1d8u: Difference between revisions
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New page: left|200px<br /> <applet load="1d8u" size="450" color="white" frame="true" align="right" spinBox="true" caption="1d8u, resolution 2.35Å" /> '''CRYSTAL STRUCTURE O... |
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== | ==CRYSTAL STRUCTURE OF NON-SYMBIOTIC PLANT HEMOGLOBIN FROM RICE== | ||
BACKGROUND: Nonsymbiotic hemoglobins (nsHbs) form a new class of plant | <StructureSection load='1d8u' size='340' side='right'caption='[[1d8u]], [[Resolution|resolution]] 2.35Å' scene=''> | ||
== Structural highlights == | |||
<table><tr><td colspan='2'>[[1d8u]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Oryza_sativa Oryza sativa]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1D8U OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1D8U FirstGlance]. <br> | |||
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.35Å</td></tr> | |||
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><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=1d8u FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1d8u OCA], [https://pdbe.org/1d8u PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1d8u RCSB], [https://www.ebi.ac.uk/pdbsum/1d8u PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1d8u ProSAT]</span></td></tr> | |||
</table> | |||
== Function == | |||
[https://www.uniprot.org/uniprot/NSHB1_ORYSJ NSHB1_ORYSJ] Phytoglobin that reduces nitrite to nitric oxide under anoxic conditions (e.g. during flooding or in waterlogged soil) (PubMed:21495624). May not function as an oxygen storage or transport protein (PubMed:17540516, PubMed:9390447). Has an unusually high affinity for O(2) through a hexacoordinate heme iron because of a very low dissociation constant (PubMed:9390447).<ref>PMID:21495624</ref> <ref>PMID:9390447</ref> <ref>PMID:17540516</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/d8/1d8u_consurf.spt"</scriptWhenChecked> | |||
<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview03.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/main_output.php?pdb_ID=1d8u ConSurf]. | |||
<div style="clear:both"></div> | |||
<div style="background-color:#fffaf0;"> | |||
== Publication Abstract from PubMed == | |||
BACKGROUND: Nonsymbiotic hemoglobins (nsHbs) form a new class of plant proteins that is distinct genetically and structurally from leghemoglobins. They are found ubiquitously in plants and are expressed in low concentrations in a variety of tissues including roots and leaves. Their function involves a biochemical response to growth under limited O(2) conditions. RESULTS: The first X-ray crystal structure of a member of this class of proteins, riceHb1, has been determined to 2.4 A resolution using a combination of phasing techniques. The active site of ferric riceHb1 differs significantly from those of traditional hemoglobins and myoglobins. The proximal and distal histidine sidechains coordinate directly to the heme iron, forming a hemichrome with spectral properties similar to those of cytochrome b(5). The crystal structure also shows that riceHb1 is a dimer with a novel interface formed by close contacts between the G helix and the region between the B and C helices of the partner subunit. CONCLUSIONS: The bis-histidyl heme coordination found in riceHb1 is unusual for a protein that binds O(2) reversibly. However, the distal His73 is rapidly displaced by ferrous ligands, and the overall O(2) affinity is ultra-high (K(D) approximately 1 nM). Our crystallographic model suggests that ligand binding occurs by an upward and outward movement of the E helix, concomitant dissociation of the distal histidine, possible repacking of the CD corner and folding of the D helix. Although the functional relevance of quaternary structure in nsHbs is unclear, the role of two conserved residues in stabilizing the dimer interface has been identified. | |||
Crystal structure of a nonsymbiotic plant hemoglobin.,Hargrove MS, Brucker EA, Stec B, Sarath G, Arredondo-Peter R, Klucas RV, Olson JS, Phillips GN Jr Structure. 2000 Sep 15;8(9):1005-14. PMID:10986467<ref>PMID:10986467</ref> | |||
== | From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | ||
</div> | |||
<div class="pdbe-citations 1d8u" style="background-color:#fffaf0;"></div> | |||
==See Also== | |||
*[[Hemoglobin 3D structures|Hemoglobin 3D structures]] | |||
== References == | |||
<references/> | |||
__TOC__ | |||
</StructureSection> | |||
[[Category: Large Structures]] | |||
[[Category: Oryza sativa]] | [[Category: Oryza sativa]] | ||
[[Category: Brucker EA]] | |||
[[Category: Brucker | [[Category: Hargrove M]] | ||
[[Category: Hargrove | [[Category: Olson JS]] | ||
[[Category: | [[Category: Phillips Jr GN]] | ||
[[Category: | [[Category: Stec B]] | ||
[[Category: Stec | |||
