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1rrc

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Revision as of 07:03, 8 March 2018

T4 POLYNUCLEOTIDE KINASE BOUND TO 5'-GTC-3' SSDNA

Structural highlights

1rrc is a 2 chain structure with sequence from Bpt4. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Ligands:	, ,
NonStd Res:
Related:	1rc8, 1rpz
Gene:	PSET (BPT4)
Activity:	Polynucleotide 5'-hydroxyl-kinase, with EC number 2.7.1.78
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

[KIPN_BPT4] Acts as a 5'-hydroxyl kinase, a 3'-phosphatase and a 2',3'-cyclic phosphodiesterase. Catalyzes the transfer of the terminal phosphate of ATP to the 5'-hydroxyl termini of ribo- and deoxyribonucleotides. In the presence of ADP the enzyme also catalyzes an exchange reaction. In the exchange reaction, an excess ADP causes the enzyme to transfer the 5' terminal phosphate from phosphorylated DNA to ADP. These activities modify the ends of nicked tRNA generated by a bacterial response to infection and facilitate repair by T4 RNA ligase.

Evolutionary Conservation

Check, as determined by ConSurfDB. You may read the explanation of the method and the full data available from ConSurf.

Publication Abstract from PubMed

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.

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^[1]

From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.

References

↑ Eastberg JH, Pelletier J, Stoddard BL. Recognition of DNA substrates by T4 bacteriophage polynucleotide kinase. Nucleic Acids Res. 2004 Jan 30;32(2):653-60. Print 2004. PMID:14754987 doi:10.1093/nar/gkh212

1 Structural highlights
2 Function
3 Evolutionary Conservation
4 Publication Abstract from PubMed
5 References

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/1rrc"

@@ Line 1: / Line 1: @@
 ==T4 POLYNUCLEOTIDE KINASE BOUND TO 5'-GTC-3' SSDNA==
 <StructureSection load='1rrc' size='340' side='right' caption='[[1rrc]], [[Resolution|resolution]] 2.46&Aring;' scene=''>
@@ Line 8: / Line 9: @@
 <tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">PSET ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=10665 BPT4])</td></tr>
 <tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Polynucleotide_5'-hydroxyl-kinase Polynucleotide 5'-hydroxyl-kinase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.7.1.78 2.7.1.78] </span></td></tr>
-<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1rrc FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1rrc OCA], [http://pdbe.org/1rrc PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1rrc RCSB], [http://www.ebi.ac.uk/pdbsum/1rrc PDBsum]</span></td></tr>
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1rrc FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1rrc OCA], [http://pdbe.org/1rrc PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1rrc RCSB], [http://www.ebi.ac.uk/pdbsum/1rrc PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1rrc ProSAT]</span></td></tr>
 </table>
 == Function ==
@@ Line 16: / Line 17: @@
 Check<jmol>
   <jmolCheckbox>
-    <scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/rr/1rrc_consurf.spt"</scriptWhenChecked>
+    <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/rr/1rrc_consurf.spt"</scriptWhenChecked>
     <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
     <text>to colour the structure by Evolutionary Conservation</text>

1rrc

From Proteopedia

Revision as of 07:03, 8 March 2018

T4 POLYNUCLEOTIDE KINASE BOUND TO 5'-GTC-3' SSDNA

Structural highlights

Function

Evolutionary Conservation

Publication Abstract from PubMed

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

Views

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