2g8k: Difference between revisions

Line 1:

[[Image:2g8k.gif|left|200px]]<br /><applet load="2g8k" size="~~450~~" color="white" frame="true" align="right" spinBox="true"

[[Image:2g8k.gif|left|200px]]<br /><applet load="2g8k" size="350" color="white" frame="true" align="right" spinBox="true"

caption="2g8k, resolution 1.65Å" />

'''B. halodurans RNase H catalytic domain D192N mutant in complex with Ca2+ and RNA/DNA hybrid (non-P nick at the active site)'''<br />

==Overview==

In two-metal catalysis, metal ion A has been proposed to activate the, nucleophile and metal ion B to stabilize the transition state. We recently, reported crystal structures of RNase H-RNA/DNA substrate complexes, obtained at 1.5-2.2 Angstroms. We have now determined and report here, structures of reaction intermediate and product complexes of RNase H at, 1.65-1.85 Angstroms. The movement of the two metal ions suggests how they, may facilitate RNA hydrolysis during the catalytic process. Firstly, metal, ion A may assist nucleophilic attack by moving towards metal ion B and, bringing the nucleophile close to the scissile phosphate. Secondly, metal, ion B transforms from an irregular coordination in the substrate complex, to a more regular geometry in the product complex. The exquisite, sensitivity of Mg(2+) to the coordination environment likely destabilizes, the enzyme-substrate complex and reduces the energy barrier to form, product. Lastly, product release probably requires dissociation of metal, ion A, which is inhibited by either high concentrations of divalent, cations or mutation of an assisting protein residue.

In two-metal catalysis, metal ion A has been proposed to activate the nucleophile and metal ion B to stabilize the transition state. We recently reported crystal structures of RNase H-RNA/DNA substrate complexes obtained at 1.5-2.2 Angstroms. We have now determined and report here structures of reaction intermediate and product complexes of RNase H at 1.65-1.85 Angstroms. The movement of the two metal ions suggests how they may facilitate RNA hydrolysis during the catalytic process. Firstly, metal ion A may assist nucleophilic attack by moving towards metal ion B and bringing the nucleophile close to the scissile phosphate. Secondly, metal ion B transforms from an irregular coordination in the substrate complex to a more regular geometry in the product complex. The exquisite sensitivity of Mg(2+) to the coordination environment likely destabilizes the enzyme-substrate complex and reduces the energy barrier to form product. Lastly, product release probably requires dissociation of metal ion A, which is inhibited by either high concentrations of divalent cations or mutation of an assisting protein residue.

==About this Structure==

2G8K is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Bacillus_halodurans Bacillus halodurans] with CA as [http://en.wikipedia.org/wiki/ligand ligand]. Active as [http://en.wikipedia.org/wiki/Ribonuclease_H Ribonuclease H], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.1.26.4 3.1.26.4] Full crystallographic information is available from [http://~~ispc~~.weizmann.ac.il/oca-bin/ocashort?id=2G8K OCA].

2G8K is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Bacillus_halodurans Bacillus halodurans] with <scene name='pdbligand=CA:'>CA</scene> as [http://en.wikipedia.org/wiki/ligand ligand]. Active as [http://en.wikipedia.org/wiki/Ribonuclease_H Ribonuclease H], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.1.26.4 3.1.26.4] Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2G8K OCA].

==Reference==

Line 21:

[[Category: rnase h]]

''Page seeded by [http://~~ispc~~.weizmann.ac.il/oca OCA ] on ~~Wed Nov~~ 21 11:02:~~01 2007~~''

''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Feb 21 17:29:14 2008''

Navigation menu

Page actions

Page actions

Personal tools

Navigation

Search

Tools

@@ Line 1: / Line 1: @@
-[[Image:2g8k.gif|left|200px]]<br /><applet load="2g8k" size="450" color="white" frame="true" align="right" spinBox="true"
+[[Image:2g8k.gif|left|200px]]<br /><applet load="2g8k" size="350" color="white" frame="true" align="right" spinBox="true"
 caption="2g8k, resolution 1.65&Aring;" />
 '''B. halodurans RNase H catalytic domain D192N mutant in complex with Ca2+ and RNA/DNA hybrid (non-P nick at the active site)'''<br />
 ==Overview==
-In two-metal catalysis, metal ion A has been proposed to activate the, nucleophile and metal ion B to stabilize the transition state. We recently, reported crystal structures of RNase H-RNA/DNA substrate complexes, obtained at 1.5-2.2 Angstroms. We have now determined and report here, structures of reaction intermediate and product complexes of RNase H at, 1.65-1.85 Angstroms. The movement of the two metal ions suggests how they, may facilitate RNA hydrolysis during the catalytic process. Firstly, metal, ion A may assist nucleophilic attack by moving towards metal ion B and, bringing the nucleophile close to the scissile phosphate. Secondly, metal, ion B transforms from an irregular coordination in the substrate complex, to a more regular geometry in the product complex. The exquisite, sensitivity of Mg(2+) to the coordination environment likely destabilizes, the enzyme-substrate complex and reduces the energy barrier to form, product. Lastly, product release probably requires dissociation of metal, ion A, which is inhibited by either high concentrations of divalent, cations or mutation of an assisting protein residue.
+In two-metal catalysis, metal ion A has been proposed to activate the nucleophile and metal ion B to stabilize the transition state. We recently reported crystal structures of RNase H-RNA/DNA substrate complexes obtained at 1.5-2.2 Angstroms. We have now determined and report here structures of reaction intermediate and product complexes of RNase H at 1.65-1.85 Angstroms. The movement of the two metal ions suggests how they may facilitate RNA hydrolysis during the catalytic process. Firstly, metal ion A may assist nucleophilic attack by moving towards metal ion B and bringing the nucleophile close to the scissile phosphate. Secondly, metal ion B transforms from an irregular coordination in the substrate complex to a more regular geometry in the product complex. The exquisite sensitivity of Mg(2+) to the coordination environment likely destabilizes the enzyme-substrate complex and reduces the energy barrier to form product. Lastly, product release probably requires dissociation of metal ion A, which is inhibited by either high concentrations of divalent cations or mutation of an assisting protein residue.
 ==About this Structure==
-G8K is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Bacillus_halodurans Bacillus halodurans] with CA as [http://en.wikipedia.org/wiki/ligand ligand]. Active as [http://en.wikipedia.org/wiki/Ribonuclease_H Ribonuclease H], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.1.26.4 3.1.26.4] Full crystallographic information is available from [http://ispc.weizmann.ac.il/oca-bin/ocashort?id=2G8K OCA].
+G8K is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Bacillus_halodurans Bacillus halodurans] with <scene name='pdbligand=CA:'>CA</scene> as [http://en.wikipedia.org/wiki/ligand ligand]. Active as [http://en.wikipedia.org/wiki/Ribonuclease_H Ribonuclease H], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.1.26.4 3.1.26.4] Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2G8K OCA].
 ==Reference==
@@ Line 21: / Line 21: @@
 [[Category: rnase h]]
-''Page seeded by [http://ispc.weizmann.ac.il/oca OCA ] on Wed Nov 21 11:02:01 2007''
+''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Feb 21 17:29:14 2008''