Membrane+Interactions).+In'>CA3</scene>, <scene name='pdbsite=CA4:C-Terminal+Ca+(Membrane+Interactions).+In'>CA4</scene>, <scene name='pdbsite=CA5:C-Terminal+Ca+(Membrane+Interactions).+In'>CA5</scene>, <scene name='pdbsite=CA6:C-Terminal+Ca+(Membrane+Interactions).+In'>CA6</scene>, <scene name='pdbsite=ZN1:Active+Site+Zn.+In+A+Molecule'>ZN1</scene>, <scene name='pdbsite=ZN2:Active+Site+Zn.+In+A+Molecule'>ZN2</scene>, <scene name='pdbsite=ZN3:Active+Site+Zn.+In+B+Molecule'>ZN3</scene> and <scene name='pdbsite=ZN4:Active+Site+Zn.+In+B+Molecule'>ZN4</scene>. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1QMD OCA].
+
-
==Reference==
+
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-
Characterisation of the calcium-binding C-terminal domain of Clostridium perfringens alpha-toxin., Naylor CE, Jepson M, Crane DT, Titball RW, Miller J, Basak AK, Bolgiano B, J Mol Biol. 1999 Dec 3;294(3):757-70. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=10610794 10610794]
+
</div>
-
[[Category: Clostridium perfringens]]
+
<div class="pdbe-citations 1qmd" style="background-color:#fffaf0;"></div>
-
[[Category: Phospholipase C]]
+
-
[[Category: Single protein]]
+
-
[[Category: Basak, A K.]]
+
-
[[Category: Miller, J.]]
+
-
[[Category: Naylor, C E.]]
+
-
[[Category: Titball, R W.]]
+
-
[[Category: CA]]
+
-
[[Category: ZN]]
+
-
[[Category: c2 domain]]
+
-
[[Category: ca and membrane binding.]]
+
-
[[Category: gangrene determinant]]
+
-
[[Category: zinc phospholipase c]]
+
-
''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Feb 21 14:41:20 2008''
+
==See Also==
 +
*[[Hemolysin 3D structures|Hemolysin 3D structures]]
 +
*[[Phospholipase C|Phospholipase C]]
 +
== References ==
 +
<references/>
 +
__TOC__
 +
</StructureSection>
 +
[[Category: Clostridium perfringens]]
 +
[[Category: Large Structures]]
 +
[[Category: Basak AK]]
 +
[[Category: Miller J]]
 +
[[Category: Naylor CE]]
 +
[[Category: Titball RW]]

Current revision

calcium bound closed form alpha-toxin from Clostridium perfringens

PDB ID 1qmd

Drag the structure with the mouse to rotate

Proteopedia Page Contributors and Editors (what is this?)

OCA

Personal tools