2olp

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[[Image:2olp.jpg|left|200px]]
 
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{{Structure
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==Structure and ligand selection of hemoglobin II from Lucina pectinata==
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|PDB= 2olp |SIZE=350|CAPTION= <scene name='initialview01'>2olp</scene>, resolution 1.932&Aring;
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<StructureSection load='2olp' size='340' side='right'caption='[[2olp]], [[Resolution|resolution]] 1.93&Aring;' scene=''>
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|SITE=
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== Structural highlights ==
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|LIGAND= <scene name='pdbligand=ACE:ACETYL+GROUP'>ACE</scene>, <scene name='pdbligand=HEM:PROTOPORPHYRIN+IX+CONTAINING+FE'>HEM</scene>, <scene name='pdbligand=OXY:OXYGEN+MOLECULE'>OXY</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene>
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<table><tr><td colspan='2'>[[2olp]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Phacoides_pectinatus Phacoides pectinatus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2OLP OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2OLP FirstGlance]. <br>
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|ACTIVITY=
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</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.932&#8491;</td></tr>
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|GENE=
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<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ACE:ACETYL+GROUP'>ACE</scene>, <scene name='pdbligand=HEM:PROTOPORPHYRIN+IX+CONTAINING+FE'>HEM</scene>, <scene name='pdbligand=OXY:OXYGEN+MOLECULE'>OXY</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
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|DOMAIN=
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<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=2olp FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2olp OCA], [https://pdbe.org/2olp PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2olp RCSB], [https://www.ebi.ac.uk/pdbsum/2olp PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2olp ProSAT]</span></td></tr>
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|RELATEDENTRY=[[1ebt|1EBT]], [[1bob|1BOB]], [[1flp|1FLP]], [[1moh|1MOH]]
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</table>
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|RESOURCES=<span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2olp FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2olp OCA], [http://www.ebi.ac.uk/pdbsum/2olp PDBsum], [http://www.rcsb.org/pdb/explore.do?structureId=2olp RCSB]</span>
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== Function ==
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}}
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[https://www.uniprot.org/uniprot/GLB2_PHAPT GLB2_PHAPT]
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== Evolutionary Conservation ==
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[[Image:Consurf_key_small.gif|200px|right]]
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Check<jmol>
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<jmolCheckbox>
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<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/ol/2olp_consurf.spt"</scriptWhenChecked>
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<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview03.spt</scriptWhenUnchecked>
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<text>to colour the structure by Evolutionary Conservation</text>
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</jmolCheckbox>
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</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=2olp ConSurf].
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<div style="clear:both"></div>
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<div style="background-color:#fffaf0;">
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== Publication Abstract from PubMed ==
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Lucina pectinata ctenidia harbor three heme proteins: sulfide-reactive hemoglobin I (HbI(Lp)) and the oxygen transporting hemoglobins II and III (HbII(Lp) and HbIII(Lp)) that remain unaffected by the presence of H(2)S. The mechanisms used by these three proteins for their function, including ligand control, remain unknown. The crystal structure of oxygen-bound HbII(Lp) shows a dimeric oxyHbII(Lp) where oxygen is tightly anchored to the heme through hydrogen bonds with Tyr(30)(B10) and Gln(65)(E7). The heme group is buried farther within HbII(Lp) than in HbI(Lp). The proximal His(97)(F8) is hydrogen bonded to a water molecule, which interacts electrostatically with a propionate group, resulting in a Fe-His vibration at 211 cm(-1). The combined effects of the HbII(Lp) small heme pocket, the hydrogen bonding network, the His(97) trans-effect, and the orientation of the oxygen molecule confer stability to the oxy-HbII(Lp) complex. Oxidation of HbI(Lp) Phe(B10) --&gt; Tyr and HbII(Lp) only occurs when the pH is decreased from pH 7.5 to 5.0. Structural and resonance Raman spectroscopy studies suggest that HbII(Lp) oxygen binding and transport to the host bacteria may be regulated by the dynamic displacements of the Gln(65)(E7) and Tyr(30)(B10) pair toward the heme to protect it from changes in the heme oxidation state from Fe(II) to Fe(III).
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'''Structure and ligand selection of hemoglobin II from Lucina pectinata'''
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Structure and ligand selection of hemoglobin II from Lucina pectinata.,Gavira JA, Camara-Artigas A, De Jesus-Bonilla W, Lopez-Garriga J, Lewis A, Pietri R, Yeh SR, Cadilla CL, Garcia-Ruiz JM J Biol Chem. 2008 Apr 4;283(14):9414-23. Epub 2008 Jan 18. PMID:18203714<ref>PMID:18203714</ref>
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From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
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</div>
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<div class="pdbe-citations 2olp" style="background-color:#fffaf0;"></div>
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==Overview==
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==See Also==
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Haemoglobin II is one of three haemoglobins present in the cytoplasm of the Lucina pectinata mollusc that inhabits the Caribbean coast. Using HBII purified from its natural source, crystallization screening was performed using the counter-diffusion method with capillaries of 0.2 mm inner diameter. Crystals of HbII suitable for data collection and structure determination were grown in the presence of agarose at 0.1%(w/v) in order to improve their quality. The crystals belong to the tetragonal space group P4(2)2(1)2, with unit-cell parameters a = b = 73.92, c = 152.35 A, and diffracted X-rays to a resolution of better than 2.0 A. The asymmetric unit is a homodimer with a corresponding Matthews coefficient (VM) of 3.15 A3 Da(-1) and a solvent content of 61% by volume.
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*[[Hemoglobin 3D structures|Hemoglobin 3D structures]]
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== References ==
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==About this Structure==
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<references/>
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2OLP is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Lucina_pectinata Lucina pectinata]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2OLP OCA].
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__TOC__
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</StructureSection>
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==Reference==
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[[Category: Large Structures]]
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Capillary crystallization and molecular-replacement solution of haemoglobin II from the clam Lucina pectinata., Gavira JA, de Jesus W, Camara-Artigas A, Lopez-Garriga J, Garcia-Ruiz JM, Acta Crystallogr Sect F Struct Biol Cryst Commun. 2006 Mar 1;62(Pt, 3):196-9. Epub 2006 Feb 10. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/16511300 16511300]
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[[Category: Phacoides pectinatus]]
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[[Category: Lucina pectinata]]
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[[Category: Camara-Artigas A]]
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[[Category: Single protein]]
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[[Category: Garcia-Ruiz JM]]
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[[Category: Camara-Artigas, A.]]
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[[Category: Gavira JA]]
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[[Category: Garcia-Ruiz, J M.]]
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[[Category: Lopez-Garriga J]]
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[[Category: Gavira, J A.]]
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[[Category: De Jesus W]]
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[[Category: Jesus, W de.]]
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[[Category: Lopez-Garriga, J.]]
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[[Category: globin]]
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[[Category: hemoprotein]]
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[[Category: oxygen storage/transport complex]]
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[[Category: oxygen transport]]
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''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Mon Mar 31 04:19:39 2008''
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Current revision

Structure and ligand selection of hemoglobin II from Lucina pectinata

PDB ID 2olp

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