6r3y

From Proteopedia

(Difference between revisions)

Current revision

M.tuberculosis nitrobindin with a cyanide molecule coordinated to the heme iron atom

Structural highlights

6r3y is a 1 chain structure with sequence from Mycobacterium tuberculosis. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	X-ray diffraction, Resolution 1.6Å
Ligands:	,
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

NB1_MYCTU Heme-binding protein able to scavenge peroxynitrite and to protect free L-tyrosine against peroxynitrite-mediated nitration, by acting as a peroxynitrite isomerase that converts peroxynitrite to nitrate. Therefore, this protein likely plays a role in peroxynitrite sensing and in the detoxification of reactive nitrogen and oxygen species (RNS and ROS, respectively). In M.tuberculosis, could be part of the pool of proteins required to scavenge RNS and ROS produced by the host during the immunity response. Is able to bind nitric oxide (NO) in vitro, but may act as a sensor of peroxynitrite levels in vivo.^[1]

Publication Abstract from PubMed

AIMS: Nitrobindins (Nbs) are evolutionary conserved all-beta-barrel heme-proteins displaying a highly solvent-exposed heme-Fe(III) atom. The physiological role(s) of Nbs is almost unknown. Here, the structural and functional properties of the Mycobacterium tuberculosis Nb (Mt-Nb(III)) and Homo sapiens Nb (Hs-Nb(III)) have been investigated and compared with those of Arabidopsis thaliana Nb (At-Nb(III), of the hematophagous bug Rodius prolixus nitrophorins (Rp-NP(III)s), and of mammalian myoglobins. RESULTS: Data here reported demonstrate that Mt-Nb(III), At-Nb(III), and Hs-Nb(III) share with Rp-NP(III)s the capability to bind selectively NO, but display a very low reactivity, if any, towards histamine. Data obtained overexpressing Hs-Nb in HEK293 cells indicate that Hs-Nb localizes mainly in the cytoplasm and partially in the nucleus thanks to a nuclear localization sequence encompassing residues Glu124-Leu154. Human Hs-Nb corresponds to the C-terminal domain of the human nuclear protein THAP4, and our data suggest that Nb may act as a sensor possibly modulating the THAP4 transcriptional activity residing in the N-terminal region. Finally, we provide strong evidence that both Mt-Nb(III) and Hs-Nb(III) are able to scavenge peroxynitrite and to protect dose-dependently free L-tyrosine against peroxynitrite-mediated nitration. INNOVATION: Data here reported suggest an evolutionarily conserved function of Nbs related to their role as gas sensors and components of the anti-oxidant system. CONCLUSION: Human THAP4 may act as a sensing protein that couples the heme-based Nb(III) reactivity with gene transcription. Besides, Mt-Nb(III) seems to be part of the pool of proteins required to scavenge RNS and ROS produced by the host during the immunity response.

Mycobacterial and human nitrobindins: structure and function.,De Simone G, di Masi A, Vita GM, Polticelli F, Pesce A, Nardini M, Bolognesi M, Ciaccio C, Coletta M, Turilli ES, Fasano M, Tognaccini L, Smulevich G, Abbruzzetti S, Viappiani C, Bruno S, Ascenzi P Antioxid Redox Signal. 2020 Apr 16. doi: 10.1089/ars.2019.7874. PMID:32295384^[2]

From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.

References

↑ De Simone G, di Masi A, Vita GM, Polticelli F, Pesce A, Nardini M, Bolognesi M, Ciaccio C, Coletta M, Turilli ES, Fasano M, Tognaccini L, Smulevich G, Abbruzzetti S, Viappiani C, Bruno S, Ascenzi P. Mycobacterial and human nitrobindins: structure and function. Antioxid Redox Signal. 2020 Apr 16. doi: 10.1089/ars.2019.7874. PMID:32295384 doi:http://dx.doi.org/10.1089/ars.2019.7874
↑ De Simone G, di Masi A, Vita GM, Polticelli F, Pesce A, Nardini M, Bolognesi M, Ciaccio C, Coletta M, Turilli ES, Fasano M, Tognaccini L, Smulevich G, Abbruzzetti S, Viappiani C, Bruno S, Ascenzi P. Mycobacterial and human nitrobindins: structure and function. Antioxid Redox Signal. 2020 Apr 16. doi: 10.1089/ars.2019.7874. PMID:32295384 doi:http://dx.doi.org/10.1089/ars.2019.7874

