2zbj: Difference between revisions

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{{Seed}}
[[Image:2zbj.png|left|200px]]


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==Crystal structure of Dioclea rostrata lectin==
The line below this paragraph, containing "STRUCTURE_2zbj", creates the "Structure Box" on the page.
<StructureSection load='2zbj' size='340' side='right'caption='[[2zbj]], [[Resolution|resolution]] 2.05&Aring;' scene=''>
You may change the PDB parameter (which sets the PDB file loaded into the applet)
== Structural highlights ==
or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
<table><tr><td colspan='2'>[[2zbj]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Macropsychanthus_bicolor Macropsychanthus bicolor]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2ZBJ OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2ZBJ FirstGlance]. <br>
or leave the SCENE parameter empty for the default display.
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.05&#8491;</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=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene></td></tr>
{{STRUCTURE_2zbj|  PDB=2zbj  |  SCENE=  }}
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=2zbj FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2zbj OCA], [https://pdbe.org/2zbj PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2zbj RCSB], [https://www.ebi.ac.uk/pdbsum/2zbj PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2zbj ProSAT]</span></td></tr>
</table>
== Function ==
[https://www.uniprot.org/uniprot/LECA_DIORO LECA_DIORO] D-mannose/D-glucose-binding lectin. Induces histamine release in mast cells from hamster and rat. Induces lymphocyte proliferation and IFNG production.<ref>PMID:18682294</ref> <ref>PMID:1398779</ref> <ref>PMID:7524287</ref> <ref>PMID:8891754</ref> <ref>PMID:9575151</ref> <ref>PMID:10747944</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/zb/2zbj_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/main_output.php?pdb_ID=2zbj ConSurf].
<div style="clear:both"></div>
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
The legume lectins from the subtribe Diocleinae, often referred to as concanavalin A-like lectins, are a typical example of highly similar proteins that show distinct biological activities. The pH-dependent oligomerization that some of these lectins undergo and the relative position of amino acids within the carbohydrate-binding site are factors that have been reported to contribute to these differences in the activities of Diocleinae lectins. In the present work, we determined the amino acid sequence and the crystal structure of the lectin of Dioclea rostrata seeds (DRL), with the aim of investigating the structural bases of the different behavior displayed by this lectin in comparison to other Diocleinae lectins and determining the reason for the distinct pH-dependent dimer-tetramer equilibrium. In addition, we discovered a novel multimeric arrangement for this lectin.


===Crystal structure of Dioclea rostrata lectin===
Crystal structure of Dioclea rostrata lectin: insights into understanding the pH-dependent dimer-tetramer equilibrium and the structural basis for carbohydrate recognition in Diocleinae lectins.,de Oliveira TM, Delatorre P, da Rocha BA, de Souza EP, Nascimento KS, Bezerra GA, Moura TR, Benevides RG, Bezerra EH, Moreno FB, Freire VN, de Azevedo WF Jr, Cavada BS J Struct Biol. 2008 Nov;164(2):177-82. Epub 2008 Jul 22. PMID:18682294<ref>PMID:18682294</ref>


 
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
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</div>
The line below this paragraph, {{ABSTRACT_PUBMED_18682294}}, adds the Publication Abstract to the page
<div class="pdbe-citations 2zbj" style="background-color:#fffaf0;"></div>
(as it appears on PubMed at http://www.pubmed.gov), where 18682294 is the PubMed ID number.
== References ==
-->
<references/>
{{ABSTRACT_PUBMED_18682294}}
__TOC__
 
</StructureSection>
==About this Structure==
[[Category: Large Structures]]
2ZBJ is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Dioclea_rostrata Dioclea rostrata]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2ZBJ OCA].
[[Category: Macropsychanthus bicolor]]
 
[[Category: Benevides RG]]
==Reference==
[[Category: Bezerra EHS]]
Crystal structure of Dioclea rostrata lectin: Insights into understanding the pH-dependent dimer-tetramer equilibrium and the structural basis for carbohydrate recognition in Diocleinae lectins., de Oliveira TM, Delatorre P, da Rocha BA, de Souza EP, Nascimento KS, Bezerra GA, Moura TR, Benevides RG, Bezerra EH, Moreno FB, Freire VN, de Azevedo WF Jr, Cavada BS, J Struct Biol. 2008 Jul 22. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/18682294 18682294]
[[Category: Bezerra GA]]
[[Category: Dioclea rostrata]]
[[Category: Cavada BS]]
[[Category: Single protein]]
[[Category: Delatorre P]]
[[Category: Benevides, R G.]]
[[Category: Freire VN]]
[[Category: Bezerra, E H.S.]]
[[Category: Moreno FBMB]]
[[Category: Bezerra, G A.]]
[[Category: Moura TR]]
[[Category: Cavada, B S.]]
[[Category: Nascimento KS]]
[[Category: Delatorre, P.]]
[[Category: Da Rocha BAM]]
[[Category: Freire, V N.]]
[[Category: De Azevedo Jr WF]]
[[Category: Jr., W F.de Azevedo.]]
[[Category: De Oliveira TM]]
[[Category: Moreno, F B.M B.]]
[[Category: De Sousa EP]]
[[Category: Moura, T R.]]
[[Category: Nascimento, K S.]]
[[Category: Oliveira, T M.de.]]
[[Category: Rocha, B A.M da.]]
[[Category: Sousa, E P.de.]]
[[Category: Calcium]]
[[Category: Dioclea rostrata]]
[[Category: Diocleinae]]
[[Category: Lectin]]
[[Category: Leguminosae]]
[[Category: Manganese]]
[[Category: Metal-binding]]
[[Category: Sugar binding protein]]
[[Category: Vacuole]]
 
