1e9n
From Proteopedia
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|PDB= 1e9n |SIZE=350|CAPTION= <scene name='initialview01'>1e9n</scene>, resolution 2.2Å | |PDB= 1e9n |SIZE=350|CAPTION= <scene name='initialview01'>1e9n</scene>, resolution 2.2Å | ||
|SITE= <scene name='pdbsite=PB1:Pb+Binding+Site+For+Residue+A1319'>PB1</scene>, <scene name='pdbsite=PB2:Pb+Binding+Site+For+Residue+A1320'>PB2</scene>, <scene name='pdbsite=PB3:Pb+Binding+Site+For+Residue+B1319'>PB3</scene> and <scene name='pdbsite=PB4:Pb+Binding+Site+For+Residue+B1320'>PB4</scene> | |SITE= <scene name='pdbsite=PB1:Pb+Binding+Site+For+Residue+A1319'>PB1</scene>, <scene name='pdbsite=PB2:Pb+Binding+Site+For+Residue+A1320'>PB2</scene>, <scene name='pdbsite=PB3:Pb+Binding+Site+For+Residue+B1319'>PB3</scene> and <scene name='pdbsite=PB4:Pb+Binding+Site+For+Residue+B1320'>PB4</scene> | ||
| - | |LIGAND= <scene name='pdbligand=PB:LEAD (II) ION'>PB</scene> | + | |LIGAND= <scene name='pdbligand=PB:LEAD+(II)+ION'>PB</scene> |
| - | |ACTIVITY= [http://en.wikipedia.org/wiki/DNA-(apurinic_or_apyrimidinic_site)_lyase DNA-(apurinic or apyrimidinic site) lyase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=4.2.99.18 4.2.99.18] | + | |ACTIVITY= <span class='plainlinks'>[http://en.wikipedia.org/wiki/DNA-(apurinic_or_apyrimidinic_site)_lyase DNA-(apurinic or apyrimidinic site) lyase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=4.2.99.18 4.2.99.18] </span> |
|GENE= APE1 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 Homo sapiens]) | |GENE= APE1 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 Homo sapiens]) | ||
| + | |DOMAIN= | ||
| + | |RELATEDENTRY= | ||
| + | |RESOURCES=<span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1e9n FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1e9n OCA], [http://www.ebi.ac.uk/pdbsum/1e9n PDBsum], [http://www.rcsb.org/pdb/explore.do?structureId=1e9n RCSB]</span> | ||
}} | }} | ||
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==Overview== | ==Overview== | ||
The major human abasic endonuclease, Ape1, is an essential DNA repair enzyme that initiates the removal of apurinic/apyrimidinic sites from DNA, excises 3' replication-blocking moieties, and modulates the DNA binding activity of several transcriptional regulators. We have determined the X-ray structure of the full-length human Ape1 enzyme in two new crystal forms, one at neutral and one at acidic pH. The new structures are generally similar to the previously determined structure of a truncated Ape1 protein, but differ in the conformation of several loop regions and in spans of residues with weak electron density. While only one active-site metal ion is present in the structure determined at low pH, the structure determined from a crystal grown at the pH optimum of Ape1 nuclease activity, pH 7.5, has two metal ions bound 5 A apart in the active site. Enzyme kinetic data indicate that at least two metal-binding sites are functionally important, since Ca(2+) exhibits complex stimulatory and inhibitory effects on the Mg(2+)-dependent catalysis of Ape1, even though Ca(2+) itself does not serve as a cofactor. In conjunction, the structural and kinetic data suggest that Ape1 catalyzes hydrolysis of the DNA backbone through a two metal ion-mediated mechanism. | The major human abasic endonuclease, Ape1, is an essential DNA repair enzyme that initiates the removal of apurinic/apyrimidinic sites from DNA, excises 3' replication-blocking moieties, and modulates the DNA binding activity of several transcriptional regulators. We have determined the X-ray structure of the full-length human Ape1 enzyme in two new crystal forms, one at neutral and one at acidic pH. The new structures are generally similar to the previously determined structure of a truncated Ape1 protein, but differ in the conformation of several loop regions and in spans of residues with weak electron density. While only one active-site metal ion is present