3qzx

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Current revision (10:51, 21 February 2024) (edit) (undo)
 
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<StructureSection load='3qzx' size='340' side='right'caption='[[3qzx]], [[Resolution|resolution]] 1.30&Aring;' scene=''>
<StructureSection load='3qzx' size='340' side='right'caption='[[3qzx]], [[Resolution|resolution]] 1.30&Aring;' scene=''>
== Structural highlights ==
== Structural highlights ==
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<table><tr><td colspan='2'>[[3qzx]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Atcc_35395 Atcc 35395]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3QZX OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3QZX FirstGlance]. <br>
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<table><tr><td colspan='2'>[[3qzx]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Methanosarcina_acetivorans Methanosarcina acetivorans]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3QZX OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3QZX FirstGlance]. <br>
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</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=HEM:PROTOPORPHYRIN+IX+CONTAINING+FE'>HEM</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene></td></tr>
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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]] 1.3&#8491;</td></tr>
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<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[2veb|2veb]], [[2vee|2vee]], [[3r0g|3r0g]], [[3qzz|3qzz]]</div></td></tr>
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<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=HEM:PROTOPORPHYRIN+IX+CONTAINING+FE'>HEM</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene></td></tr>
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<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">MA_2883 ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=2214 ATCC 35395])</td></tr>
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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=3qzx FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3qzx OCA], [https://pdbe.org/3qzx PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3qzx RCSB], [https://www.ebi.ac.uk/pdbsum/3qzx PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3qzx 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=3qzx FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3qzx OCA], [https://pdbe.org/3qzx PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3qzx RCSB], [https://www.ebi.ac.uk/pdbsum/3qzx PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3qzx ProSAT]</span></td></tr>
</table>
</table>
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<div style="background-color:#fffaf0;">
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== Function ==
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== Publication Abstract from PubMed ==
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[https://www.uniprot.org/uniprot/Q8TLY9_METAC Q8TLY9_METAC]
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Protoglobin from Methanosarcina acetivorans C2A (MaPgb), a strictly anaerobic methanogenic Archaea, displays peculiar structural and functional properties within members of the hemoglobin superfamily. In fact, MaPgb-specific loops and a N-terminal extension (20 amino acid residues) completely bury the heme within the protein matrix. Therefore, the access of diatomic gaseous molecules to the heme is granted by two apolar tunnels reaching the heme distal site from locations at the B/G and B/E helix interfaces. The presence of two tunnels within the protein matrix could be partly responsible for the slightly biphasic ligand binding behavior. Unusually, MaPgb oxygenation is favored with respect to carbonylation. Here, the crucial role of Tyr(B10)61 and Ile(G11)149 residues, located in the heme distal site and lining the protein matrix tunnels 1 and 2, respectively, on ligand binding to the heme-Fe-atom and on distal site structural organization is reported. In particular, tunnel 1 accessibility is modulated by a complex reorganization of the Trp(B9)60 and Phe(E11)93 side-chains, triggered by mutations of the Tyr(B10)61 and Ile(G11)149 residues, and affected by the presence and type of the distal heme-bound ligand. (c) 2011 IUBMB IUBMB Life, 63(5): 287-294, 2011.
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Structural heterogeneity and ligand gating in ferric methanosarcina acetivorans protoglobin mutants.,Pesce A, Tilleman L, Dewilde S, Ascenzi P, Coletta M, Ciaccio C, Bruno S, Moens L, Bolognesi M, Nardini M IUBMB Life. 2011 May;63(5):287-94. doi: 10.1002/iub.484. PMID:21618401<ref>PMID:21618401</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 3qzx" style="background-color:#fffaf0;"></div>
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== References ==
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<references/>
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__TOC__
__TOC__
</StructureSection>
</StructureSection>
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[[Category: Atcc 35395]]
 
[[Category: Large Structures]]
[[Category: Large Structures]]
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[[Category: Ascenzi, P]]
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[[Category: Methanosarcina acetivorans]]
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[[Category: Bolognesi, M]]
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[[Category: Ascenzi P]]
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[[Category: Bruno, S]]
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[[Category: Bolognesi M]]
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[[Category: Ciaccio, C]]
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[[Category: Bruno S]]
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[[Category: Coletta, M]]
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[[Category: Ciaccio C]]
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[[Category: Dewilde, S]]
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[[Category: Coletta M]]
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[[Category: Moens, L]]
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[[Category: Dewilde S]]
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[[Category: Nardini, M]]
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[[Category: Moens L]]
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[[Category: Pesce, A]]
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[[Category: Nardini M]]
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[[Category: Tilleman, L]]
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[[Category: Pesce A]]
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[[Category: Archaea protein]]
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[[Category: Tilleman L]]
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[[Category: Globin fold]]
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[[Category: Methanogenesis]]
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[[Category: Oxygen binding]]
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[[Category: Oxygen transport]]
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[[Category: Protoglobin]]
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Current revision

3D Structure of ferric methanosarcina acetivorans protoglobin Y61A mutant with unknown ligand

PDB ID 3qzx

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