1ykd

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(New page: 200px<br /><applet load="1ykd" size="450" color="white" frame="true" align="right" spinBox="true" caption="1ykd, resolution 1.90&Aring;" /> '''Crystal Structure of...)
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[[Image:1ykd.gif|left|200px]]<br /><applet load="1ykd" size="450" color="white" frame="true" align="right" spinBox="true"
 
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caption="1ykd, resolution 1.90&Aring;" />
 
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'''Crystal Structure of the Tandem GAF Domains from a Cyanobacterial Adenylyl Cyclase: Novel Modes of Ligand-Binding and Dimerization'''<br />
 
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==Overview==
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==Crystal Structure of the Tandem GAF Domains from a Cyanobacterial Adenylyl Cyclase: Novel Modes of Ligand-Binding and Dimerization==
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In several species, GAF domains, which are widely expressed, small-molecule-binding domains that regulate enzyme activity, are known to, bind cyclic nucleotides. However, the molecular mechanism by which cyclic, nucleotide binding affects enzyme activity is not known for any GAF, domain. In the cyanobacterium, Anabaena, the cyaB1 and cyaB2 genes encode, adenylyl cyclases that are stimulated by binding of cAMP to their, N-terminal GAF domains. Replacement of the tandem GAF-A/B domains in cyaB1, with the mammalian phosphodiesterase 2A GAF-A/B tandem domains allows, regulation of the chimeric protein by cGMP, suggesting a highly conserved, mechanism of activation. Here, we describe the 1.9-A crystal structure of, the tandem GAF-A/B domains of cyaB2 with bound cAMP and compare it to the, previously reported structure of the PDE2A GAF-A/B. Unexpectedly, the, cyaB2 GAF-A/B dimer is antiparallel, unlike the parallel dimer of PDE2A., Moreover, there is clear electron density for cAMP in both GAF-A and -B, whereas in PDE2A, cGMP is found only in GAF-B. Phosphate and ribose group, contacts are similar to those in PDE2A. However, the purine-binding, pockets appear very different from that in PDE2A GAF-B. Differences in the, beta2-beta3 loop suggest that this loop confers much of the ligand, specificity in this and perhaps in many other GAF domains. Finally, a, conserved asparagine appears to be a new addition to the signature NKFDE, motif, and a mechanism for this motif to stabilize the cNMP-binding pocket, is proposed.
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<StructureSection load='1ykd' size='340' side='right'caption='[[1ykd]], [[Resolution|resolution]] 1.90&Aring;' scene=''>
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== Structural highlights ==
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<table><tr><td colspan='2'>[[1ykd]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Anabaena_sp. Anabaena sp.]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1YKD OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1YKD FirstGlance]. <br>
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</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.9&#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=CMP:ADENOSINE-3,5-CYCLIC-MONOPHOSPHATE'>CMP</scene></td></tr>
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<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1ykd FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1ykd OCA], [https://pdbe.org/1ykd PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1ykd RCSB], [https://www.ebi.ac.uk/pdbsum/1ykd PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1ykd ProSAT]</span></td></tr>
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</table>
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== Function ==
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[https://www.uniprot.org/uniprot/P94182_9NOST P94182_9NOST]
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== Evolutionary Conservation ==
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[[Image:Consurf_key_small.gif|200px|right]]
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Check<jmol>
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<jmolCheckbox>
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<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/yk/1ykd_consurf.spt"</scriptWhenChecked>
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<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
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<text>to colour the structure by Evolutionary Conservation</text>
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</jmolCheckbox>
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</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=1ykd ConSurf].
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<div style="clear:both"></div>
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==About this Structure==
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==See Also==
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1YKD is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Anabaena_sp. Anabaena sp.] with CMP as [http://en.wikipedia.org/wiki/ligand ligand]. Active as [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] Full crystallographic information is available from [http://ispc.weizmann.ac.il/oca-bin/ocashort?id=1YKD OCA].
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*[[3D Adenylyl cyclase 3D structures|3D Adenylyl cyclase 3D structures]]
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__TOC__
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==Reference==
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</StructureSection>
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Crystal structure of the tandem GAF domains from a cyanobacterial adenylyl cyclase: modes of ligand binding and dimerization., Martinez SE, Bruder S, Schultz A, Zheng N, Schultz JE, Beavo JA, Linder JU, Proc Natl Acad Sci U S A. 2005 Feb 22;102(8):3082-7. Epub 2005 Feb 11. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=15708973 15708973]
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[[Category: Anabaena sp]]
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[[Category: Adenylate cyclase]]
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[[Category: Large Structures]]
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[[Category: Anabaena sp.]]
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[[Category: Beavo JA]]
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[[Category: Single protein]]
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[[Category: Bruder S]]
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[[Category: Beavo, J.A.]]
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[[Category: Linder JU]]
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[[Category: Bruder, S.]]
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[[Category: Martinez SE]]
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[[Category: Linder, J.U.]]
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[[Category: Schultz A]]
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[[Category: Martinez, S.E.]]
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[[Category: Schultz JE]]
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[[Category: Schultz, A.]]
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[[Category: Zheng N]]
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[[Category: Schultz, J.E.]]
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[[Category: Zheng, N.]]
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[[Category: CMP]]
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[[Category: bound cyclic amp ligand]]
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[[Category: gaf domain]]
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''Page seeded by [http://ispc.weizmann.ac.il/oca OCA ] on Sun Nov 25 04:14:10 2007''
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Current revision

Crystal Structure of the Tandem GAF Domains from a Cyanobacterial Adenylyl Cyclase: Novel Modes of Ligand-Binding and Dimerization

PDB ID 1ykd

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