1gwf: Difference between revisions

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<StructureSection load='1gwf' size='340' side='right'caption='[[1gwf]], [[Resolution|resolution]] 1.96&Aring;' scene=''>
<StructureSection load='1gwf' size='340' side='right'caption='[[1gwf]], [[Resolution|resolution]] 1.96&Aring;' scene=''>
== Structural highlights ==
== Structural highlights ==
<table><tr><td colspan='2'>[[1gwf]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/"bacteridium_luteum"_schroeter_1872 "bacteridium luteum" schroeter 1872]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1GWF OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=1GWF FirstGlance]. <br>
<table><tr><td colspan='2'>[[1gwf]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Micrococcus_luteus Micrococcus luteus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1GWF OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1GWF FirstGlance]. <br>
</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ACT:ACETATE+ION'>ACT</scene>, <scene name='pdbligand=HEM:PROTOPORPHYRIN+IX+CONTAINING+FE'>HEM</scene>, <scene name='pdbligand=O:OXYGEN+ATOM'>O</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.96&#8491;</td></tr>
<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=SME:METHIONINE+SULFOXIDE'>SME</scene></td></tr>
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ACT:ACETATE+ION'>ACT</scene>, <scene name='pdbligand=HEM:PROTOPORPHYRIN+IX+CONTAINING+FE'>HEM</scene>, <scene name='pdbligand=O:OXYGEN+ATOM'>O</scene>, <scene name='pdbligand=SME:METHIONINE+SULFOXIDE'>SME</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[1gwe|1gwe]], [[1gwh|1gwh]]</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=1gwf FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1gwf OCA], [https://pdbe.org/1gwf PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1gwf RCSB], [https://www.ebi.ac.uk/pdbsum/1gwf PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1gwf ProSAT]</span></td></tr>
<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">katA ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1270 "Bacteridium luteum" Schroeter 1872])</td></tr>
<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Catalase Catalase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.11.1.6 1.11.1.6] </span></td></tr>
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://proteopedia.org/fgij/fg.htm?mol=1gwf FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1gwf OCA], [http://pdbe.org/1gwf PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1gwf RCSB], [http://www.ebi.ac.uk/pdbsum/1gwf PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1gwf ProSAT]</span></td></tr>
</table>
</table>
== Function ==
== Function ==
[[http://www.uniprot.org/uniprot/CATA_MICLU CATA_MICLU]] Decomposes hydrogen peroxide into water and oxygen; serves to protect cells from the toxic effects of hydrogen peroxide.  
[https://www.uniprot.org/uniprot/CATA_MICLU CATA_MICLU] Decomposes hydrogen peroxide into water and oxygen; serves to protect cells from the toxic effects of hydrogen peroxide.
== Evolutionary Conservation ==
== Evolutionary Conservation ==
[[Image:Consurf_key_small.gif|200px|right]]
[[Image:Consurf_key_small.gif|200px|right]]
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</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=1gwf ConSurf].
</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=1gwf ConSurf].
<div style="clear:both"></div>
<div style="clear:both"></div>
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
The crystal structure of the bacterial catalase from Micrococcus lysodeikticus has been refined using the gene-derived sequence both at 0.88 A resolution using data recorded at 110 K and at 1.5 A resolution with room-temperature data. The atomic resolution structure has been refined with individual anisotropic atomic thermal parameters. This has revealed the geometry of the haem and surrounding protein, including many of the H atoms, with unprecedented accuracy and has characterized functionally important hydrogen-bond interactions in the active site. The positions of the H atoms are consistent with the enzymatic mechanism previously suggested for beef liver catalase. The structure reveals that a 25 A long channel leading to the haem is filled by partially occupied water molecules, suggesting an inherent facile access to the active site. In addition, the structures of the ferryl intermediate of the catalase, the so-called compound II, at 1.96 A resolution and the catalase complex with NADPH at 1.83 A resolution have been determined. Comparison of compound II and the resting state of the enzyme shows that the binding of the O atom to the iron (bond length 1.87 A) is associated with increased haem bending and is accompanied by a distal movement of the iron and the side chain of the proximal tyrosine. Finally, the structure of the NADPH complex shows that the cofactor is bound to the molecule in an equivalent position to that found in beef liver catalase, but that only the adenine part of NADPH is visible in the present structure.
The structures of Micrococcus lysodeikticus catalase, its ferryl intermediate (compound II) and NADPH complex.,Murshudov GN, Grebenko AI, Brannigan JA, Antson AA, Barynin VV, Dodson GG, Dauter Z, Wilson KS, Melik-Adamyan WR Acta Crystallogr D Biol Crystallogr. 2002 Dec;58(Pt 12):1972-82. Epub 2002, Nov 23. PMID:12454454<ref>PMID:12454454</ref>
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
</div>
<div class="pdbe-citations 1gwf" style="background-color:#fffaf0;"></div>


==See Also==
==See Also==
*[[Catalase 3D structures|Catalase 3D structures]]
*[[Catalase 3D structures|Catalase 3D structures]]
== References ==
<references/>
__TOC__
__TOC__
</StructureSection>
</StructureSection>
[[Category: Bacteridium luteum schroeter 1872]]
[[Category: Catalase]]
[[Category: Large Structures]]
[[Category: Large Structures]]
[[Category: Antson, A A]]
[[Category: Micrococcus luteus]]
[[Category: Barynin, V V]]
[[Category: Antson AA]]
[[Category: Brannigan, J A]]
[[Category: Barynin VV]]
[[Category: Dauter, Z]]
[[Category: Brannigan JA]]
[[Category: Dodson, G G]]
[[Category: Dauter Z]]
[[Category: Grebenko, A I]]
[[Category: Dodson GG]]
[[Category: Melik-Adamyan, W R]]
[[Category: Grebenko AI]]
[[Category: Murshudov, G N]]
[[Category: Melik-Adamyan WR]]
[[Category: Wilson, K S]]
[[Category: Murshudov GN]]
[[Category: Hydrogen peroxide oxidoreductase]]
[[Category: Wilson KS]]
[[Category: Oxidoreductase]]

Latest revision as of 14:24, 27 March 2024

Compound II structure of Micrococcus Lysodeikticus catalaseCompound II structure of Micrococcus Lysodeikticus catalase

Structural highlights

1gwf is a 1 chain structure with sequence from Micrococcus luteus. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:X-ray diffraction, Resolution 1.96Å
Ligands:, , , ,
Resources:FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

CATA_MICLU Decomposes hydrogen peroxide into water and oxygen; serves to protect cells from the toxic effects of hydrogen peroxide.

Evolutionary Conservation

Check, as determined by ConSurfDB. You may read the explanation of the method and the full data available from ConSurf.

See Also

1gwf, resolution 1.96Å

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