Proteopedia

2c1u: Difference between revisions

← Older edit
No edit summary
No edit summary
 
(16 intermediate revisions by the same user not shown)
Line 1: Line 1:
[[Image:2c1u.jpg|left|200px]]<br /><applet load="2c1u" size="450" color="white" frame="true" align="right" spinBox="true"
caption="2c1u, resolution 1.952&Aring;" />
'''CRYSTAL STRUCTURE OF THE DI-HAEM CYTOCHROME C PEROXIDASE FROM PARACOCCUS PANTOTROPHUS- OXIDISED FORM'''<br />


==Overview==
==CRYSTAL STRUCTURE OF THE DI-HAEM CYTOCHROME C PEROXIDASE FROM PARACOCCUS PANTOTROPHUS - OXIDISED FORM==
Bacterial cytochrome c peroxidases contain an electron transferring (E), heme domain and a peroxidatic (P) heme domain. All but one of these, enzymes are isolated in an inactive oxidized state and require reduction, of the E heme by a small redox donor protein in order to activate the P, heme. Here we present the structures of the inactive oxidized and active, mixed valence enzyme from Paracoccus pantotrophus. Chain flexibility in, the former, as expressed by the crystallographic temperature factors, is, strikingly distributed in certain loop regions, and these coincide with, the regions of conformational change that occur in forming the active, mixed valence enzyme. On the basis of these changes, we postulate a series, of events that occur to link the trigger of the electron entering the E, heme from either pseudoazurin or cytochrome c(550) and the dissociation of, a coordinating histidine at the P heme, which allows substrate access.
<StructureSection load='2c1u' size='340' side='right'caption='[[2c1u]], [[Resolution|resolution]] 1.95&Aring;' scene=''>
== Structural highlights ==
<table><tr><td colspan='2'>[[2c1u]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Paracoccus_pantotrophus Paracoccus pantotrophus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2C1U OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2C1U 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]] 1.95&#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=HEC:HEME+C'>HEC</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=2c1u FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2c1u OCA], [https://pdbe.org/2c1u PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2c1u RCSB], [https://www.ebi.ac.uk/pdbsum/2c1u PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2c1u ProSAT]</span></td></tr>
</table>
== 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/c1/2c1u_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=2c1u ConSurf].
<div style="clear:both"></div>
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
Bacterial cytochrome c peroxidases contain an electron transferring (E) heme domain and a peroxidatic (P) heme domain. All but one of these enzymes are isolated in an inactive oxidized state and require reduction of the E heme by a small redox donor protein in order to activate the P heme. Here we present the structures of the inactive oxidized and active mixed valence enzyme from Paracoccus pantotrophus. Chain flexibility in the former, as expressed by the crystallographic temperature factors, is strikingly distributed in certain loop regions, and these coincide with the regions of conformational change that occur in forming the active mixed valence enzyme. On the basis of these changes, we postulate a series of events that occur to link the trigger of the electron entering the E heme from either pseudoazurin or cytochrome c(550) and the dissociation of a coordinating histidine at the P heme, which allows substrate access.


==About this Structure==
Activation and catalysis of the di-heme cytochrome c peroxidase from Paracoccus pantotrophus.,Echalier A, Goodhew CF, Pettigrew GW, Fulop V Structure. 2006 Jan;14(1):107-17. PMID:16407070<ref>PMID:16407070</ref>
2C1U is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Paracoccus_pantotrophus Paracoccus pantotrophus] with CA and HEC as [http://en.wikipedia.org/wiki/ligands ligands]. Active as [http://en.wikipedia.org/wiki/Cytochrome-c_peroxidase Cytochrome-c peroxidase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.11.1.5 1.11.1.5] Known structural/functional Site: <scene name='pdbsite=AC1:Ca Binding Site For Chain D'>AC1</scene>. Full crystallographic information is available from [http://ispc.weizmann.ac.il/oca-bin/ocashort?id=2C1U OCA].


==Reference==
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
Activation and catalysis of the di-heme cytochrome c peroxidase from Paracoccus pantotrophus., Echalier A, Goodhew CF, Pettigrew GW, Fulop V, Structure. 2006 Jan;14(1):107-17. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=16407070 16407070]
</div>
[[Category: Cytochrome-c peroxidase]]
<div class="pdbe-citations 2c1u" style="background-color:#fffaf0;"></div>
 
==See Also==
*[[Cytochrome c peroxidase 3D structures|Cytochrome c peroxidase 3D structures]]
== References ==
<references/>
__TOC__
</StructureSection>
[[Category: Large Structures]]
[[Category: Paracoccus pantotrophus]]
[[Category: Paracoccus pantotrophus]]
[[Category: Single protein]]
[[Category: Echalier A]]
[[Category: Echalier, A.]]
[[Category: Fulop V]]
[[Category: Fulop, V.]]
[[Category: CA]]
[[Category: HEC]]
[[Category: electron transport]]
[[Category: heme]]
[[Category: oxidoreductase]]
[[Category: periplasmic]]
[[Category: peroxidase]]
 
''Page seeded by [http://ispc.weizmann.ac.il/oca OCA ] on Tue Dec 18 19:06:22 2007''

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

OCA
Retrieved from "https://proteopedia.openfox.io/w/2c1u"