1pbx: Difference between revisions

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[[Image:1pbx.png|left|200px]]
==HAEMOGLOBIN OF THE ANTARCTIC FISH PAGOTHENIA BERNACCHII: AMINO ACID SEQUENCE, OXYGEN EQUILIBRIA AND CRYSTAL STRUCTURE OF ITS CARBONMONOXY DERIVATIVE==
<StructureSection load='1pbx' size='340' side='right' caption='[[1pbx]], [[Resolution|resolution]] 2.50&Aring;' scene=''>
== Structural highlights ==
<table><tr><td colspan='2'>[[1pbx]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Trematomus_bernacchii Trematomus bernacchii]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1PBX OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1PBX FirstGlance]. <br>
</td></tr><tr><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CMO:CARBON+MONOXIDE'>CMO</scene>, <scene name='pdbligand=HEM:PROTOPORPHYRIN+IX+CONTAINING+FE'>HEM</scene><br>
<tr><td class="sblockLbl"><b>[[Non-Standard_Residue|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=ACE:ACETYL+GROUP'>ACE</scene></td></tr>
<tr><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1pbx FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1pbx OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1pbx RCSB], [http://www.ebi.ac.uk/pdbsum/1pbx PDBsum]</span></td></tr>
<table>
== 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/pb/1pbx_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].
<div style="clear:both"></div>
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
The Antarctic fish Pagothenia bernacchii has one major haemoglobin, Hb1 (over 95% of the total blood content). Hb1 has a strong alkaline Bohr effect and at low pH exhibits the reduced ligand affinity and co-operativity that comprise the Root effect. We have determined the complete amino acid sequence of P. bernacchii Hb1 and also the structure of its carbonmonoxy derivative by X-ray crystallography, to a resolution of 2.5 A. The crystallographic R-factor of the refined structure is 18%. The three-dimensional structure of this fish haemoglobin is similar to that of human haemoglobin A, with a root-mean-square difference in main-chain atom positions of 1.4 A after superimposition of the two structures, despite only 48% homology of their amino acid sequences (including insertion of a single residue in the CD region of the fish alpha-chain). Large structural differences occur only at the N and C termini of both the alpha- and beta-chains. Neither these nor other smaller structural differences provide any obvious explanation of the Root effect of this or other fish haemoglobins.


{{STRUCTURE_1pbx|  PDB=1pbx  |  SCENE=  }}
Haemoglobin of the antarctic fish Pagothenia bernacchii. Amino acid sequence, oxygen equilibria and crystal structure of its carbonmonoxy derivative.,Camardella L, Caruso C, D'Avino R, di Prisco G, Rutigliano B, Tamburrini M, Fermi G, Perutz MF J Mol Biol. 1992 Mar 20;224(2):449-60. PMID:1560461<ref>PMID:1560461</ref>


===HAEMOGLOBIN OF THE ANTARCTIC FISH PAGOTHENIA BERNACCHII: AMINO ACID SEQUENCE, OXYGEN EQUILIBRIA AND CRYSTAL STRUCTURE OF ITS CARBONMONOXY DERIVATIVE===
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
 
</div>
{{ABSTRACT_PUBMED_1560461}}
 
==About this Structure==
[[1pbx]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Trematomus_bernacchii Trematomus bernacchii]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1PBX OCA].


==See Also==
==See Also==
*[[Hemoglobin|Hemoglobin]]
*[[Hemoglobin 3D structures|Hemoglobin 3D structures]]
 
== References ==
==Reference==
<references/>
<ref group="xtra">PMID:001560461</ref><ref group="xtra">PMID:010222199</ref><references group="xtra"/>
__TOC__
</StructureSection>
[[Category: Trematomus bernacchii]]
[[Category: Trematomus bernacchii]]
[[Category: Fermi, G.]]
[[Category: Fermi, G.]]
[[Category: Oxygen transport]]
[[Category: Oxygen transport]]

Revision as of 22:44, 28 September 2014

HAEMOGLOBIN OF THE ANTARCTIC FISH PAGOTHENIA BERNACCHII: AMINO ACID SEQUENCE, OXYGEN EQUILIBRIA AND CRYSTAL STRUCTURE OF ITS CARBONMONOXY DERIVATIVEHAEMOGLOBIN OF THE ANTARCTIC FISH PAGOTHENIA BERNACCHII: AMINO ACID SEQUENCE, OXYGEN EQUILIBRIA AND CRYSTAL STRUCTURE OF ITS CARBONMONOXY DERIVATIVE

Structural highlights

1pbx is a 2 chain structure with sequence from Trematomus bernacchii. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Ligands:,
NonStd Res:
Resources:FirstGlance, OCA, RCSB, PDBsum

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 Antarctic fish Pagothenia bernacchii has one major haemoglobin, Hb1 (over 95% of the total blood content). Hb1 has a strong alkaline Bohr effect and at low pH exhibits the reduced ligand affinity and co-operativity that comprise the Root effect. We have determined the complete amino acid sequence of P. bernacchii Hb1 and also the structure of its carbonmonoxy derivative by X-ray crystallography, to a resolution of 2.5 A. The crystallographic R-factor of the refined structure is 18%. The three-dimensional structure of this fish haemoglobin is similar to that of human haemoglobin A, with a root-mean-square difference in main-chain atom positions of 1.4 A after superimposition of the two structures, despite only 48% homology of their amino acid sequences (including insertion of a single residue in the CD region of the fish alpha-chain). Large structural differences occur only at the N and C termini of both the alpha- and beta-chains. Neither these nor other smaller structural differences provide any obvious explanation of the Root effect of this or other fish haemoglobins.

Haemoglobin of the antarctic fish Pagothenia bernacchii. Amino acid sequence, oxygen equilibria and crystal structure of its carbonmonoxy derivative.,Camardella L, Caruso C, D'Avino R, di Prisco G, Rutigliano B, Tamburrini M, Fermi G, Perutz MF J Mol Biol. 1992 Mar 20;224(2):449-60. PMID:1560461[1]

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

See Also

References

  1. ↑ Camardella L, Caruso C, D'Avino R, di Prisco G, Rutigliano B, Tamburrini M, Fermi G, Perutz MF. Haemoglobin of the antarctic fish Pagothenia bernacchii. Amino acid sequence, oxygen equilibria and crystal structure of its carbonmonoxy derivative. J Mol Biol. 1992 Mar 20;224(2):449-60. PMID:1560461

1pbx, resolution 2.50Å

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