1uyu: Difference between revisions
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[[Image: | ==Xenon COMPLEX OF wildtype P450CAM FROM PSEUDOMONAS PUTIDA== | ||
<StructureSection load='1uyu' size='340' side='right' caption='[[1uyu]], [[Resolution|resolution]] 2.00Å' scene=''> | |||
== Structural highlights == | |||
<table><tr><td colspan='2'>[[1uyu]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Pseudomonas_putida Pseudomonas putida]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1UYU OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1UYU FirstGlance]. <br> | |||
</td></tr><tr><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CAM:CAMPHOR'>CAM</scene>, <scene name='pdbligand=HEM:PROTOPORPHYRIN+IX+CONTAINING+FE'>HEM</scene>, <scene name='pdbligand=K:POTASSIUM+ION'>K</scene>, <scene name='pdbligand=XE:XENON'>XE</scene><br> | |||
<tr><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[1akd|1akd]], [[1c8j|1c8j]], [[1cp4|1cp4]], [[1dz4|1dz4]], [[1dz6|1dz6]], [[1dz8|1dz8]], [[1dz9|1dz9]], [[1geb|1geb]], [[1gek|1gek]], [[1gem|1gem]], [[1gjm|1gjm]], [[1iwi|1iwi]], [[1iwj|1iwj]], [[1iwk|1iwk]], [[1j51|1j51]], [[1k2o|1k2o]], [[1lwl|1lwl]], [[1mpw|1mpw]], [[1noo|1noo]], [[1o76|1o76]], [[1p2y|1p2y]], [[1p7r|1p7r]], [[1pha|1pha]], [[1phb|1phb]], [[1phc|1phc]], [[1phd|1phd]], [[1phe|1phe]], [[1phf|1phf]], [[1phg|1phg]], [[1qmq|1qmq]], [[2cp4|2cp4]], [[2cpp|2cpp]], [[3cp4|3cp4]], [[3cpp|3cpp]], [[4cp4|4cp4]], [[4cpp|4cpp]], [[5cp4|5cp4]], [[5cpp|5cpp]], [[6cp4|6cp4]], [[6cpp|6cpp]], [[7cpp|7cpp]], [[8cpp|8cpp]]</td></tr> | |||
<tr><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1uyu FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1uyu OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1uyu RCSB], [http://www.ebi.ac.uk/pdbsum/1uyu PDBsum]</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/uy/1uyu_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/chain_selection.php?pdb_ID=2ata ConSurf]. | |||
<div style="clear:both"></div> | |||
<div style="background-color:#fffaf0;"> | |||
== Publication Abstract from PubMed == | |||
In cytochrome P450s, the active site is situated deep inside the protein next to the heme cofactor, and is often completely isolated from the surrounding solvent. To identify routes by which substrates may enter into and products exit from the active site, random expulsion molecular dynamics simulations were performed for three cytochrome P450s: CYP101, CYP102A1 and CYP107A1 [J. Mol. Biol. 303 (2000) 797; Proc. Natl. Acad. Sci. USA 99 (2002) 5361]. Amongst the different pathways identified, one pathway was found to be common to all three cytochrome P450s although the mechanism of ligand passage along it was different in each case and apparently adapted to the substrate specificity of the enzyme. Recently, a number of new crystal structures of cytochrome P450s have been solved. Here, we analyse the open channels leading to the active site that these structures reveal. We find that in addition to showing the common pathway, they provide experimental evidence for the existence of three additional channels that were identified by simulation. We also discuss how the location of xenon binding sites in CYP101 suggests a role for one of the pathways identified by molecular dynamics simulations as a route for gaseous species, such as oxygen, to access the active site. | |||
A survey of active site access channels in cytochromes P450.,Wade RC, Winn PJ, Schlichting I, Sudarko J Inorg Biochem. 2004 Jul;98(7):1175-82. PMID:15219983<ref>PMID:15219983</ref> | |||
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | |||
</div> | |||
==See Also== | ==See Also== | ||
*[[Cytochrome P450|Cytochrome P450]] | *[[Cytochrome P450|Cytochrome P450]] | ||
== References == | |||
== | <references/> | ||
< | __TOC__ | ||
</StructureSection> | |||
[[Category: Pseudomonas putida]] | [[Category: Pseudomonas putida]] | ||
[[Category: Schlichting, I.]] | [[Category: Schlichting, I.]] | ||
Revision as of 02:58, 29 September 2014
Xenon COMPLEX OF wildtype P450CAM FROM PSEUDOMONAS PUTIDAXenon COMPLEX OF wildtype P450CAM FROM PSEUDOMONAS PUTIDA
Structural highlights
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 PubMedIn cytochrome P450s, the active site is situated deep inside the protein next to the heme cofactor, and is often completely isolated from the surrounding solvent. To identify routes by which substrates may enter into and products exit from the active site, random expulsion molecular dynamics simulations were performed for three cytochrome P450s: CYP101, CYP102A1 and CYP107A1 [J. Mol. Biol. 303 (2000) 797; Proc. Natl. Acad. Sci. USA 99 (2002) 5361]. Amongst the different pathways identified, one pathway was found to be common to all three cytochrome P450s although the mechanism of ligand passage along it was different in each case and apparently adapted to the substrate specificity of the enzyme. Recently, a number of new crystal structures of cytochrome P450s have been solved. Here, we analyse the open channels leading to the active site that these structures reveal. We find that in addition to showing the common pathway, they provide experimental evidence for the existence of three additional channels that were identified by simulation. We also discuss how the location of xenon binding sites in CYP101 suggests a role for one of the pathways identified by molecular dynamics simulations as a route for gaseous species, such as oxygen, to access the active site. A survey of active site access channels in cytochromes P450.,Wade RC, Winn PJ, Schlichting I, Sudarko J Inorg Biochem. 2004 Jul;98(7):1175-82. PMID:15219983[1] From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine. See AlsoReferences
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