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| | ==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]] 1.60Å' scene=''> | + | <StructureSection load='4j6o' size='340' side='right'caption='[[4j6o]], [[Resolution|resolution]] 1.60Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[4j6o]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Cloth Cloth]. 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> | + | <table><tr><td colspan='2'>[[4j6o]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Acetivibrio_thermocellus_ATCC_27405 Acetivibrio thermocellus 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 [https://proteopedia.org/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> | + | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><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='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=4j6o FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4j6o OCA], [https://pdbe.org/4j6o PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4j6o RCSB], [https://www.ebi.ac.uk/pdbsum/4j6o PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4j6o ProSAT]</span></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 CLOTH])</td></tr>
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| - | <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://pdbe.org/4j6o PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4j6o RCSB], [http://www.ebi.ac.uk/pdbsum/4j6o PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4j6o ProSAT]</span></td></tr> | + | |
| | </table> | | </table> |
| | + | == Function == |
| | + | [https://www.uniprot.org/uniprot/A3DJ38_ACET2 A3DJ38_ACET2] |
| | <div style="background-color:#fffaf0;"> | | <div style="background-color:#fffaf0;"> |
| | == Publication Abstract from PubMed == | | == Publication Abstract from PubMed == |
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| | __TOC__ | | __TOC__ |
| | </StructureSection> | | </StructureSection> |
| - | [[Category: Cloth]] | + | [[Category: Acetivibrio thermocellus ATCC 27405]] |
| - | [[Category: Phosphoprotein phosphatase]] | + | [[Category: Large Structures]] |
| - | [[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]]
| + | |
| - | [[Category: Hydrolase]]
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| - | [[Category: Metalloenzyme]]
| + | |
| - | [[Category: Phosphatase]]
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| Structural highlights
Function
A3DJ38_ACET2
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.
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[1]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
References
- ↑ Wang LK, Smith P, Shuman S. Structure and mechanism of the 2',3' phosphatase component of the bacterial Pnkp-Hen1 RNA repair system. Nucleic Acids Res. 2013 Apr 16. PMID:23595150 doi:10.1093/nar/gkt221
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