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| | ==Product complex of adenylate cyclase class IV== | | ==Product complex of adenylate cyclase class IV== |
| - | <StructureSection load='3n10' size='340' side='right' caption='[[3n10]], [[Resolution|resolution]] 1.60Å' scene=''> | + | <StructureSection load='3n10' size='340' side='right'caption='[[3n10]], [[Resolution|resolution]] 1.60Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[3n10]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/"bacillus_pestis"_(lehmann_and_neumann_1896)_migula_1900 "bacillus pestis" (lehmann and neumann 1896) migula 1900]. This structure supersedes the now removed PDB entry [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=3ghx 3ghx]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3N10 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3N10 FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[3n10]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Yersinia_pestis Yersinia pestis]. This structure supersedes the now removed PDB entry [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=3ghx 3ghx]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3N10 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3N10 FirstGlance]. <br> |
| - | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CMP:ADENOSINE-3,5-CYCLIC-MONOPHOSPHATE'>CMP</scene>, <scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</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]] 1.6Å</td></tr> |
| - | <tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[3n0y|3n0y]], [[3n0z|3n0z]], [[2fjt|2fjt]]</td></tr>
| + | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CMP:ADENOSINE-3,5-CYCLIC-MONOPHOSPHATE'>CMP</scene>, <scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr> |
| - | <tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">cyaB, y3011, YPO1178, YP_0959 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=632 "Bacillus pestis" (Lehmann and Neumann 1896) Migula 1900])</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=3n10 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3n10 OCA], [https://pdbe.org/3n10 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3n10 RCSB], [https://www.ebi.ac.uk/pdbsum/3n10 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3n10 ProSAT]</span></td></tr> |
| - | <tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Adenylate_cyclase Adenylate cyclase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=4.6.1.1 4.6.1.1] </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=3n10 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3n10 OCA], [http://pdbe.org/3n10 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3n10 RCSB], [http://www.ebi.ac.uk/pdbsum/3n10 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=3n10 ProSAT]</span></td></tr> | + | |
| | </table> | | </table> |
| | + | == Function == |
| | + | [https://www.uniprot.org/uniprot/A0A5P8YEL9_YERPE A0A5P8YEL9_YERPE] |
| | == Evolutionary Conservation == | | == Evolutionary Conservation == |
| | [[Image:Consurf_key_small.gif|200px|right]] | | [[Image:Consurf_key_small.gif|200px|right]] |
| | Check<jmol> | | Check<jmol> |
| | <jmolCheckbox> | | <jmolCheckbox> |
| - | <scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/n1/3n10_consurf.spt"</scriptWhenChecked> | + | <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/n1/3n10_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> |
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| | __TOC__ | | __TOC__ |
| | </StructureSection> | | </StructureSection> |
| - | [[Category: Adenylate cyclase]] | + | [[Category: Large Structures]] |
| - | [[Category: Gallagher, D T]] | + | [[Category: Yersinia pestis]] |
| - | [[Category: Reddy, P T]] | + | [[Category: Gallagher DT]] |
| - | [[Category: Antiparallel barrel]] | + | [[Category: Reddy PT]] |
| - | [[Category: Cyclic amp]]
| + | |
| - | [[Category: Cyth domain]]
| + | |
| - | [[Category: Lyase]]
| + | |
| - | [[Category: Product complex]]
| + | |
| Structural highlights
Function
A0A5P8YEL9_YERPE
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
Adenylyl cyclases (ACs) belonging to three nonhomologous classes (II, III, and IV) have been structurally characterized, enabling a comparison of the mechanisms of cyclic adenosine 3',5'-monophosphate biosynthesis. We report the crystal structures of three active-site complexes for Yersinia pestis class IV AC (AC-IV)-two with substrate analogs and one with product. Mn(2+) binds to all three phosphates, and to Glu12 and Glu136. Electropositive residues Lys14, Arg63, Lys76, Lys111, and Arg113 also form hydrogen bonds to phosphates. The conformation of the analogs is suitable for in-line nucleophilic attack by the ribose O3' on alpha-phosphate (distance approximately 4 A). In the product complex, a second Mn ion is observed to be coordinated to both ribose 2' oxygen and ribose 3' oxygen. Observation of both metal sites, together with kinetic measurements, provides strong support for a two-cation mechanism. Eleven active-site mutants were also made and kinetically characterized. These findings and comparisons with class II and class III enzymes enable a detailed transphyletic analysis of the AC mechanism. Consistent with its lack of coordination to purine, Y. pestis AC-IV cyclizes both ATP and GTP. As in other classes of AC, the ribose is loosely bound, and as in class III, no base appears to ionize the O3' nucleophile. Different syn/anti conformations suggest that the mechanism involves a conformational transition, and further evidence suggests a role for ribosyl pseudorotation. With resolutions of 1.6-1.7 A, these are the most detailed active-site ligand complexes for any class of this ubiquitous signaling enzyme.
Active-Site Structure of Class IV Adenylyl Cyclase and Transphyletic Mechanism.,Gallagher DT, Kim SK, Robinson H, Reddy PT J Mol Biol. 2011 Jan 21;405(3):787-803. Epub 2010 Nov 20. PMID:21094652[1]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
References
- ↑ Gallagher DT, Kim SK, Robinson H, Reddy PT. Active-Site Structure of Class IV Adenylyl Cyclase and Transphyletic Mechanism. J Mol Biol. 2011 Jan 21;405(3):787-803. Epub 2010 Nov 20. PMID:21094652 doi:10.1016/j.jmb.2010.11.026
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