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2a13

From Proteopedia

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X-ray structure of protein from Arabidopsis thaliana AT1G79260

Structural highlights

2a13 is a 1 chain structure with sequence from Arabidopsis thaliana. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	X-ray diffraction, Resolution 1.32Å
Ligands:
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT, TOPSAN

Function

NB_ARATH 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) (PubMed:32295384). Is able to bind nitric oxide (NO) in vitro, but may act as a sensor of peroxynitrite levels in vivo (PubMed:32295384, PubMed:19938152).^[1] ^[2]

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 PubMed

The protein from Arabidopsis thaliana gene locus At1g79260.1 is comprised of 166-residues and is of previously unknown function. Initial structural studies by the Center for Eukaryotic Structural Genomics (CESG) suggested that this protein might bind heme, and consequently, the crystal structures of apo and heme-bound forms were solved to near atomic resolution of 1.32 A and 1.36 A, respectively. The rate of hemin loss from the protein was measured to be 3.6 x 10(-5) s(-1), demonstrating that it binds heme specifically and with high affinity. The protein forms a compact 10-stranded beta-barrel that is structurally similar to the lipocalins and fatty acid binding proteins (FABPs). One group of lipocalins, the nitrophorins (NP), are heme proteins involved in nitric oxide (NO) transport and show both sequence and structural similarity to the protein from At1g79260.1 and two human homologues, all of which contain a proximal histidine capable of coordinating a heme iron. Rapid-mixing and laser photolysis techniques were used to determine the rate constants for carbon monoxide (CO) binding to the ferrous form of the protein (k'(CO) = 0.23 microM(-1) s(-1), k(CO) = 0.050 s(-1)) and NO binding to the ferric form (k'(NO) = 1.2 microM(-1) s(-1), k(NO) = 73 s(-1)). Based on both structural and functional similarity to the nitrophorins, we have named the protein nitrobindin and hypothesized that it plays a role in NO transport. However, one of the two human homologs of nitrobindin contains a THAP domain, implying a possible role in apoptosis. Proteins 2010. (c) 2009 Wiley-Liss, Inc.

The structure and NO binding properties of the nitrophorin-like heme-binding protein from Arabidopsis thaliana gene locus At1g79260.1.,Bianchetti CM, Blouin GC, Bitto E, Olson JS, Phillips GN Jr Proteins. 2010 Mar;78(4):917-31. PMID:19938152^[3]

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

References

↑ Bianchetti CM, Blouin GC, Bitto E, Olson JS, Phillips GN Jr. The structure and NO binding properties of the nitrophorin-like heme-binding protein from Arabidopsis thaliana gene locus At1g79260.1. Proteins. 2010 Mar;78(4):917-31. PMID:19938152 doi:10.1002/prot.22617
↑ 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
↑ Bianchetti CM, Blouin GC, Bitto E, Olson JS, Phillips GN Jr. The structure and NO binding properties of the nitrophorin-like heme-binding protein from Arabidopsis thaliana gene locus At1g79260.1. Proteins. 2010 Mar;78(4):917-31. PMID:19938152 doi:10.1002/prot.22617

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

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/2a13"

@@ Line 1: / Line 1: @@
 ==X-ray structure of protein from Arabidopsis thaliana AT1G79260==
-<StructureSection load='2a13' size='340' side='right' caption='[[2a13]], [[Resolution|resolution]] 1.32&Aring;' scene=''>
+<StructureSection load='2a13' size='340' side='right'caption='[[2a13]], [[Resolution|resolution]] 1.32&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[2a13]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Arabidopsis_thaliana Arabidopsis thaliana]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2A13 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2A13 FirstGlance]. <br>
+<table><tr><td colspan='2'>[[2a13]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Arabidopsis_thaliana Arabidopsis thaliana]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2A13 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2A13 FirstGlance]. <br>
-</td></tr><tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</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]] 1.32&#8491;</td></tr>
-<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">AT1G79260 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=3702 Arabidopsis thaliana])</td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene></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=2a13 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2a13 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2a13 RCSB], [http://www.ebi.ac.uk/pdbsum/2a13 PDBsum], [http://www.topsan.org/Proteins/CESG/2a13 TOPSAN]</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=2a13 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2a13 OCA], [https://pdbe.org/2a13 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2a13 RCSB], [https://www.ebi.ac.uk/pdbsum/2a13 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2a13 ProSAT], [https://www.topsan.org/Proteins/CESG/2a13 TOPSAN]</span></td></tr>
 </table>
 == Function ==
-[[http://www.uniprot.org/uniprot/Y1926_ARATH Y1926_ARATH]] May play a role in the intracellular transport of hydrophobic ligands (Potential).
+[https://www.uniprot.org/uniprot/NB_ARATH NB_ARATH] 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) (PubMed:32295384). Is able to bind nitric oxide (NO) in vitro, but may act as a sensor of peroxynitrite levels in vivo (PubMed:32295384, PubMed:19938152).<ref>PMID:19938152</ref> <ref>PMID:32295384</ref>
 == 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/a1/2a13_consurf.spt"</scriptWhenChecked>
+    <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/a1/2a13_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].
+</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=2a13 ConSurf].
 <div style="clear:both"></div>
 <div style="background-color:#fffaf0;">
@@ Line 27: / Line 28: @@
 From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
 </div>
+<div class="pdbe-citations 2a13" style="background-color:#fffaf0;"></div>
 == References ==
 <references/>
@@ Line 32: / Line 34: @@
 </StructureSection>
 [[Category: Arabidopsis thaliana]]
-[[Category: Allard, S T.M]]
+[[Category: Large Structures]]
-[[Category: Bingman, C A]]
+[[Category: Allard STM]]
-[[Category: Bitto, E]]
+[[Category: Bingman CA]]
-[[Category: Structural genomic]]
+[[Category: Bitto E]]
-[[Category: McCoy, J G]]
+[[Category: McCoy JG]]
-[[Category: Phillips, G N]]
+[[Category: Phillips Jr GN]]
-[[Category: Wesenberg, G E]]
+[[Category: Wesenberg GE]]
-[[Category: At1g79260]]
-[[Category: Cesg]]
-[[Category: PSI, Protein structure initiative]]
-[[Category: Unknown function]]

2a13

From Proteopedia

Current revision

X-ray structure of protein from Arabidopsis thaliana AT1G79260

Structural highlights

Function

Evolutionary Conservation

Publication Abstract from PubMed

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

Views

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