1zm8
From Proteopedia
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|PDB= 1zm8 |SIZE=350|CAPTION= <scene name='initialview01'>1zm8</scene>, resolution 1.90Å | |PDB= 1zm8 |SIZE=350|CAPTION= <scene name='initialview01'>1zm8</scene>, resolution 1.90Å | ||
|SITE= | |SITE= | ||
| - | |LIGAND= <scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</scene>, <scene name='pdbligand= | + | |LIGAND= <scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene> |
|ACTIVITY= | |ACTIVITY= | ||
|GENE= nucA ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1167 Anabaena sp.]) | |GENE= nucA ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1167 Anabaena sp.]) | ||
| + | |DOMAIN= | ||
| + | |RELATEDENTRY= | ||
| + | |RESOURCES=<span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1zm8 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1zm8 OCA], [http://www.ebi.ac.uk/pdbsum/1zm8 PDBsum], [http://www.rcsb.org/pdb/explore.do?structureId=1zm8 RCSB]</span> | ||
}} | }} | ||
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[[Category: Pedersen, L C.]] | [[Category: Pedersen, L C.]] | ||
[[Category: Pingoud, A.]] | [[Category: Pingoud, A.]] | ||
| - | [[Category: MN]] | ||
| - | [[Category: NA]] | ||
| - | [[Category: SO4]] | ||
[[Category: metal dependent]] | [[Category: metal dependent]] | ||
[[Category: nuca]] | [[Category: nuca]] | ||
[[Category: nuclease]] | [[Category: nuclease]] | ||
| - | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on | + | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Mon Mar 31 01:38:36 2008'' |
Revision as of 22:38, 30 March 2008
| |||||||
| , resolution 1.90Å | |||||||
|---|---|---|---|---|---|---|---|
| Ligands: | , , | ||||||
| Gene: | nucA (Anabaena sp.) | ||||||
| Resources: | FirstGlance, OCA, PDBsum, RCSB | ||||||
| Coordinates: | save as pdb, mmCIF, xml | ||||||
Apo Crystal structure of Nuclease A from Anabaena sp.
Overview
Nuclease A (NucA) is a nonspecific endonuclease from Anabaena sp. capable of degrading single- and double-stranded DNA and RNA in the presence of divalent metal ions. We have determined the structure of the delta(2-24),D121A mutant of NucA in the presence of Zn2+ and Mn2+ (PDB code 1ZM8). The mutations were introduced to remove the N-terminal signal peptide and to reduce the activity of the nonspecific nuclease, thereby reducing its toxicity to the Escherichia coli expression system. NucA contains a betabeta alpha metal finger motif and a hydrated Mn2+ ion at the active site. Unexpectedly, NucA was found to contain additional metal binding sites approximately 26 A apart from the catalytic metal binding site. A structural comparison between NucA and the closest analog for which structural data exist, the Serratia nuclease, indicates several interesting differences. First, NucA is a monomer rather than a dimer. Second, there is an unexpected structural homology between the N-terminal segments despite a poorly conserved sequence, which in Serratia includes a cysteine bridge thought to play a regulatory role. In addition, although a sequence alignment had suggested that NucA lacks a proposed catalytic residue corresponding to Arg57 in Serratia, the structure determined here indicates that Arg93 in NucA is positioned to fulfill this role. Based on comparison with DNA-bound nuclease structures of the betabeta alpha metal finger nuclease family and available mutational data on NucA, we propose that His124 acts as a catalytic base, and Arg93 participates in the catalysis possibly through stabilization of the transition state.
About this Structure
1ZM8 is a Single protein structure of sequence from Anabaena sp.. Full crystallographic information is available from OCA.
Reference
Structural insights into the mechanism of nuclease A, a betabeta alpha metal nuclease from Anabaena., Ghosh M, Meiss G, Pingoud A, London RE, Pedersen LC, J Biol Chem. 2005 Jul 29;280(30):27990-7. Epub 2005 May 15. PMID:15897201
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