in the structure determined at low pH, the structure determined from a crystal grown at the pH optimum of Ape1 nuclease activity, pH 7.5, has two metal ions bound 5 A apart in the active site. Enzyme kinetic data indicate that at least two metal-binding sites are functionally important, since Ca(2+) exhibits complex stimulatory and inhibitory effects on the Mg(2+)-dependent catalysis of Ape1, even though Ca(2+) itself does not serve as a cofactor. In conjunction, the structural and kinetic data suggest that Ape1 catalyzes hydrolysis of the DNA backbone through a two metal ion-mediated mechanism. | ||
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| - | ==Disease== | ||
| - | Known diseases associated with this structure: Autoimmune polyglandular disease, type I OMIM:[[http://www.ncbi.nlm.nih.gov/entrez/dispomim.cgi?id=607358 607358]], Sveinsson choreoretinal atrophy OMIM:[[http://www.ncbi.nlm.nih.gov/entrez/dispomim.cgi?id=189967 189967]] | ||
==About this Structure== | ==About this Structure== | ||
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[[Category: Rupp, B.]] | [[Category: Rupp, B.]] | ||
[[Category: Segelke, B W.]] | [[Category: Segelke, B W.]] | ||
| - | [[Category: PB]] | ||
[[Category: abasic endonuclease]] | [[Category: abasic endonuclease]] | ||
[[Category: alpha]] | [[Category: alpha]] | ||
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[[Category: ref-1]] | [[Category: ref-1]] | ||
| - | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on | + | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sun Mar 30 19:58:08 2008'' |
Revision as of 16:58, 30 March 2008
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| , resolution 2.2Å | |||||||
|---|---|---|---|---|---|---|---|
| Sites: | , , and | ||||||
| Ligands: | |||||||
| Gene: | APE1 (Homo sapiens) | ||||||
| Activity: | DNA-(apurinic or apyrimidinic site) lyase, with EC number 4.2.99.18 | ||||||
| Resources: | FirstGlance, OCA, PDBsum, RCSB | ||||||
| Coordinates: | save as pdb, mmCIF, xml | ||||||
A SECOND DIVALENT METAL ION IN THE ACTIVE SITE OF A NEW CRYSTAL FORM OF HUMAN APURINIC/APYRIMIDINIC ENDONUCLEASE, APE1, AND ITS IMPLICATIONS FOR THE CATALYTIC MECHANISM
Overview
The major human abasic endonuclease, Ape1, is an essential DNA repair enzyme that initiates the removal of apurinic/apyrimidinic sites from DNA, excises 3' replication-blocking moieties, and modulates the DNA binding activity of several transcriptional regulators. We have determined the X-ray structure of the full-length human Ape1 enzyme in two new crystal forms, one at neutral and one at acidic pH. The new structures are generally similar to the previously determined structure of a truncated Ape1 protein, but differ in the conformation of several loop regions and in spans of residues with weak electron density. While only one active-site metal ion is present in the structure determined at low pH, the structure determined from a crystal grown at the pH optimum of Ape1 nuclease activity, pH 7.5, has two metal ions bound 5 A apart in the active site. Enzyme kinetic data indicate that at least two metal-binding sites are functionally important, since Ca(2+) exhibits complex stimulatory and inhibitory effects on the Mg(2+)-dependent catalysis of Ape1, even though Ca(2+) itself does not serve as a cofactor. In conjunction, the structural and kinetic data suggest that Ape1 catalyzes hydrolysis of the DNA backbone through a two metal ion-mediated mechanism.
About this Structure
1E9N is a Single protein structure of sequence from Homo sapiens. Full crystallographic information is available from OCA.
Reference
Two divalent metal ions in the active site of a new crystal form of human apurinic/apyrimidinic endonuclease, Ape1: implications for the catalytic mechanism., Beernink PT, Segelke BW, Hadi MZ, Erzberger JP, Wilson DM 3rd, Rupp B, J Mol Biol. 2001 Apr 6;307(4):1023-34. PMID:11286553
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