Structural insights to the metal specificity of an archaeal member of the LigD 3′-phosphoesterase DNA repair enzyme family Journal Article

   

Authors:	Das, U.; Smith, P.; Shuman, S.
Article Title:	Structural insights to the metal specificity of an archaeal member of the LigD 3′-phosphoesterase DNA repair enzyme family
Abstract:	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 (10mM), but is less sensitive to phosphate (IC 50 50mM) or chloride (IC 50 150mM). 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 1.5Å 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 CkoPEMn 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. © The Author(s) 2011. Published by Oxford University Press.
Keywords:	controlled study; unclassified drug; protein function; dna repair; enzyme inhibition; phosphatase; enzyme activity; substrate specificity; dna repair enzymes; temperature; crystal structure; molecular interaction; cobalt; zinc; crystallization; ic 50; structure analysis; enzyme specificity; enzyme structure; enzyme substrate complex; catalytic domain; phosphate; aspartic acid; nickel; archaebacterium; histidine; enzyme mechanism; enzyme active site; cations, divalent; calcium ion; zinc ion; manganese; anions; temperature dependence; phosphoric diester hydrolases; chloride ion; copper ion; ligase d 3' phosphoesterase; vanadic acid; candidatus korarchaeum; korarchaeota
Journal Title:	Nucleic Acids Research
Volume:	40
Issue:	2
ISSN:	0305-1048
Publisher:	Oxford University Press
Date Published:	2012-01-01
Start Page:	828
End Page:	836
Language:	English
DOI:	10.1093/nar/gkr767
PROVIDER:	scopus
PMCID:	PMC3258152
PUBMED:	21965539
DOI/URL:	http://www.scopus.com/inward/record.url?eid=2-s2.0-84863395749&partnerID=40&md5=01ad0609721c7307bbcdec85866acd54
Notes:	--- - "Export Date: 1 March 2012" - "CODEN: NARHA" - "Source: Scopus"

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