''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Oct 29 09:57:15 2008''

Latest revision as of 16:30, 1 November 2023

Crystal structure of Dioclea rostrata lectinCrystal structure of Dioclea rostrata lectin

Structural highlights

2zbj is a 1 chain structure with sequence from Macropsychanthus bicolor. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:X-ray diffraction, Resolution 2.05Å
Ligands:, ,
Resources:FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

LECA_DIORO D-mannose/D-glucose-binding lectin. Induces histamine release in mast cells from hamster and rat. Induces lymphocyte proliferation and IFNG production.[1] [2] [3] [4] [5] [6]

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 legume lectins from the subtribe Diocleinae, often referred to as concanavalin A-like lectins, are a typical example of highly similar proteins that show distinct biological activities. The pH-dependent oligomerization that some of these lectins undergo and the relative position of amino acids within the carbohydrate-binding site are factors that have been reported to contribute to these differences in the activities of Diocleinae lectins. In the present work, we determined the amino acid sequence and the crystal structure of the lectin of Dioclea rostrata seeds (DRL), with the aim of investigating the structural bases of the different behavior displayed by this lectin in comparison to other Diocleinae lectins and determining the reason for the distinct pH-dependent dimer-tetramer equilibrium. In addition, we discovered a novel multimeric arrangement for this lectin.

Crystal structure of Dioclea rostrata lectin: insights into understanding the pH-dependent dimer-tetramer equilibrium and the structural basis for carbohydrate recognition in Diocleinae lectins.,de Oliveira TM, Delatorre P, da Rocha BA, de Souza EP, Nascimento KS, Bezerra GA, Moura TR, Benevides RG, Bezerra EH, Moreno FB, Freire VN, de Azevedo WF Jr, Cavada BS J Struct Biol. 2008 Nov;164(2):177-82. Epub 2008 Jul 22. PMID:18682294[7]

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

References

  1. ↑ de Oliveira TM, Delatorre P, da Rocha BA, de Souza EP, Nascimento KS, Bezerra GA, Moura TR, Benevides RG, Bezerra EH, Moreno FB, Freire VN, de Azevedo WF Jr, Cavada BS. Crystal structure of Dioclea rostrata lectin: insights into understanding the pH-dependent dimer-tetramer equilibrium and the structural basis for carbohydrate recognition in Diocleinae lectins. J Struct Biol. 2008 Nov;164(2):177-82. Epub 2008 Jul 22. PMID:18682294 doi:10.1016/j.jsb.2008.05.012
  2. ↑ Barral-Netto M, Santos SB, Barral A, Moreira LI, Santos CF, Moreira RA, Oliveira JT, Cavada BS. Human lymphocyte stimulation by legume lectins from the Diocleae tribe. Immunol Invest. 1992 Jul;21(4):297-303. PMID:1398779
  3. ↑ Gomes JC, Ferreira RR, Cavada BS, Moreira RA, Oliveira JT. Histamine release induced by glucose (mannose)-specific lectins isolated from Brazilian beans. Comparison with concanavalin A. Agents Actions. 1994 May;41(3-4):132-5. PMID:7524287
  4. ↑ Ferreira RR, Cavada BS, Moreira RA, Oliveira JT, Gomes JC. Characteristics of the histamine release from hamster cheek pouch mast cells stimulated by lectins from Brazilian beans and concanavalin A. Inflamm Res. 1996 Sep;45(9):442-7. PMID:8891754
  5. ↑ Dam TK, Cavada BS, Grangeiro TB, Santos CF, de Sousa FA, Oscarson S, Brewer CF. Diocleinae lectins are a group of proteins with conserved binding sites for the core trimannoside of asparagine-linked oligosaccharides and differential specificities for complex carbohydrates. J Biol Chem. 1998 May 15;273(20):12082-8. PMID:9575151
  6. ↑ Dam TK, Cavada BS, Grangeiro TB, Santos CF, Ceccatto VM, de Sousa FA, Oscarson S, Brewer CF. Thermodynamic binding studies of lectins from the diocleinae subtribe to deoxy analogs of the core trimannoside of asparagine-linked oligosaccharides. J Biol Chem. 2000 May 26;275(21):16119-26. PMID:10747944 doi:http://dx.doi.org/10.1074/jbc.M000670200
  7. ↑ de Oliveira TM, Delatorre P, da Rocha BA, de Souza EP, Nascimento KS, Bezerra GA, Moura TR, Benevides RG, Bezerra EH, Moreno FB, Freire VN, de Azevedo WF Jr, Cavada BS. Crystal structure of Dioclea rostrata lectin: insights into understanding the pH-dependent dimer-tetramer equilibrium and the structural basis for carbohydrate recognition in Diocleinae lectins. J Struct Biol. 2008 Nov;164(2):177-82. Epub 2008 Jul 22. PMID:18682294 doi:10.1016/j.jsb.2008.05.012

2zbj, resolution 2.05Å

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