1 Structural highlights
2 Function
3 Publication Abstract from PubMed
4 References

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/6r3y"

@@ Line 3: / Line 3: @@
 <StructureSection load='6r3y' size='340' side='right'caption='[[6r3y]], [[Resolution|resolution]] 1.60&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[6r3y]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/"bacillus_tuberculosis"_(zopf_1883)_klein_1884 "bacillus tuberculosis" (zopf 1883) klein 1884]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6R3Y OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=6R3Y FirstGlance]. <br>
+<table><tr><td colspan='2'>[[6r3y]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Mycobacterium_tuberculosis Mycobacterium tuberculosis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6R3Y OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6R3Y FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CYN:CYANIDE+ION'>CYN</scene>, <scene name='pdbligand=HEM:PROTOPORPHYRIN+IX+CONTAINING+FE'>HEM</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]] 1.6&#8491;</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=6r3y FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6r3y OCA], [http://pdbe.org/6r3y PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6r3y RCSB], [http://www.ebi.ac.uk/pdbsum/6r3y PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6r3y ProSAT]</span></td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CYN:CYANIDE+ION'>CYN</scene>, <scene name='pdbligand=HEM:PROTOPORPHYRIN+IX+CONTAINING+FE'>HEM</scene></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=6r3y FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6r3y OCA], [https://pdbe.org/6r3y PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6r3y RCSB], [https://www.ebi.ac.uk/pdbsum/6r3y PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6r3y ProSAT]</span></td></tr>
 </table>
 == Function ==
-[[http://www.uniprot.org/uniprot/A0A0E8TXJ8_MYCTX A0A0E8TXJ8_MYCTX]] May play a role in the intracellular transport of hydrophobic ligands.[HAMAP-Rule:MF_01297][SAAS:SAAS00728027]
+[https://www.uniprot.org/uniprot/NB1_MYCTU NB1_MYCTU] Heme-binding protein able to scavenge peroxynitrite and to protect free L-tyrosine against peroxynitrite-mediated nitration, by acting as a peroxynitrite isomerase that converts peroxynitrite to nitrate. Therefore, this protein likely plays a role in peroxynitrite sensing and in the detoxification of reactive nitrogen and oxygen species (RNS and ROS, respectively). In M.tuberculosis, could be part of the pool of proteins required to scavenge RNS and ROS produced by the host during the immunity response. Is able to bind nitric oxide (NO) in vitro, but may act as a sensor of peroxynitrite levels in vivo.<ref>PMID:32295384</ref>
 <div style="background-color:#fffaf0;">
 == Publication Abstract from PubMed ==
@@ Line 23: / Line 24: @@
 </StructureSection>
 [[Category: Large Structures]]
-[[Category: Abbruzzetti, S]]
+[[Category: Mycobacterium tuberculosis]]
-[[Category: Ascenzi, P]]
+[[Category: Abbruzzetti S]]
-[[Category: Bolognesi, M]]
+[[Category: Ascenzi P]]
-[[Category: Bruno, S]]
+[[Category: Bolognesi M]]
-[[Category: Ciaccio, C]]
+[[Category: Bruno S]]
-[[Category: Coletta, M]]
+[[Category: Ciaccio C]]
-[[Category: Fasano, M]]
+[[Category: Coletta M]]
-[[Category: Masi, A di]]
+[[Category: De Simone G]]
-[[Category: Nardini, M]]
+[[Category: Fasano M]]
-[[Category: Pesce, A]]
+[[Category: Nardini M]]
-[[Category: Polticelli, F]]
+[[Category: Pesce A]]
-[[Category: Simone, G De]]
+[[Category: Polticelli F]]
-[[Category: Smulevich, G]]
+[[Category: Smulevich G]]
-[[Category: Tognaccini, L]]
+[[Category: Tognaccini L]]
-[[Category: Turilli, E S]]
+[[Category: Turilli ES]]
-[[Category: Viappiani, C]]
+[[Category: Viappiani C]]
-[[Category: Beta-barrel]]
+[[Category: Di Masi A]]
-[[Category: Hemeprotein]]
-[[Category: Peroxynitrite detoxification]]
-[[Category: Protein binding]]

6r3y

From Proteopedia

Current revision

M.tuberculosis nitrobindin with a cyanide molecule coordinated to the heme iron atom

Structural highlights

Function

Publication Abstract from PubMed

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

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