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==Human AdoMetDC with 5'-Deoxy-5'-(dimethylsulfonio) adenosine== | ==Human AdoMetDC with 5'-Deoxy-5'-(dimethylsulfonio) adenosine== | ||
<StructureSection load='3h0v' size='340' side='right' caption='[[3h0v]], [[Resolution|resolution]] 2.24Å' scene=''> | <StructureSection load='3h0v' size='340' side='right'caption='[[3h0v]], [[Resolution|resolution]] 2.24Å' scene=''> | ||
== Structural highlights == | == Structural highlights == | ||
<table><tr><td colspan='2'>[[3h0v]] is a 2 chain structure with sequence from [ | <table><tr><td colspan='2'>[[3h0v]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Human Human]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3H0V OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3H0V FirstGlance]. <br> | ||
</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=M2T:5-DEOXY-5-(DIMETHYL-LAMBDA~4~-SULFANYL)ADENOSINE'>M2T</scene>, <scene name='pdbligand=PUT:1,4-DIAMINOBUTANE'>PUT</scene>, <scene name='pdbligand=PYR:PYRUVIC+ACID'>PYR</scene></td></tr> | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=M2T:5-DEOXY-5-(DIMETHYL-LAMBDA~4~-SULFANYL)ADENOSINE'>M2T</scene>, <scene name='pdbligand=PUT:1,4-DIAMINOBUTANE'>PUT</scene>, <scene name='pdbligand=PYR:PYRUVIC+ACID'>PYR</scene></td></tr> | ||
<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[1jen|1jen]], [[1i7b|1i7b]], [[1i7c|1i7c]], [[1i7m|1i7m]], [[1i72|1i72]], [[1i79|1i79]], [[3h0w|3h0w]]</td></tr> | <tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[1jen|1jen]], [[1i7b|1i7b]], [[1i7c|1i7c]], [[1i7m|1i7m]], [[1i72|1i72]], [[1i79|1i79]], [[3h0w|3h0w]]</div></td></tr> | ||
<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">AMD1, AMD ([ | <tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">AMD1, AMD ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 HUMAN])</td></tr> | ||
<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[ | <tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/Adenosylmethionine_decarboxylase Adenosylmethionine decarboxylase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=4.1.1.50 4.1.1.50] </span></td></tr> | ||
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[ | <tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=3h0v FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3h0v OCA], [https://pdbe.org/3h0v PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3h0v RCSB], [https://www.ebi.ac.uk/pdbsum/3h0v PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3h0v ProSAT]</span></td></tr> | ||
</table> | </table> | ||
== Evolutionary Conservation == | == Evolutionary Conservation == | ||
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Check<jmol> | Check<jmol> | ||
<jmolCheckbox> | <jmolCheckbox> | ||
<scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/h0/3h0v_consurf.spt"</scriptWhenChecked> | <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/h0/3h0v_consurf.spt"</scriptWhenChecked> | ||
<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked> | <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked> | ||
<text>to colour the structure by Evolutionary Conservation</text> | <text>to colour the structure by Evolutionary Conservation</text> | ||
| Line 29: | Line 29: | ||
</div> | </div> | ||
<div class="pdbe-citations 3h0v" style="background-color:#fffaf0;"></div> | <div class="pdbe-citations 3h0v" style="background-color:#fffaf0;"></div> | ||
==See Also== | |||
*[[SAM decarboxylase|SAM decarboxylase]] | |||
== References == | == References == | ||
<references/> | <references/> | ||
| Line 35: | Line 38: | ||
[[Category: Adenosylmethionine decarboxylase]] | [[Category: Adenosylmethionine decarboxylase]] | ||
[[Category: Human]] | [[Category: Human]] | ||
[[Category: Large Structures]] | |||
[[Category: Bale, S]] | [[Category: Bale, S]] | ||
[[Category: Brooks, W H]] | [[Category: Brooks, W H]] | ||
Revision as of 11:00, 16 March 2022
Human AdoMetDC with 5'-Deoxy-5'-(dimethylsulfonio) adenosineHuman AdoMetDC with 5'-Deoxy-5'-(dimethylsulfonio) adenosine
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 PubMedS-Adenosylmethionine decarboxylase (AdoMetDC) is a key enzyme in the polyamine biosynthetic pathway. Inhibition of this pathway and subsequent depletion of polyamine levels is a viable strategy for cancer chemotherapy and for the treatment of parasitic diseases. Substrate analogue inhibitors display an absolute requirement for a positive charge at the position equivalent to the sulfonium of S-adenosylmethionine. We investigated the ligand specificity of AdoMetDC through crystallography, quantum chemical calculations, and stopped-flow experiments. We determined crystal structures of the enzyme cocrystallized with 5'-deoxy-5'-dimethylthioadenosine and 5'-deoxy-5'-(N-dimethyl)amino-8-methyladenosine. The crystal structures revealed a favorable cation-pi interaction between the ligand and the aromatic side chains of Phe7 and Phe223. The estimated stabilization from this interaction is 4.5 kcal/mol as determined by quantum chemical calculations. Stopped-flow kinetic experiments showed that the rate of the substrate binding to the enzyme greatly depends on Phe7 and Phe223, thus supporting the importance of the cation-pi interaction. Role of the Sulfonium Center in Determining the Ligand Specificity of Human S-Adenosylmethionine Decarboxylase.,Bale S, Brooks W, Hanes JW, Mahesan AM, Guida WC, Ealick SE Biochemistry. 2009 Jun 15. PMID:19527050[1] From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine. See AlsoReferences
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Proteopedia Page Contributors and Editors (what is this?)Proteopedia Page Contributors and Editors (what is this?)
OCACategories:
- Adenosylmethionine decarboxylase
- Human
- Large Structures
- Bale, S
- Brooks, W H
- Ealick, S E
- Guida, W C
- Hanes, J W
- Mahesan, A M
- Adometdc with competitive substrate analog
- Autocatalytic cleavage
- Decarboxylase
- Lyase
- Phosphoprotein
- Polyamine biosynthesis
- Pyruvate
- S-adenosyl-l-methionine
- Schiff base
- Spermidine biosynthesis
- Zymogen