3ta5 | pdb_00003ta5

Cobalt bound structure of an archaeal member of the LigD 3'-phosphoesterase DNA repair enzyme family

spinqualitylabelsall models 3ta5, resolution 1.52Å Show:Asymmetric Unit Biological Assembly Drag the structure with the mouse to rotate   Export Animated Image   Print3D Structural highlights 3ta5 is a 1 chain structure with sequence from "candidatus_korarchaeum_cryptofilum"_elkins_et_al._2008 "candidatus korarchaeum cryptofilum" elkins et al. 2008. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance. Ligands: CO, PEG, PO4 Related: 3p4h, 3ta7 Gene: Kcr_0736 ("Candidatus Korarchaeum cryptofilum" Elkins et al. 2008) Resources: FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT Publication Abstract from PubMed LigD 3'-phosphoesterase (PE) enzymes perform end-healing reactions at DNA breaks. Here we characterize the 3'-ribonucleoside-resecting activity of Candidatus Korarchaeum PE. CkoPE prefers a single-stranded substrate versus a primer-template. Activity is abolished by vanadate (10 mM), but is less sensitive to phosphate (IC(50) 50 mM) or chloride (IC(50) 150 mM). The metal requirement is satisfied by manganese, cobalt, copper or cadmium, but not magnesium, calcium, nickel or zinc. Insights to CkoPE metal specificity were gained by solving new 1.5 A crystal structures of CkoPE in complexes with Co(2+) and Zn(2+). His9, His15 and Asp17 coordinate cobalt in an octahedral complex that includes a phosphate anion, which is in turn coordinated by Arg19 and His51. The cobalt and phosphate positions and the atomic contacts in the active site are virtually identical to those in the CkoPE.Mn(2+) structure. By contrast, Zn(2+) binds in the active site in a tetrahedral complex, wherein the position, orientation and atomic contacts of the phosphate are shifted and its interaction with His51 is lost. We conclude that: (i) PE selectively binds to 'soft' metals in either productive or non-productive modes and (ii) PE catalysis depends acutely on proper metal and scissile phosphate geometry. Structural insights to the metal specificity of an archaeal member of the LigD 3'-phosphoesterase DNA repair enzyme family.,Das U, Smith P, Shuman S Nucleic Acids Res. 2012 Jan 1;40(2):828-36. Epub 2011 Sep 28. PMID:21965539 From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine. See Also DNA ligase 3D structures

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