4gp6

<StructureSection load='4gp6' size='340' side='right' caption='[[4gp6]], [[Resolution|resolution]] 2.10&Aring;' scene=''>

<table><tr><td colspan='2'>[[4gp6]] 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=4GP6 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4GP6 FirstGlance]. <br>

</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ADP:ADENOSINE-5-DIPHOSPHATE'>ADP</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></td></tr>

<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[4gp7|4gp7]], [[3ty5|3ty5]], [[3ty8|3ty8]], [[3ty9|3ty9]], [[4drf|4drf]], [[4e6n|4e6n]]</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/Polynucleotide_5'-hydroxyl-kinase Polynucleotide 5'-hydroxyl-kinase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.7.1.78 2.7.1.78] </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=4gp6 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4gp6 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4gp6 RCSB], [http://www.ebi.ac.uk/pdbsum/4gp6 PDBsum]</span></td></tr>

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== 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. Here we report the crystal structure of the kinase domain of Clostridium thermocellum Pnkp bound to ATP*Mg(2+) (substrate complex) and ADP*Mg(2+) (product complex). The protein consists of a core P-loop phosphotransferase fold embellished by a distinctive homodimerization module composed of secondary structure elements derived from the N and C termini of the kinase domain. ATP is bound within a crescent-shaped groove formed by the P-loop ((15)GSSGSGKST(23)) and an overlying helix-loop-helix "lid." The alpha and beta phosphates are engaged by a network of hydrogen bonds from Thr23 and the P-loop main-chain amides; the gamma phosphate is anchored by the lid residues Arg120 and Arg123. The P-loop lysine (Lys21) and the catalytic Mg(2+) bridge the ATP beta and gamma phosphates. The P-loop serine (Ser22) is the sole enzymic constituent of the octahedral metal coordination complex. Structure-guided mutational analysis underscored the essential contributions of Lys21 and Ser22 in the ATP donor site and Asp38 and Arg41 in the phosphoacceptor site. Our studies suggest a catalytic mechanism whereby Asp38 (as general base) activates the polynucleotide 5'-OH for its nucleophilic attack on the gamma phosphorus and Lys21 and Mg(2+) stabilize the transition state.

 

Structure and mechanism of the polynucleotide kinase component of the bacterial Pnkp-Hen1 RNA repair system.,Wang LK, Das U, Smith P, Shuman S RNA. 2012 Nov 1. PMID:23118415<ref>PMID:23118415</ref>

 

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

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<references/>

[[Category: Clostridium thermocellum atcc 27405]]

[[Category: Polynucleotide 5'-hydroxyl-kinase]]

[[Category: Das, U]]

[[Category: Shuman, S]]

[[Category: Smith, P]]

[[Category: Wang, L K]]

[[Category: Transferase]]