4cab: Difference between revisions
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The | ==The refined structure of catalase DR1998 from Deinococcus radiodurans at 2.6 A resolution== | ||
<StructureSection load='4cab' size='340' side='right'caption='[[4cab]], [[Resolution|resolution]] 2.60Å' scene=''> | |||
== Structural highlights == | |||
<table><tr><td colspan='2'>[[4cab]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Deinococcus_radiodurans_R1 Deinococcus radiodurans R1]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4CAB OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4CAB 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]] 2.599Å</td></tr> | |||
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=HEM:PROTOPORPHYRIN+IX+CONTAINING+FE'>HEM</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=4cab FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4cab OCA], [https://pdbe.org/4cab PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4cab RCSB], [https://www.ebi.ac.uk/pdbsum/4cab PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4cab ProSAT]</span></td></tr> | |||
</table> | |||
== Function == | |||
[https://www.uniprot.org/uniprot/CATA_DEIRA CATA_DEIRA] Decomposes hydrogen peroxide into water and oxygen; serves to protect cells from the toxic effects of hydrogen peroxide.<ref>PMID:16716939</ref> | |||
<div style="background-color:#fffaf0;"> | |||
== Publication Abstract from PubMed == | |||
Deinococcus radiodurans is an aerobic organism with the ability to survive under conditions of high radiation doses or desiccation. As part of its protection system against oxidative stress, this bacterium encodes three mono-functional catalases. The DR1998 catalase belongs to the clade 1, and is present at high levels under normal growth conditions. The crystals of DR1998 catalase diffracted very weakly and the merged diffraction data showed a Rsym of 0.308. Its crystal structure was determined and refined to 2.6 A. The four molecules present in the asymmetric unit originate, by crystallographic symmetry, two homotetramers with 222 point-group symmetry. The overall structure of DR1998 catalase is similar to that of other mono-functional catalases, displaying higher structural homology with the catalase structures of clade 1. Each monomer exhibits the typical catalase fold and contains one heme b in the active site. The heme is coordinated by the proximal ligand Tyr369, and on the heme distal side the essential His81 and Asn159 are hydrogen-bonded to a water molecule. A 25 A long channel is the main channel connecting the active site to the external surface. This channel starts with a hydrophobic region from the catalytic heme site, followed by a hydrophilic region that begins on Asp139 and expands up to the protein surface. Apart from this channel, an alternative channel also nearby the heme active site is presented and discussed. This article is protected by copyright. All rights reserved. | |||
Structure of the mono-functional heme catalase DR1998 from Deinococcus radiodurans.,Borges PT, Frazao C, Miranda CS, Carrondo MA, Romao CV FEBS J. 2014 Jun 26. doi: 10.1111/febs.12895. PMID:24975828<ref>PMID:24975828</ref> | |||
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | |||
</div> | |||
<div class="pdbe-citations 4cab" style="background-color:#fffaf0;"></div> | |||
==See Also== | |||
*[[Catalase 3D structures|Catalase 3D structures]] | |||
== References == | |||
<references/> | |||
__TOC__ | |||
</StructureSection> | |||
[[Category: Deinococcus radiodurans R1]] | |||
[[Category: Large Structures]] | |||
[[Category: Borges PT]] | |||
[[Category: Frazao C]] | |||
[[Category: Miranda CS]] | |||
[[Category: Romao CV]] | |||
[[Category: Santos SP]] | |||
Latest revision as of 15:06, 20 December 2023
The refined structure of catalase DR1998 from Deinococcus radiodurans at 2.6 A resolutionThe refined structure of catalase DR1998 from Deinococcus radiodurans at 2.6 A resolution
Structural highlights
FunctionCATA_DEIRA Decomposes hydrogen peroxide into water and oxygen; serves to protect cells from the toxic effects of hydrogen peroxide.[1] Publication Abstract from PubMedDeinococcus radiodurans is an aerobic organism with the ability to survive under conditions of high radiation doses or desiccation. As part of its protection system against oxidative stress, this bacterium encodes three mono-functional catalases. The DR1998 catalase belongs to the clade 1, and is present at high levels under normal growth conditions. The crystals of DR1998 catalase diffracted very weakly and the merged diffraction data showed a Rsym of 0.308. Its crystal structure was determined and refined to 2.6 A. The four molecules present in the asymmetric unit originate, by crystallographic symmetry, two homotetramers with 222 point-group symmetry. The overall structure of DR1998 catalase is similar to that of other mono-functional catalases, displaying higher structural homology with the catalase structures of clade 1. Each monomer exhibits the typical catalase fold and contains one heme b in the active site. The heme is coordinated by the proximal ligand Tyr369, and on the heme distal side the essential His81 and Asn159 are hydrogen-bonded to a water molecule. A 25 A long channel is the main channel connecting the active site to the external surface. This channel starts with a hydrophobic region from the catalytic heme site, followed by a hydrophilic region that begins on Asp139 and expands up to the protein surface. Apart from this channel, an alternative channel also nearby the heme active site is presented and discussed. This article is protected by copyright. All rights reserved. Structure of the mono-functional heme catalase DR1998 from Deinococcus radiodurans.,Borges PT, Frazao C, Miranda CS, Carrondo MA, Romao CV FEBS J. 2014 Jun 26. doi: 10.1111/febs.12895. PMID:24975828[2] From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine. See AlsoReferences
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