2ia5
From Proteopedia
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|PDB= 2ia5 |SIZE=350|CAPTION= <scene name='initialview01'>2ia5</scene>, resolution 2.90Å | |PDB= 2ia5 |SIZE=350|CAPTION= <scene name='initialview01'>2ia5</scene>, resolution 2.90Å | ||
|SITE= | |SITE= | ||
| - | |LIGAND= <scene name='pdbligand= | + | |LIGAND= <scene name='pdbligand=ARS:ARSENIC'>ARS</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene> |
| - | |ACTIVITY= [http://en.wikipedia.org/wiki/Polynucleotide_5'-hydroxy-kinase Polynucleotide 5'-hydroxy-kinase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.7.1.78 2.7.1.78] | + | |ACTIVITY= <span class='plainlinks'>[http://en.wikipedia.org/wiki/Polynucleotide_5'-hydroxy-kinase Polynucleotide 5'-hydroxy-kinase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.7.1.78 2.7.1.78] </span> |
| - | |GENE= pseT ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id= | + | |GENE= pseT ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=10665 Enterobacteria phage T4]) |
| + | |DOMAIN= | ||
| + | |RELATEDENTRY= | ||
| + | |RESOURCES=<span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2ia5 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2ia5 OCA], [http://www.ebi.ac.uk/pdbsum/2ia5 PDBsum], [http://www.rcsb.org/pdb/explore.do?structureId=2ia5 RCSB]</span> | ||
}} | }} | ||
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==About this Structure== | ==About this Structure== | ||
| - | 2IA5 is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/ | + | 2IA5 is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Enterobacteria_phage_t4 Enterobacteria phage t4]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2IA5 OCA]. |
==Reference== | ==Reference== | ||
Structure-function analysis of the 3' phosphatase component of T4 polynucleotide kinase/phosphatase., Zhu H, Smith P, Wang LK, Shuman S, Virology. 2007 Sep 15;366(1):126-36. Epub 2007 May 9. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/17493655 17493655] | Structure-function analysis of the 3' phosphatase component of T4 polynucleotide kinase/phosphatase., Zhu H, Smith P, Wang LK, Shuman S, Virology. 2007 Sep 15;366(1):126-36. Epub 2007 May 9. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/17493655 17493655] | ||
| - | [[Category: | + | [[Category: Enterobacteria phage t4]] |
[[Category: Polynucleotide 5'-hydroxy-kinase]] | [[Category: Polynucleotide 5'-hydroxy-kinase]] | ||
[[Category: Single protein]] | [[Category: Single protein]] | ||
| Line 28: | Line 31: | ||
[[Category: Wang, L K.]] | [[Category: Wang, L K.]] | ||
[[Category: Zhu, H.]] | [[Category: Zhu, H.]] | ||
| - | [[Category: ARS]] | ||
| - | [[Category: MG]] | ||
| - | [[Category: SO4]] | ||
[[Category: polynucleotide kinase phosphatase sulfate-complex]] | [[Category: polynucleotide kinase phosphatase sulfate-complex]] | ||
| - | ''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 03:41:31 2008'' |
Revision as of 00:41, 31 March 2008
| |||||||
| , resolution 2.90Å | |||||||
|---|---|---|---|---|---|---|---|
| Ligands: | , , | ||||||
| Gene: | pseT (Enterobacteria phage T4) | ||||||
| Activity: | Polynucleotide 5'-hydroxy-kinase, with EC number 2.7.1.78 | ||||||
| Resources: | FirstGlance, OCA, PDBsum, RCSB | ||||||
| Coordinates: | save as pdb, mmCIF, xml | ||||||
T4 polynucleotide kinase/phosphatase with bound sulfate and magnesium.
Overview
T4 polynucleotide kinase/phosphatase (Pnkp) exemplifies a family of bifunctional enzymes with 5'-kinase and 3' phosphatase activities that function in nucleic acid repair. T4 Pnkp is a homotetramer of a 301-aa polypeptide, which consists of an N-terminal kinase domain of the P-loop phosphotransferase superfamily and a C-terminal phosphatase domain of the DxD acylphosphatase superfamily. The homotetramer is formed via pairs of phosphatase-phosphatase and kinase-kinase homodimer interfaces. Here we identify four side chains-Asp187, Ser211, Lys258, and Asp277-that are required for 3' phosphatase activity. Alanine mutations at these positions abolished phosphatase activity without affecting kinase function or tetramerization. Conservative substitutions of asparagine or glutamate for Asp187 did not revive the 3' phosphatase, nor did arginine or glutamine substitutions for Lys258. Threonine in lieu of Ser211 and glutamate in lieu of Asp277 restored full activity, whereas asparagine at position 277 had no salutary effect. We report a 3.0 A crystal structure of the Pnkp tetramer, in which a sulfate ion is coordinated between Arg246 and Arg279 in a position that we propose mimics one of the penultimate phosphodiesters (5'NpNpNp-3') of the polynucleotide 3'-PO(4) substrate. The amalgam of mutational and structural data engenders a plausible catalytic mechanism for the phosphatase that includes covalent catalysis (via Asp165), general acid-base catalysis (via Asp167), metal coordination (by Asp165, Asp277 and Asp278), and transition state stabilization (via Lys258, Ser211, backbone amides, and the divalent cation). Other critical side chains play architectural roles (Arg176, Asp187, Arg213, Asp254). To probe the role of oligomerization in phosphatase function, we introduced six double-alanine cluster mutations at the phosphatase-phosphatase domain interface, two of which (R297A-Q295A and E292A-D300A) converted Pnkp from a tetramer to a dimer and ablated phosphatase activity.
About this Structure
2IA5 is a Single protein structure of sequence from Enterobacteria phage t4. Full crystallographic information is available from OCA.
Reference
Structure-function analysis of the 3' phosphatase component of T4 polynucleotide kinase/phosphatase., Zhu H, Smith P, Wang LK, Shuman S, Virology. 2007 Sep 15;366(1):126-36. Epub 2007 May 9. PMID:17493655
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