1rc8
From Proteopedia
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|PDB= 1rc8 |SIZE=350|CAPTION= <scene name='initialview01'>1rc8</scene>, resolution 2.75Å | |PDB= 1rc8 |SIZE=350|CAPTION= <scene name='initialview01'>1rc8</scene>, resolution 2.75Å | ||
|SITE= | |SITE= | ||
| - | |LIGAND= <scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=DMS:DIMETHYL+SULFOXIDE'>DMS</scene> | + | |LIGAND= <scene name='pdbligand=ADP:ADENOSINE-5'-DIPHOSPHATE'>ADP</scene>, <scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=DA:2'-DEOXYADENOSINE-5'-MONOPHOSPHATE'>DA</scene>, <scene name='pdbligand=DC:2'-DEOXYCYTIDINE-5'-MONOPHOSPHATE'>DC</scene>, <scene name='pdbligand=DG:2'-DEOXYGUANOSINE-5'-MONOPHOSPHATE'>DG</scene>, <scene name='pdbligand=DMS:DIMETHYL+SULFOXIDE'>DMS</scene>, <scene name='pdbligand=DT:THYMIDINE-5'-MONOPHOSPHATE'>DT</scene>, <scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</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=[[1rpz|1RPZ]], [[1rrc|1RRC]] | ||
| + | |RESOURCES=<span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1rc8 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1rc8 OCA], [http://www.ebi.ac.uk/pdbsum/1rc8 PDBsum], [http://www.rcsb.org/pdb/explore.do?structureId=1rc8 RCSB]</span> | ||
}} | }} | ||
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==About this Structure== | ==About this Structure== | ||
| - | 1RC8 is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/ | + | 1RC8 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=1RC8 OCA]. |
==Reference== | ==Reference== | ||
Recognition of DNA substrates by T4 bacteriophage polynucleotide kinase., Eastberg JH, Pelletier J, Stoddard BL, Nucleic Acids Res. 2004 Jan 30;32(2):653-60. Print 2004. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/14754987 14754987] | Recognition of DNA substrates by T4 bacteriophage polynucleotide kinase., Eastberg JH, Pelletier J, Stoddard BL, Nucleic Acids Res. 2004 Jan 30;32(2):653-60. Print 2004. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/14754987 14754987] | ||
| - | [[Category: | + | [[Category: Enterobacteria phage t4]] |
[[Category: Polynucleotide 5'-hydroxy-kinase]] | [[Category: Polynucleotide 5'-hydroxy-kinase]] | ||
[[Category: Single protein]] | [[Category: Single protein]] | ||
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[[Category: Pelletier, J.]] | [[Category: Pelletier, J.]] | ||
[[Category: Stoddard, B L.]] | [[Category: Stoddard, B L.]] | ||
| - | [[Category: ADP]] | ||
| - | [[Category: CA]] | ||
| - | [[Category: DMS]] | ||
[[Category: alpha/beta]] | [[Category: alpha/beta]] | ||
[[Category: kinase]] | [[Category: kinase]] | ||
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[[Category: ssdna]] | [[Category: ssdna]] | ||
| - | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sun Mar 23 | + | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sun Mar 30 23:26:08 2008'' |
Revision as of 20:26, 30 March 2008
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| , resolution 2.75Å | |||||||
|---|---|---|---|---|---|---|---|
| Ligands: | , , , , , , , | ||||||
| Gene: | PSET (Enterobacteria phage T4) | ||||||
| Activity: | Polynucleotide 5'-hydroxy-kinase, with EC number 2.7.1.78 | ||||||
| Related: | 1RPZ, 1RRC
| ||||||
| Resources: | FirstGlance, OCA, PDBsum, RCSB | ||||||
| Coordinates: | save as pdb, mmCIF, xml | ||||||
T4 Polynucleotide Kinase bound to 5'-GTCAC-3' ssDNA
Overview
T4 phage polynucleotide kinase (PNK) displays 5'-hydroxyl kinase, 3'-phosphatase and 2',3'-cyclic phosphodiesterase activities. The enzyme phosphorylates the 5' hydroxyl termini of a wide variety of nucleic acid substrates, a behavior studied here through the determination of a series of crystal structures with single-stranded (ss)DNA oligonucleotide substrates of various lengths and sequences. In these structures, the 5' ribose hydroxyl is buried in the kinase active site in proper alignment for phosphoryl transfer. Depending on the ssDNA length, the first two or three nucleotide bases are well ordered. Numerous contacts are made both to the phosphoribosyl backbone and to the ordered bases. The position, side chain contacts and internucleotide stacking interactions of the ordered bases are strikingly different for a 5'-GT DNA end than for a 5'-TG end. The base preferences displayed at those positions by PNK are attributable to differences in the enzyme binding interactions and in the DNA conformation for each unique substrate molecule.
About this Structure
1RC8 is a Single protein structure of sequence from Enterobacteria phage t4. Full crystallographic information is available from OCA.
Reference
Recognition of DNA substrates by T4 bacteriophage polynucleotide kinase., Eastberg JH, Pelletier J, Stoddard BL, Nucleic Acids Res. 2004 Jan 30;32(2):653-60. Print 2004. PMID:14754987
Page seeded by OCA on Sun Mar 30 23:26:08 2008
