4x0x: Difference between revisions

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 ==The structure of AhpE from Mycobacterium tuberculosis revisited==
-<StructureSection load='4x0x' size='340' side='right' caption='[[4x0x]], [[Resolution|resolution]] 1.90&Aring;' scene=''>
+<StructureSection load='4x0x' size='340' side='right'caption='[[4x0x]], [[Resolution|resolution]] 1.90&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[4x0x]] is a 4 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4X0X OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4X0X FirstGlance]. <br>
+<table><tr><td colspan='2'>[[4x0x]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Mycobacterium_tuberculosis_CDC1551 Mycobacterium tuberculosis CDC1551]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4X0X OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4X0X FirstGlance]. <br>
-</td></tr><tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Peroxiredoxin Peroxiredoxin], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.11.1.15 1.11.1.15] </span></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]] 1.9&#8491;</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=4x0x FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4x0x OCA], [http://pdbe.org/4x0x PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4x0x RCSB], [http://www.ebi.ac.uk/pdbsum/4x0x PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4x0x ProSAT]</span></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=4x0x FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4x0x OCA], [https://pdbe.org/4x0x PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4x0x RCSB], [https://www.ebi.ac.uk/pdbsum/4x0x PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4x0x ProSAT]</span></td></tr>
 </table>
+== Function ==
+[https://www.uniprot.org/uniprot/AHPE_MYCTO AHPE_MYCTO] Thiol-specific peroxidase that catalyzes the reduction of hydrogen peroxide and organic hydroperoxides to water and alcohols, respectively. Plays a role in cell protection against oxidative stress by detoxifying peroxides. May represent an important antioxidant defense against cytotoxic peroxides, especially peroxynitrite, which can be formed by activated macrophages during infection.[UniProtKB:P9WIE3]
 <div style="background-color:#fffaf0;">
 == Publication Abstract from PubMed ==
-All living systems require protection against the damaging effects of reactive oxygen species. The genome of Mycobacterium tuberculosis, the cause of TB, encodes a number of peroxidases that are thought to be active against organic and inorganic peroxides, and are likely to play a key role in the ability of this organism to survive within the phagosomes of macrophages. The open reading frame Rv2238c in M.tuberculosis encodes a 153-residue protein AhpE, which is a peroxidase of the 1-Cys peroxiredoxin (Prx) family. The crystal structure of AhpE, determined at 1.87 A resolution (R(cryst)=0.179, R(free)=0.210), reveals a compact single-domain protein with a thioredoxin fold. AhpE forms both dimers and octamers; a tightly-associated dimer and a ring-like octamer, generated by crystallographic 4-fold symmetry. In this native structure, the active site Cys45 is in its oxidized, sulfenic acid (S-O-H) state. A second crystal form of AhpE, obtained after soaking in sodium bromide and refined at 1.90 A resolution (R(cryst)=0.242, R(free)=0.286), reveals the reduced structure. In this structure, a conformational change in an external loop, in two of the four molecules in the asymmetric unit, allows Arg116 to stabilise the Cys45 thiolate ion, and concomitantly closes a surface channel. This channel is identified as the likely binding site for a physiological reductant, and the conformational change is inferred to be important for the reaction cycle of AhpE.
+In many established methods, identification of hydrogen bonds (H-bonds) is primarily based on pairwise comparison of distances between atoms. These methods often give rise to systematic errors when sulfur is involved. A more accurate method is the non-covalent interaction index, which determines the strength of the H-bonds based on the associated electron density and its gradient. We applied the NCI index on the active site of a single-cysteine peroxiredoxin. We found a different sulfur hydrogen-bonding network to that typically found by established methods, and we propose a more accurate equation for determining sulfur H-bonds based on geometrical criteria. This new algorithm will be implemented in the next release of the widely-used CHARMM program (version 41b), and will be particularly useful for analyzing water molecule-mediated H-bonds involving different atom types. Furthermore, based on the identification of the weakest sulfur-water H-bond, the location of hydrogen peroxide for the nucleophilic attack by the cysteine sulfur can be predicted. In general, current methods to determine H-bonds will need to be reevaluated, thereby leading to better understanding of the catalytic mechanisms in which sulfur chemistry is involved.
-Crystal Structure of AhpE from Mycobacterium tuberculosis, a 1-Cys peroxiredoxin.,Li S, Peterson NA, Kim MY, Kim CY, Hung LW, Yu M, Lekin T, Segelke BW, Lott JS, Baker EN J Mol Biol. 2005 Mar 4;346(4):1035-46. Epub 2005 Jan 25. PMID:15701515<ref>PMID:15701515</ref>
+Revisiting sulfur H-bonds in proteins: The example of peroxiredoxin AhpE.,van Bergen LA, Alonso M, Pallo A, Nilsson L, De Proft F, Messens J Sci Rep. 2016 Jul 29;6:30369. doi: 10.1038/srep30369. PMID:27468924<ref>PMID:27468924</ref>
 From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
 </div>
 <div class="pdbe-citations 4x0x" style="background-color:#fffaf0;"></div>
+==See Also==
+*[[Thioredoxin reductase 3D structures|Thioredoxin reductase 3D structures]]
 == References ==
 <references/>
 __TOC__
 </StructureSection>
-[[Category: Peroxiredoxin]]
+[[Category: Large Structures]]
-[[Category: Messens, J]]
+[[Category: Mycobacterium tuberculosis CDC1551]]
-[[Category: Pallo, A]]
+[[Category: Messens J]]
-[[Category: Oxidoreductase]]
+[[Category: Pallo A]]
-[[Category: Protein structure]]