4j6o: Difference between revisions

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~~{{STRUCTURE_4j6o| PDB=4j6o | SCENE= }}~~

==Crystal Structure of the Phosphatase Domain of C. thermocellum (Bacterial) PnkP==

===Crystal Structure of the Phosphatase Domain of C. thermocellum (Bacterial) PnkP===

~~{{ABSTRACT_PUBMED_23595150}}~~

== Structural highlights ==

<table><tr><td colspan='2'>[[4j6o]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Clostridium_thermocellum_atcc_27405 Clostridium thermocellum atcc 27405]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4J6O OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4J6O FirstGlance]. <br>

</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CIT:CITRIC+ACID'>CIT</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</scene>, <scene name='pdbligand=PG4:TETRAETHYLENE+GLYCOL'>PG4</scene>, <scene name='pdbligand=PGE:TRIETHYLENE+GLYCOL'>PGE</scene></td></tr>

<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">Cthe_2768 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=203119 Clostridium thermocellum ATCC 27405])</td></tr>

<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Phosphoprotein_phosphatase Phosphoprotein phosphatase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.1.3.16 3.1.3.16] </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=4j6o FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4j6o OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4j6o RCSB], [http://www.ebi.ac.uk/pdbsum/4j6o PDBsum]</span></td></tr>

</table>

== Publication Abstract from PubMed ==

Pnkp is the end-healing and end-sealing component of an RNA repair system present in diverse bacteria from many phyla. Pnkp is composed of three catalytic modules: an N-terminal polynucleotide 5' kinase, a central 2',3' phosphatase and a C-terminal ligase. The phosphatase module is a Mn2+-dependent phosphodiesterase-monoesterase that dephosphorylates 2',3'-cyclic phosphate RNA ends. Here we report the crystal structure of the phosphatase domain of Clostridium thermocellum Pnkp with Mn2+ and citrate in the active site. The protein consists of a core binuclear metallo-phosphoesterase fold (exemplified by bacteriophage lambda phosphatase) embellished by distinctive secondary structure elements. The active site contains a single Mn2+ in an octahedral coordination complex with Asp187, His189, Asp233, two citrate oxygens and a water. The citrate fills the binding site for the scissile phosphate, wherein it is coordinated by Arg237, Asn263 and His264. The citrate invades the site normally occupied by a second metal (engaged by Asp233, Asn263, His323 and His376), and thereby dislocates His376. A continuous tract of positive surface potential flanking the active site suggests an RNA binding site. The structure illuminates a large body of mutational data regarding the metal and substrate specificity of Clostridium thermocellum Pnkp phosphatase.

~~==About this~~ Structure==

Structure and mechanism of the 2',3' phosphatase component of the bacterial Pnkp-Hen1 RNA repair system.,Wang LK, Smith P, Shuman S Nucleic Acids Res. 2013 Apr 16. PMID:23595150<ref>PMID:23595150</ref>

~~[[4j6o]] is a~~ 2 ~~chain structure with sequence from [http://en~~.~~wikipedia~~.~~org/wiki/Clostridium_thermocellum_atcc_27405 Clostridium thermocellum atcc 27405]~~. ~~Full crystallographic information is available from [http~~:/~~/oca.weizmann.ac.il/oca-bin/ocashort?id=4J6O OCA].~~

==~~Reference~~==

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

~~<ref group="xtra">PMID:023595150</ref>~~<references ~~group="xtra"~~/><~~references~~/>

</div>

== References ==

__TOC__

</StructureSection>

[[Category: Clostridium thermocellum atcc 27405]]

[[Category: Phosphoprotein phosphatase]]

[[Category: Shuman, S.]]

[[Category: Shuman, S]]

[[Category: Smith, P.]]

[[Category: Smith, P]]

[[Category: Wang, L.]]

