2nqh: Difference between revisions

Revision as of 09:25, 24 April 2008

High Resolution crystal structure of Escherichia coli endonuclease IV (Endo IV) E261Q mutant

OverviewOverview

Escherichia coli endonuclease IV is an archetype for an abasic or apurinic-apyrimidinic endonuclease superfamily crucial for DNA base excision repair. Here biochemical, mutational and crystallographic characterizations reveal a three-metal ion mechanism for damage binding and incision. The 1.10-A resolution DNA-free and the 2.45-A resolution DNA-substrate complex structures capture substrate stabilization by Arg37 and reveal a distorted Zn(3)-ligand arrangement that reverts, after catalysis, to an ideal geometry suitable to hold rather than release cleaved DNA product. The 1.45-A resolution DNA-product complex structure shows how Tyr72 caps the active site, tunes its dielectric environment and promotes catalysis by Glu261-activated hydroxide, bound to two Zn(2+) ions throughout catalysis. These structural, mutagenesis and biochemical results suggest general requirements for abasic site removal in contrast to features specific to the distinct endonuclease IV alpha-beta triose phosphate isomerase (TIM) barrel and APE1 four-layer alpha-beta folds of the apurinic-apyrimidinic endonuclease families.

About this StructureAbout this Structure

2NQH is a Single protein structure of sequence from Escherichia coli. Full crystallographic information is available from OCA.

ReferenceReference

DNA apurinic-apyrimidinic site binding and excision by endonuclease IV., Garcin ED, Hosfield DJ, Desai SA, Haas BJ, Bjoras M, Cunningham RP, Tainer JA, Nat Struct Mol Biol. 2008 Apr 13;. PMID:18408731 Page seeded by OCA on Thu Apr 24 09:25:19 2008

Proteopedia Page Contributors and Editors (what is this?)Proteopedia Page Contributors and Editors (what is this?)

OCA

@@ Line 1: / Line 1: @@
 [[Image:2nqh.jpg|left|200px]]
- {{Structure
+<!--
-|PDB= 2nqh |SIZE=350|CAPTION= <scene name='initialview01'>2nqh</scene>, resolution 1.1&Aring;
+The line below this paragraph, containing "STRUCTURE_2nqh", creates the "Structure Box" on the page.
-|SITE=
+You may change the PDB parameter (which sets the PDB file loaded into the applet)
-|LIGAND= <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene>
+or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
-|ACTIVITY= <span class='plainlinks'>[http://en.wikipedia.org/wiki/Deoxyribonuclease_IV_(phage-T(4)-induced) Deoxyribonuclease IV (phage-T(4)-induced)], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.1.21.2 3.1.21.2] </span>
+or leave the SCENE parameter empty for the default display.
-|GENE= nfo ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=562 Escherichia coli])
+-->
-|DOMAIN=
+{{STRUCTURE_2nqh|  PDB=2nqh  |  SCENE=  }}
-|RELATEDENTRY=[[2nq9|2NQ9]], [[2nqj|2NQJ]]
-|RESOURCES=<span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2nqh FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2nqh OCA], [http://www.ebi.ac.uk/pdbsum/2nqh PDBsum], [http://www.rcsb.org/pdb/explore.do?structureId=2nqh RCSB]</span>
-}}
 '''High Resolution crystal structure of Escherichia coli endonuclease IV (Endo IV) E261Q mutant'''
+==Overview==
+Escherichia coli endonuclease IV is an archetype for an abasic or apurinic-apyrimidinic endonuclease superfamily crucial for DNA base excision repair. Here biochemical, mutational and crystallographic characterizations reveal a three-metal ion mechanism for damage binding and incision. The 1.10-A resolution DNA-free and the 2.45-A resolution DNA-substrate complex structures capture substrate stabilization by Arg37 and reveal a distorted Zn(3)-ligand arrangement that reverts, after catalysis, to an ideal geometry suitable to hold rather than release cleaved DNA product. The 1.45-A resolution DNA-product complex structure shows how Tyr72 caps the active site, tunes its dielectric environment and promotes catalysis by Glu261-activated hydroxide, bound to two Zn(2+) ions throughout catalysis. These structural, mutagenesis and biochemical results suggest general requirements for abasic site removal in contrast to features specific to the distinct endonuclease IV alpha-beta triose phosphate isomerase (TIM) barrel and APE1 four-layer alpha-beta folds of the apurinic-apyrimidinic endonuclease families.
 ==About this Structure==
 NQH is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2NQH OCA].
-[[Category: Deoxyribonuclease IV (phage-T(4)-induced)]]
+==Reference==
+DNA apurinic-apyrimidinic site binding and excision by endonuclease IV., Garcin ED, Hosfield DJ, Desai SA, Haas BJ, Bjoras M, Cunningham RP, Tainer JA, Nat Struct Mol Biol. 2008 Apr 13;. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/18408731 18408731]
 [[Category: Escherichia coli]]
 [[Category: Single protein]]
@@ Line 23: / Line 25: @@
 [[Category: Hosfield, D J.]]
 [[Category: Tainer, J A.]]
-[[Category: hydrolase]]
+[[Category: Hydrolase]]
-[[Category: tim-barrel]]
+[[Category: Tim-barrel]]
-[[Category: trinuclear zinc center]]
+[[Category: Trinuclear zinc center]]
+''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Apr 24 09:25:19 2008''
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Mon Mar 31 04:06:50 2008''