3TA5

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

Summary for 3TA5

• Entry DOI: 10.2210/pdb3ta5/pdb
• Related: 3P4H 3TA7
• Descriptor: ATP-dependent DNA ligase, N-terminal domain protein, COBALT (II) ION, PHOSPHATE ION, ... (5 entities in total)
• Functional Keywords: 3'-phosphoesterase, hydrolase
• Biological source: Candidatus Korarchaeum cryptofilum
• Total number of polymer chains: 1
• Total formula weight: 14110.12

Authors

Das, U.,Smith, P.,Shuman, S. (deposition date: 2011-08-03, release date: 2011-10-12, Last modification date: 2023-09-13)

Primary citation

Das, U.,Smith, P.,Shuman, S.
Structural insights to the metal specificity of an archaeal member of the LigD 3'-phosphoesterase DNA repair enzyme family.
Nucleic Acids Res., 40:828-836, 2012

PubMed 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 (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 Å 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.

PubMed: 21965539
DOI: 10.1093/nar/gkr767

Experimental method

X-RAY DIFFRACTION (1.52 Å)