2c05: Difference between revisions
No edit summary |
No edit summary |
||
| (8 intermediate revisions by the same user not shown) | |||
| Line 1: | Line 1: | ||
==CRYSTAL STRUCTURES OF EOSINOPHIL-DERIVED NEUROTOXIN IN COMPLEX WITH THE INHIBITORS 5'-ATP, AP3A, AP4A AND AP5A== | |||
[[Image: | <StructureSection load='2c05' size='340' side='right' caption='[[2c05]], [[Resolution|resolution]] 1.86Å' scene=''> | ||
== Structural highlights == | |||
<table><tr><td colspan='2'>[[2c05]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Human Human]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2C05 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2C05 FirstGlance]. <br> | |||
</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ACY:ACETIC+ACID'>ACY</scene>, <scene name='pdbligand=B4P:BIS(ADENOSINE)-5-TETRAPHOSPHATE'>B4P</scene></td></tr> | |||
<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[1gqv|1gqv]], [[1hi2|1hi2]], [[1hi3|1hi3]], [[1hi4|1hi4]], [[1hi5|1hi5]], [[1k2a|1k2a]], [[2bex|2bex]], [[2bzz|2bzz]], [[2c01|2c01]], [[2c02|2c02]]</td></tr> | |||
<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Pancreatic_ribonuclease Pancreatic ribonuclease], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.1.27.5 3.1.27.5] </span></td></tr> | |||
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2c05 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2c05 OCA], [http://pdbe.org/2c05 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2c05 RCSB], [http://www.ebi.ac.uk/pdbsum/2c05 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/c0/2c05_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=2c05 ConSurf]. | |||
<div style="clear:both"></div> | |||
<div style="background-color:#fffaf0;"> | |||
== Publication Abstract from PubMed == | |||
Eosinophil-derived neurotoxin (EDN) is a catalytically proficient member of the pancreatic ribonuclease superfamily secreted along with other eosinophil granule proteins during innate host defense responses and various eosinophil-related inflammatory and allergic diseases. The ribonucleolytic activity of EDN is central to its antiviral and neurotoxic activities and possibly to other facets of its biological activity. To probe the importance of this enzymatic activity further, specific inhibitors will be of great aid. Derivatives of 5'-ADP are among the most potent inhibitors currently known. Here, we use X-ray crystallography to investigate the binding of four natural nucleotides containing this moiety. 5'-ATP binds in two alternative orientations, one occupying the B2 subsite in a conventional manner and one being a retro orientation with no ordered adenosine moiety. Diadenosine triphosphate (Ap3A) and diadenosine tetraphosphate (Ap4A) bind with one adenine positioned at the B2 subsite, the polyphosphate chain extending across the P1 subsite in an ill-defined conformation, and a disordered second adenosine moiety. Diadenosine pentaphosphate (Ap5A), the most avid inhibitor of this series, binds in a completely ordered fashion with one adenine positioned conventionally at the B2 subsite, the polyphosphate chain occupying the P1 and putative P(-1) subsites, and the other adenine bound in a retro-like manner at the edge of the B1 subsite. The binding mode of each of these inhibitors has features seen in previously determined structures of adenosine diphosphates. We examine the structure-affinity relationships of these inhibitors and discuss the implications for the design of improved inhibitors. | |||
Crystal structures of eosinophil-derived neurotoxin (EDN) in complex with the inhibitors 5'-ATP, Ap3A, Ap4A, and Ap5A.,Baker MD, Holloway DE, Swaminathan GJ, Acharya KR Biochemistry. 2006 Jan 17;45(2):416-26. PMID:16401072<ref>PMID:16401072</ref> | |||
== | From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | ||
</div> | |||
<div class="pdbe-citations 2c05" style="background-color:#fffaf0;"></div> | |||
==See Also== | |||
*[[Ribonuclease|Ribonuclease]] | |||
*[[Temp|Temp]] | |||
== References == | |||
<references/> | |||
__TOC__ | |||
</StructureSection> | |||
== | [[Category: Human]] | ||
== | |||
[[Category: | |||
[[Category: Pancreatic ribonuclease]] | [[Category: Pancreatic ribonuclease]] | ||
[[Category: Acharya, K R]] | |||
[[Category: Acharya, K R | [[Category: Baker, M D]] | ||
[[Category: Baker, M D | [[Category: Holloway, D E]] | ||
[[Category: Holloway, D E | [[Category: Swaminathan, G J]] | ||
[[Category: Swaminathan, G J | |||
[[Category: 5'-atp]] | [[Category: 5'-atp]] | ||
[[Category: Ap3a]] | [[Category: Ap3a]] | ||
| Line 42: | Line 52: | ||
[[Category: Inhibitor]] | [[Category: Inhibitor]] | ||
[[Category: Nuclease]] | [[Category: Nuclease]] | ||
[[Category: Ribonuclease]] | [[Category: Ribonuclease]] | ||
[[Category: Rnase us]] | [[Category: Rnase us]] | ||
[[Category: Rnase-2]] | [[Category: Rnase-2]] | ||
[[Category: Sensory transduction]] | [[Category: Sensory transduction]] | ||
Latest revision as of 07:10, 7 February 2016
CRYSTAL STRUCTURES OF EOSINOPHIL-DERIVED NEUROTOXIN IN COMPLEX WITH THE INHIBITORS 5'-ATP, AP3A, AP4A AND AP5ACRYSTAL STRUCTURES OF EOSINOPHIL-DERIVED NEUROTOXIN IN COMPLEX WITH THE INHIBITORS 5'-ATP, AP3A, AP4A AND AP5A
Structural highlights
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 PubMedEosinophil-derived neurotoxin (EDN) is a catalytically proficient member of the pancreatic ribonuclease superfamily secreted along with other eosinophil granule proteins during innate host defense responses and various eosinophil-related inflammatory and allergic diseases. The ribonucleolytic activity of EDN is central to its antiviral and neurotoxic activities and possibly to other facets of its biological activity. To probe the importance of this enzymatic activity further, specific inhibitors will be of great aid. Derivatives of 5'-ADP are among the most potent inhibitors currently known. Here, we use X-ray crystallography to investigate the binding of four natural nucleotides containing this moiety. 5'-ATP binds in two alternative orientations, one occupying the B2 subsite in a conventional manner and one being a retro orientation with no ordered adenosine moiety. Diadenosine triphosphate (Ap3A) and diadenosine tetraphosphate (Ap4A) bind with one adenine positioned at the B2 subsite, the polyphosphate chain extending across the P1 subsite in an ill-defined conformation, and a disordered second adenosine moiety. Diadenosine pentaphosphate (Ap5A), the most avid inhibitor of this series, binds in a completely ordered fashion with one adenine positioned conventionally at the B2 subsite, the polyphosphate chain occupying the P1 and putative P(-1) subsites, and the other adenine bound in a retro-like manner at the edge of the B1 subsite. The binding mode of each of these inhibitors has features seen in previously determined structures of adenosine diphosphates. We examine the structure-affinity relationships of these inhibitors and discuss the implications for the design of improved inhibitors. Crystal structures of eosinophil-derived neurotoxin (EDN) in complex with the inhibitors 5'-ATP, Ap3A, Ap4A, and Ap5A.,Baker MD, Holloway DE, Swaminathan GJ, Acharya KR Biochemistry. 2006 Jan 17;45(2):416-26. PMID:16401072[1] From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine. See AlsoReferences
|
| ||||||||||||||||||||