2d2m

From Proteopedia

(Difference between revisions)

Current revision

Structure of an extracellular giant hemoglobin of the gutless beard worm Oligobrachia mashikoi

Structural highlights

2d2m is a 4 chain structure with sequence from Oligobrachia mashikoi. The March 2013 RCSB PDB Molecule of the Month feature on Erythrocruorin by David Goodsell is 10.2210/rcsb_pdb/mom_2013_3. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	X-ray diffraction, Resolution 2.85Å
Ligands:	,
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

GLBA1_OLIMA The extracellular giant hemoglobin is able to bind and transport oxygen and hydrosulfide simultaneously and reversibly at two different sites.

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

Mouthless and gutless marine animals, pogonophorans and vestimentiferans, obtain their nutrition solely from their symbiotic chemoautotrophic sulfur-oxidizing bacteria. These animals have sulfide-binding 400-kDa and/or 3,500-kDa Hb, which transports oxygen and sulfide simultaneously. The symbiotic bacteria are supplied with sulfide by Hb of the host animal and use it to provide carbon compounds. Here, we report the crystal structure of a 400-kDa Hb from pogonophoran Oligobrachia mashikoi at 2.85-A resolution. The structure is hollow-spherical, composed of a total of 24 globins as a dimer of dodecamer. This dodecameric assemblage would be a fundamental structural unit of both 400-kDa and 3,500-kDa Hbs. The structure of the mercury derivative used for phasing provides insights into the sulfide-binding mechanism. The mercury compounds bound to all free Cys residues that have been expected as sulfide-binding sites. Some of the free Cys residues are surrounded by Phe aromatic rings, and mercury atoms come into contact with these residues in the derivative structure. It is strongly suggested that sulfur atoms bound to these sites could be stabilized by aromatic-electrostatic interactions by the surrounding Phe residues.

Structure of an extracellular giant hemoglobin of the gutless beard worm Oligobrachia mashikoi.,Numoto N, Nakagawa T, Kita A, Sasayama Y, Fukumori Y, Miki K Proc Natl Acad Sci U S A. 2005 Oct 11;102(41):14521-6. Epub 2005 Oct 3. PMID:16204001^[1]

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

References

↑ Numoto N, Nakagawa T, Kita A, Sasayama Y, Fukumori Y, Miki K. Structure of an extracellular giant hemoglobin of the gutless beard worm Oligobrachia mashikoi. Proc Natl Acad Sci U S A. 2005 Oct 11;102(41):14521-6. Epub 2005 Oct 3. PMID:16204001

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

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/2d2m"

@@ Line 4: / Line 4: @@
 == Structural highlights ==
 <table><tr><td colspan='2'>[[2d2m]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Oligobrachia_mashikoi Oligobrachia mashikoi]. The March 2013 RCSB PDB [https://pdb.rcsb.org/pdb/static.do?p=education_discussion/molecule_of_the_month/index.html Molecule of the Month] feature on ''Erythrocruorin''  by David Goodsell is [https://dx.doi.org/10.2210/rcsb_pdb/mom_2013_3 10.2210/rcsb_pdb/mom_2013_3]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2D2M OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2D2M FirstGlance]. <br>
-</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>, <scene name='pdbligand=OXY:OXYGEN+MOLECULE'>OXY</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]] 2.85&#8491;</td></tr>
-<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[2d2n|2d2n]]</div></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>, <scene name='pdbligand=OXY:OXYGEN+MOLECULE'>OXY</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=2d2m FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2d2m OCA], [https://pdbe.org/2d2m PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2d2m RCSB], [https://www.ebi.ac.uk/pdbsum/2d2m PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2d2m ProSAT]</span></td></tr>
 </table>
 == Function ==
-[[https://www.uniprot.org/uniprot/GLBB1_OLIMA GLBB1_OLIMA]] The extracellular giant hemoglobin is able to bind and transport oxygen and sulfide simultaneously and reversibly at two different sites. [[https://www.uniprot.org/uniprot/GLBA1_OLIMA GLBA1_OLIMA]] The extracellular giant hemoglobin is able to bind and transport oxygen and hydrosulfide simultaneously and reversibly at two different sites. [[https://www.uniprot.org/uniprot/GLBB2_OLIMA GLBB2_OLIMA]] The extracellular giant hemoglobin is able to bind and transport oxygen and hydrosulfide simultaneously and reversibly at two different sites. [[https://www.uniprot.org/uniprot/GLBA2_OLIMA GLBA2_OLIMA]] The extracellular giant hemoglobin is able to bind and transport oxygen and hydrosulfide simultaneously and reversibly at two different sites.
+[https://www.uniprot.org/uniprot/GLBA1_OLIMA GLBA1_OLIMA] The extracellular giant hemoglobin is able to bind and transport oxygen and hydrosulfide simultaneously and reversibly at two different sites.
 == Evolutionary Conservation ==
 [[Image:Consurf_key_small.gif|200px|right]]
@@ Line 15: / Line 15: @@
   <jmolCheckbox>
     <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/d2/2d2m_consurf.spt"</scriptWhenChecked>
-    <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
+    <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview03.spt</scriptWhenUnchecked>
     <text>to colour the structure by Evolutionary Conservation</text>
   </jmolCheckbox>
@@ Line 41: / Line 41: @@
 [[Category: Oligobrachia mashikoi]]
 [[Category: RCSB PDB Molecule of the Month]]
-[[Category: Fukumori, Y]]
+[[Category: Fukumori Y]]
-[[Category: Kita, A]]
+[[Category: Kita A]]
-[[Category: Miki, K]]
+[[Category: Miki K]]
-[[Category: Nakagawa, T]]
+[[Category: Nakagawa T]]
-[[Category: Numoto, N]]
+[[Category: Numoto N]]
-[[Category: Sasayama, Y]]
+[[Category: Sasayama Y]]
-[[Category: Giant hemoglobin]]
-[[Category: Invertebrate]]
-[[Category: Oxygen storage-transport complex]]
-[[Category: Pogonophora]]
-[[Category: Sulfide binding]]

2d2m

From Proteopedia

Current revision

Structure of an extracellular giant hemoglobin of the gutless beard worm Oligobrachia mashikoi

Structural highlights

Function

Evolutionary Conservation

Publication Abstract from PubMed

See Also

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

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