This old version of Proteopedia is provided for student assignments while the new version is undergoing repairs. Content and edits done in this old version of Proteopedia after March 1, 2026 will eventually be lost when it is retired in about June of 2026.

Apply for new accounts at the new Proteopedia. Your logins will work in both the old and new versions.

3dba

From Proteopedia

(Difference between revisions)

Jump to: navigation, search

Revision as of 10:03, 14 November 2018

Crystal structure of the cGMP-bound GAF a domain from the photoreceptor phosphodiesterase 6C

Structural highlights

3dba is a 2 chain structure with sequence from Chick. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Ligands:	,
Gene:	PDE6C (CHICK)
Activity:	3',5'-cyclic-GMP phosphodiesterase, with EC number 3.1.4.35
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

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 photoreceptor phosphodiesterase (PDE6) regulates the intracellular levels of the second messenger cGMP in the outer segments of cone and rod photoreceptor cells. PDE6 contains two regulatory GAF domains, of which one (GAF A) binds cGMP and regulates the activity of the PDE6 holoenzyme. To increase our understanding of this allosteric regulation mechanism, we present the 2.6A crystal structure of the cGMP-bound GAF A domain of chicken cone PDE6. Nucleotide specificity appears to be provided in part by the orientation of Asn-116, which makes two hydrogen bonds to the guanine ring of cGMP but is not strictly conserved among PDE6 isoforms. The isolated PDE6C GAF A domain is monomeric and does not contain sufficient structural determinants to form a homodimer as found in full-length PDE6C. A highly conserved surface patch on GAF A indicates a potential binding site for the inhibitory subunit Pgamma. NMR studies reveal that the apo-PDE6C GAF A domain is structured but adopts a significantly altered structural state indicating a large conformational change with rearrangement of secondary structure elements upon cGMP binding. The presented crystal structure will help to define the cGMP-dependent regulation mechanism of the PDE6 holoenzyme and its inhibition through Pgamma binding.

The structure of the GAF A domain from phosphodiesterase 6C reveals determinants of cGMP binding, a conserved binding surface, and a large cGMP-dependent conformational change.,Martinez SE, Heikaus CC, Klevit RE, Beavo JA J Biol Chem. 2008 Sep 19;283(38):25913-9. Epub 2008 Jul 9. PMID:18614542^[1]

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

References

↑ Martinez SE, Heikaus CC, Klevit RE, Beavo JA. The structure of the GAF A domain from phosphodiesterase 6C reveals determinants of cGMP binding, a conserved binding surface, and a large cGMP-dependent conformational change. J Biol Chem. 2008 Sep 19;283(38):25913-9. Epub 2008 Jul 9. PMID:18614542 doi:10.1074/jbc.M802891200

1 Structural highlights
2 Evolutionary Conservation
3 Publication Abstract from PubMed
4 See Also
5 References

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/3dba"

@@ Line 1: / Line 1: @@
 ==Crystal structure of the cGMP-bound GAF a domain from the photoreceptor phosphodiesterase 6C==
 <StructureSection load='3dba' size='340' side='right' caption='[[3dba]], [[Resolution|resolution]] 2.57&Aring;' scene=''>
@@ Line 6: / Line 7: @@
 <tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">PDE6C ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9031 CHICK])</td></tr>
 <tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/3',5'-cyclic-GMP_phosphodiesterase 3',5'-cyclic-GMP phosphodiesterase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.1.4.35 3.1.4.35] </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=3dba FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3dba OCA], [http://pdbe.org/3dba PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3dba RCSB], [http://www.ebi.ac.uk/pdbsum/3dba PDBsum]</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=3dba FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3dba OCA], [http://pdbe.org/3dba PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3dba RCSB], [http://www.ebi.ac.uk/pdbsum/3dba PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=3dba ProSAT]</span></td></tr>
 </table>
 == Evolutionary Conservation ==
@@ Line 12: / Line 13: @@
 Check<jmol>
   <jmolCheckbox>
-    <scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/db/3dba_consurf.spt"</scriptWhenChecked>
+    <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/db/3dba_consurf.spt"</scriptWhenChecked>
     <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
     <text>to colour the structure by Evolutionary Conservation</text>
@@ Line 40: / Line 41: @@
 [[Category: Klevit, R E]]
 [[Category: Martinez, S E]]
-[[Category: 3s']]
+[[Category: 3ss']]
 [[Category: 5' cgmp]]
 [[Category: Cgmp]]

3dba

From Proteopedia

Revision as of 10:03, 14 November 2018

Crystal structure of the cGMP-bound GAF a domain from the photoreceptor phosphodiesterase 6C

Structural highlights

Evolutionary Conservation

Publication Abstract from PubMed

See Also

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

Views

Personal tools

Navigation

Search

Toolbox