5n8h: Difference between revisions
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==Serial Cu nitrite reductase structures at elevated cryogenic temperature, 240K. Dataset 3.== | |||
<StructureSection load='5n8h' size='340' side='right' caption='[[5n8h]], [[Resolution|resolution]] 1.65Å' scene=''> | |||
== Structural highlights == | |||
<table><tr><td colspan='2'>[[5n8h]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5N8H OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5N8H FirstGlance]. <br> | |||
</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CU:COPPER+(II)+ION'>CU</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr> | |||
<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Nitrite_reductase_(NO-forming) Nitrite reductase (NO-forming)], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.7.2.1 1.7.2.1] </span></td></tr> | |||
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5n8h FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5n8h OCA], [http://pdbe.org/5n8h PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5n8h RCSB], [http://www.ebi.ac.uk/pdbsum/5n8h PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5n8h ProSAT]</span></td></tr> | |||
</table> | |||
<div style="background-color:#fffaf0;"> | |||
== Publication Abstract from PubMed == | |||
Microbial nitrite reductases are denitrifying enzymes that are a major component of the global nitrogen cycle. Multiple structures measured from one crystal (MSOX data) of copper nitrite reductase at 240 K, together with molecular-dynamics simulations, have revealed protein dynamics at the type 2 copper site that are significant for its catalytic properties and for the entry and exit of solvent or ligands to and from the active site. Molecular-dynamics simulations were performed using different protonation states of the key catalytic residues (AspCAT and HisCAT) involved in the nitrite-reduction mechanism of this enzyme. Taken together, the crystal structures and simulations show that the AspCAT protonation state strongly influences the active-site solvent accessibility, while the dynamics of the active-site 'capping residue' (IleCAT), a determinant of ligand binding, are influenced both by temperature and by the protonation state of AspCAT. A previously unobserved conformation of IleCAT is seen in the elevated temperature series compared with 100 K structures. DFT calculations also show that the loss of a bound water ligand at the active site during the MSOX series is consistent with reduction of the type 2 Cu atom. | |||
Active-site protein dynamics and solvent accessibility in native Achromobacter cycloclastes copper nitrite reductase.,Sen K, Horrell S, Kekilli D, Yong CW, Keal TW, Atakisi H, Moreau DW, Thorne RE, Hough MA, Strange RW IUCrJ. 2017 Jun 16;4(Pt 4):495-505. doi: 10.1107/S2052252517007527. eCollection, 2017 Jul 1. PMID:28875036<ref>PMID:28875036</ref> | |||
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | |||
[[Category: | </div> | ||
<div class="pdbe-citations 5n8h" style="background-color:#fffaf0;"></div> | |||
==See Also== | |||
*[[Nitrite reductase|Nitrite reductase]] | |||
== References == | |||
<references/> | |||
__TOC__ | |||
</StructureSection> | |||
[[Category: Horrell, S]] | |||
[[Category: Hough, M]] | |||
[[Category: Kekilli, D]] | [[Category: Kekilli, D]] | ||
[[Category: Strange, R]] | [[Category: Strange, R]] | ||
[[Category: | [[Category: Copper enzyme]] | ||
[[Category: | [[Category: Cupredoxid domain]] | ||
[[Category: Nitrite reductase]] | |||
[[Category: Oxidoreductase]] | |||
[[Category: Trimer]] | |||
Revision as of 07:46, 21 September 2017
Serial Cu nitrite reductase structures at elevated cryogenic temperature, 240K. Dataset 3.Serial Cu nitrite reductase structures at elevated cryogenic temperature, 240K. Dataset 3.
Structural highlights
Publication Abstract from PubMedMicrobial nitrite reductases are denitrifying enzymes that are a major component of the global nitrogen cycle. Multiple structures measured from one crystal (MSOX data) of copper nitrite reductase at 240 K, together with molecular-dynamics simulations, have revealed protein dynamics at the type 2 copper site that are significant for its catalytic properties and for the entry and exit of solvent or ligands to and from the active site. Molecular-dynamics simulations were performed using different protonation states of the key catalytic residues (AspCAT and HisCAT) involved in the nitrite-reduction mechanism of this enzyme. Taken together, the crystal structures and simulations show that the AspCAT protonation state strongly influences the active-site solvent accessibility, while the dynamics of the active-site 'capping residue' (IleCAT), a determinant of ligand binding, are influenced both by temperature and by the protonation state of AspCAT. A previously unobserved conformation of IleCAT is seen in the elevated temperature series compared with 100 K structures. DFT calculations also show that the loss of a bound water ligand at the active site during the MSOX series is consistent with reduction of the type 2 Cu atom. Active-site protein dynamics and solvent accessibility in native Achromobacter cycloclastes copper nitrite reductase.,Sen K, Horrell S, Kekilli D, Yong CW, Keal TW, Atakisi H, Moreau DW, Thorne RE, Hough MA, Strange RW IUCrJ. 2017 Jun 16;4(Pt 4):495-505. doi: 10.1107/S2052252517007527. eCollection, 2017 Jul 1. PMID:28875036[1] From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine. See AlsoReferences
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