1ynr: Difference between revisions
No edit summary |
No edit summary |
||
| (5 intermediate revisions by the same user not shown) | |||
| Line 1: | Line 1: | ||
==Crystal structure of the cytochrome c-552 from Hydrogenobacter thermophilus at 2.0 resolution== | ==Crystal structure of the cytochrome c-552 from Hydrogenobacter thermophilus at 2.0 resolution== | ||
<StructureSection load='1ynr' size='340' side='right' caption='[[1ynr]], [[Resolution|resolution]] 2.00Å' scene=''> | <StructureSection load='1ynr' size='340' side='right'caption='[[1ynr]], [[Resolution|resolution]] 2.00Å' scene=''> | ||
== Structural highlights == | == Structural highlights == | ||
<table><tr><td colspan='2'>[[1ynr]] is a 4 chain structure with sequence from [ | <table><tr><td colspan='2'>[[1ynr]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Hydrogenobacter_thermophilus Hydrogenobacter thermophilus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1YNR OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1YNR FirstGlance]. <br> | ||
</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=HEC:HEME+C'>HEC</scene>, <scene name='pdbligand=MPD:(4S)-2-METHYL-2,4-PENTANEDIOL'>MPD</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene> | </td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2Å</td></tr> | ||
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=HEC:HEME+C'>HEC</scene>, <scene name='pdbligand=MPD:(4S)-2-METHYL-2,4-PENTANEDIOL'>MPD</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr> | |||
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[ | <tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1ynr FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1ynr OCA], [https://pdbe.org/1ynr PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1ynr RCSB], [https://www.ebi.ac.uk/pdbsum/1ynr PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1ynr ProSAT]</span></td></tr> | ||
</table> | </table> | ||
== Function == | == Function == | ||
[ | [https://www.uniprot.org/uniprot/CY552_HYDTT CY552_HYDTT] Reacts with hydrogenase. | ||
== Evolutionary Conservation == | == Evolutionary Conservation == | ||
[[Image:Consurf_key_small.gif|200px|right]] | [[Image:Consurf_key_small.gif|200px|right]] | ||
Check<jmol> | Check<jmol> | ||
<jmolCheckbox> | <jmolCheckbox> | ||
<scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/yn/1ynr_consurf.spt"</scriptWhenChecked> | <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/yn/1ynr_consurf.spt"</scriptWhenChecked> | ||
<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/ | <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview03.spt</scriptWhenUnchecked> | ||
<text>to colour the structure by Evolutionary Conservation</text> | <text>to colour the structure by Evolutionary Conservation</text> | ||
</jmolCheckbox> | </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/ | </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=1ynr ConSurf]. | ||
<div style="clear:both"></div> | <div style="clear:both"></div> | ||
<div style="background-color:#fffaf0;"> | <div style="background-color:#fffaf0;"> | ||
| Line 30: | Line 31: | ||
==See Also== | ==See Also== | ||
*[[ | *[[Cytochrome c nitrite reductase|Cytochrome c nitrite reductase]] | ||
== References == | == References == | ||
<references/> | <references/> | ||
__TOC__ | __TOC__ | ||
</StructureSection> | </StructureSection> | ||
[[Category: | [[Category: Hydrogenobacter thermophilus]] | ||
[[Category: Bonivento | [[Category: Large Structures]] | ||
[[Category: Borgia | [[Category: Bonivento D]] | ||
[[Category: Bren | [[Category: Borgia A]] | ||
[[Category: Brunori | [[Category: Bren KL]] | ||
[[Category: Cutruzzola | [[Category: Brunori M]] | ||
[[Category: | [[Category: Cutruzzola F]] | ||
[[Category: | [[Category: Di Matteo A]] | ||
[[Category: | [[Category: Dubey VK]] | ||
[[Category: Travaglini-Allocatelli | [[Category: Gianni S]] | ||
[[Category: Travaglini-Allocatelli C]] | |||
Latest revision as of 08:02, 17 October 2024
Crystal structure of the cytochrome c-552 from Hydrogenobacter thermophilus at 2.0 resolutionCrystal structure of the cytochrome c-552 from Hydrogenobacter thermophilus at 2.0 resolution
Structural highlights
FunctionCY552_HYDTT Reacts with hydrogenase. 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 PubMedThe folding mechanism of many proteins involves the population of partially organized structures en route to the native state. Identification and characterization of these intermediates is particularly difficult, as they are often only transiently populated and may play different mechanistic roles, being either on-pathway productive species or off-pathway kinetic traps. Following different spectroscopic probes, and employing state-of-the-art kinetic analysis, we present evidence that the folding mechanism of the thermostable cytochrome c552 from Hydrogenobacter thermophilus does involve the presence of an elusive, yet compact, on-pathway intermediate. Characterization of the folding mechanism of this cytochrome c is particularly interesting for the purpose of comparative folding studies, because H. thermophilus cytochrome c552 shares high sequence identity and structural homology with its homologue from the mesophilic bacterium Pseudomonas aeruginosa cytochrome c551, which refolds through a broad energy barrier without the accumulation of intermediates. Analysis of the folding kinetics and correlation with the three-dimensional structure add new evidence for the validity of a consensus folding mechanism in the cytochrome c family. An obligatory intermediate in the folding pathway of cytochrome c552 from Hydrogenobacter thermophilus.,Travaglini-Allocatelli C, Gianni S, Dubey VK, Borgia A, Di Matteo A, Bonivento D, Cutruzzola F, Bren KL, Brunori M J Biol Chem. 2005 Jul 8;280(27):25729-34. Epub 2005 May 9. PMID:15883159[1] From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine. See AlsoReferences
|
| ||||||||||||||||||