2kzz
From Proteopedia
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| - | [[Image:2kzz.gif|left|200px]]<br /><applet load="2kzz" size=" | + | [[Image:2kzz.gif|left|200px]]<br /><applet load="2kzz" size="350" color="white" frame="true" align="right" spinBox="true" |
caption="2kzz, resolution 2.25Å" /> | caption="2kzz, resolution 2.25Å" /> | ||
'''KLENOW FRAGMENT WITH NORMAL SUBSTRATE AND ZINC ONLY'''<br /> | '''KLENOW FRAGMENT WITH NORMAL SUBSTRATE AND ZINC ONLY'''<br /> | ||
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==About this Structure== | ==About this Structure== | ||
| - | 2KZZ is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli] with ZN as [http://en.wikipedia.org/wiki/ligand ligand]. Active as [http://en.wikipedia.org/wiki/DNA-directed_DNA_polymerase DNA-directed DNA polymerase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.7.7.7 2.7.7.7] Known structural/functional Site: <scene name='pdbsite=EXO:Exonuclease Active Site'>EXO</scene>. Full crystallographic information is available from [http:// | + | 2KZZ is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli] with <scene name='pdbligand=ZN:'>ZN</scene> as [http://en.wikipedia.org/wiki/ligand ligand]. Active as [http://en.wikipedia.org/wiki/DNA-directed_DNA_polymerase DNA-directed DNA polymerase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.7.7.7 2.7.7.7] Known structural/functional Site: <scene name='pdbsite=EXO:Exonuclease+Active+Site'>EXO</scene>. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2KZZ OCA]. |
==Reference== | ==Reference== | ||
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[[Category: two metal ion]] | [[Category: two metal ion]] | ||
| - | ''Page seeded by [http:// | + | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sun Feb 3 10:46:28 2008'' |
Revision as of 08:46, 3 February 2008
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KLENOW FRAGMENT WITH NORMAL SUBSTRATE AND ZINC ONLY
Overview
The interaction of a divalent metal ion with a leaving 3' oxygen is a, central component of several proposed mechanisms of phosphoryl transfer., In support of this are recent kinetic studies showing that thiophilic, metal ions (e.g., Mn2+) stimulate the hydrolysis of compounds in which, sulfur takes the place of the leaving oxygen. To examine the structural, basis of this phenomenon, we have solved four crystal structures of, single-stranded DNA's containing either oxygen or sulfur at a 3'-bridging, position bound in conjunction with various metal ions at the 3'-5', exonucleolytic active site of the Klenow fragment (KF) of DNA polymerase I, from Escherichia coli. Two structures of normal ssDNA bound to KF in the, presence of Zn2+ and Mn2+ or Zn2+ alone were refined at 2.6- and 2.25-A, resolution, respectively. They serve as standards for comparison with, other Mn2+- and Zn2+-containing structures. In these cases, Mn2+ and Zn2+, bind at metal ion site B in a nearly identical position to Mg2+ (Brautigam, and Steitz (1998) J. Mol. Biol. 277, 363-377). Two structures of KF bound, to a deoxyoligonucleotide that contained a 3'-bridging sulfur at the, scissile phosphate were refined at 2.03-A resolution. Although the, bridging sulfur compounds bind in a manner very similar to that of the, normal oligonucleotides, the presence of the sulfur changes the metal ion, binding properties of the active site such that Mn2+ and Zn2+ are observed, at metal ion site B, but Mg2+ is not. It therefore appears that the, ability of the bridging sulfur compounds to exclude nonthiophilic metal, ions from metal ion site B explains the low activity of KF exonuclease on, these substrates in the presence of Mg2+ (Curley et al. (1997) J. Am., Chem. Soc. 119, 12691-12692) and that the 3'-bridging atom of the, substrate is influencing the binding of metal ion B prior to catalysis.
About this Structure
2KZZ is a Single protein structure of sequence from Escherichia coli with as ligand. Active as DNA-directed DNA polymerase, with EC number 2.7.7.7 Known structural/functional Site: . Full crystallographic information is available from OCA.
Reference
Structures of normal single-stranded DNA and deoxyribo-3'-S-phosphorothiolates bound to the 3'-5' exonucleolytic active site of DNA polymerase I from Escherichia coli., Brautigam CA, Sun S, Piccirilli JA, Steitz TA, Biochemistry. 1999 Jan 12;38(2):696-704. PMID:9888810
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