[[Category: Wang, L]]

[[Category: Alpha/beta fold]]

[[Category: Calcineurin-like]]

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@@ Line 1: / Line 1: @@
-{{STRUCTURE_4j6o|  PDB=4j6o  |  SCENE=  }}
+==Crystal Structure of the Phosphatase Domain of C. thermocellum (Bacterial) PnkP==
-===Crystal Structure of the Phosphatase Domain of C. thermocellum (Bacterial) PnkP===
+<StructureSection load='4j6o' size='340' side='right' caption='[[4j6o]], [[Resolution|resolution]] 1.60&Aring;' scene=''>
-{{ABSTRACT_PUBMED_23595150}}
+== Structural highlights ==
+<table><tr><td colspan='2'>[[4j6o]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Clostridium_thermocellum_atcc_27405 Clostridium thermocellum atcc 27405]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4J6O OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4J6O FirstGlance]. <br>
+</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CIT:CITRIC+ACID'>CIT</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</scene>, <scene name='pdbligand=PG4:TETRAETHYLENE+GLYCOL'>PG4</scene>, <scene name='pdbligand=PGE:TRIETHYLENE+GLYCOL'>PGE</scene></td></tr>
+<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[3ty5|3ty5]], [[3ty8|3ty8]], [[3ty9|3ty9]], [[4gp6|4gp6]], [[4gp7|4gp7]]</td></tr>
+<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">Cthe_2768 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=203119 Clostridium thermocellum ATCC 27405])</td></tr>
+<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Phosphoprotein_phosphatase Phosphoprotein phosphatase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.1.3.16 3.1.3.16] </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=4j6o FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4j6o OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4j6o RCSB], [http://www.ebi.ac.uk/pdbsum/4j6o PDBsum]</span></td></tr>
+</table>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+Pnkp is the end-healing and end-sealing component of an RNA repair system present in diverse bacteria from many phyla. Pnkp is composed of three catalytic modules: an N-terminal polynucleotide 5' kinase, a central 2',3' phosphatase and a C-terminal ligase. The phosphatase module is a Mn2+-dependent phosphodiesterase-monoesterase that dephosphorylates 2',3'-cyclic phosphate RNA ends. Here we report the crystal structure of the phosphatase domain of Clostridium thermocellum Pnkp with Mn2+ and citrate in the active site. The protein consists of a core binuclear metallo-phosphoesterase fold (exemplified by bacteriophage lambda phosphatase) embellished by distinctive secondary structure elements. The active site contains a single Mn2+ in an octahedral coordination complex with Asp187, His189, Asp233, two citrate oxygens and a water. The citrate fills the binding site for the scissile phosphate, wherein it is coordinated by Arg237, Asn263 and His264. The citrate invades the site normally occupied by a second metal (engaged by Asp233, Asn263, His323 and His376), and thereby dislocates His376. A continuous tract of positive surface potential flanking the active site suggests an RNA binding site. The structure illuminates a large body of mutational data regarding the metal and substrate specificity of Clostridium thermocellum Pnkp phosphatase.
-==About this Structure==
+Structure and mechanism of the 2',3' phosphatase component of the bacterial Pnkp-Hen1 RNA repair system.,Wang LK, Smith P, Shuman S Nucleic Acids Res. 2013 Apr 16. PMID:23595150<ref>PMID:23595150</ref>
-[[4j6o]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Clostridium_thermocellum_atcc_27405 Clostridium thermocellum atcc 27405]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4J6O OCA].
-==Reference==
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-<ref group="xtra">PMID:023595150</ref><references group="xtra"/><references/>
+</div>
+== References ==
+<references/>
+__TOC__
+</StructureSection>
 [[Category: Clostridium thermocellum atcc 27405]]
 [[Category: Phosphoprotein phosphatase]]
-[[Category: Shuman, S.]]
+[[Category: Shuman, S]]
-[[Category: Smith, P.]]
+[[Category: Smith, P]]
-[[Category: Wang, L.]]
+[[Category: Wang, L]]
 [[Category: Alpha/beta fold]]
 [[Category: Calcineurin-like]]