2kqb: Difference between revisions

Revision as of 08:47, 14 June 2023

First PBZ domain of human APLF protein

Structural highlights

2kqb is a 1 chain structure with sequence from Homo sapiens. Full experimental information is available from OCA. For a guided tour on the structure components use FirstGlance.
Ligands:	ZN
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

APLF_HUMAN Nuclease involved in single-strand and double-strand DNA break repair. Recruited to sites of DNA damage through interaction with poly(ADP-ribose), a polymeric post-translational modification synthesized transiently at sites of chromosomal damage to accelerate DNA strand break repair reactions. Displays apurinic-apyrimidinic (AP) endonuclease and 3'-5' exonuclease activities in vitro. Also able to introduce nicks at hydroxyuracil and other types of pyrimidine base damage.^[1] ^[2]

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

Addition of poly(ADP-ribose) (PAR) is an important post-translational modification in higher eukaryotes. Several DNA repair and checkpoint proteins possess specific PAR-binding zinc-finger (PBZ) modules critical for function. Here, we present solution structures of the two PBZ modules of aprataxin and PNK-like factor (APLF), revealing a novel type of zinc finger. By combining in vivo PAR-binding data with NMR interaction data using PAR fragments, we propose a structural basis for PBZ-PAR recognition.

Solution structures of the two PBZ domains from human APLF and their interaction with poly(ADP-ribose).,Eustermann S, Brockmann C, Mehrotra PV, Yang JC, Loakes D, West SC, Ahel I, Neuhaus D Nat Struct Mol Biol. 2010 Feb;17(2):241-3. Epub 2010 Jan 24. PMID:20098424^[3]

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

References

↑ Kanno S, Kuzuoka H, Sasao S, Hong Z, Lan L, Nakajima S, Yasui A. A novel human AP endonuclease with conserved zinc-finger-like motifs involved in DNA strand break responses. EMBO J. 2007 Apr 18;26(8):2094-103. Epub 2007 Mar 29. PMID:17396150 doi:https://dx.doi.org/10.1038/sj.emboj.7601663
↑ Iles N, Rulten S, El-Khamisy SF, Caldecott KW. APLF (C2orf13) is a novel human protein involved in the cellular response to chromosomal DNA strand breaks. Mol Cell Biol. 2007 May;27(10):3793-803. Epub 2007 Mar 12. PMID:17353262 doi:https://dx.doi.org/MCB.02269-06
↑ Eustermann S, Brockmann C, Mehrotra PV, Yang JC, Loakes D, West SC, Ahel I, Neuhaus D. Solution structures of the two PBZ domains from human APLF and their interaction with poly(ADP-ribose). Nat Struct Mol Biol. 2010 Feb;17(2):241-3. Epub 2010 Jan 24. PMID:20098424 doi:10.1038/nsmb.1747

Proteopedia Page Contributors and Editors (what is this?)

OCA

[1] Kanno S, Kuzuoka H, Sasao S, Hong Z, Lan L, Nakajima S, Yasui A. A novel human AP endonuclease with conserved zinc-finger-like motifs involved in DNA strand break responses. EMBO J. 2007 Apr 18;26(8):2094-103. Epub 2007 Mar 29. PMID:17396150 doi:https://dx.doi.org/10.1038/sj.emboj.7601663

[2] Iles N, Rulten S, El-Khamisy SF, Caldecott KW. APLF (C2orf13) is a novel human protein involved in the cellular response to chromosomal DNA strand breaks. Mol Cell Biol. 2007 May;27(10):3793-803. Epub 2007 Mar 12. PMID:17353262 doi:https://dx.doi.org/MCB.02269-06

[3] Eustermann S, Brockmann C, Mehrotra PV, Yang JC, Loakes D, West SC, Ahel I, Neuhaus D. Solution structures of the two PBZ domains from human APLF and their interaction with poly(ADP-ribose). Nat Struct Mol Biol. 2010 Feb;17(2):241-3. Epub 2010 Jan 24. PMID:20098424 doi:10.1038/nsmb.1747

[1]

[2]

[3]

@@ Line 1: / Line 1: @@
 ==First PBZ domain of human APLF protein==
-<StructureSection load='2kqb' size='340' side='right'caption='[[2kqb]], [[NMR_Ensembles_of_Models | 25 NMR models]]' scene=''>
+<StructureSection load='2kqb' size='340' side='right'caption='[[2kqb]]' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[2kqb]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Human Human]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2KQB OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2KQB FirstGlance]. <br>
+<table><tr><td colspan='2'>[[2kqb]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2KQB OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2KQB FirstGlance]. <br>
 </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
-<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[2kqc|2kqc]], [[2kqd|2kqd]], [[2kqe|2kqe]]</div></td></tr>
-<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">APLF, C2orf13, PALF, XIP1 ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 HUMAN])</td></tr>
-<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/DNA-(apurinic_or_apyrimidinic_site)_lyase DNA-(apurinic or apyrimidinic site) lyase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=4.2.99.18 4.2.99.18] </span></td></tr>
 <tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=2kqb FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2kqb OCA], [https://pdbe.org/2kqb PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2kqb RCSB], [https://www.ebi.ac.uk/pdbsum/2kqb PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2kqb ProSAT]</span></td></tr>
 </table>
 == Function ==
-[[https://www.uniprot.org/uniprot/APLF_HUMAN APLF_HUMAN]] Nuclease involved in single-strand and double-strand DNA break repair. Recruited to sites of DNA damage through interaction with poly(ADP-ribose), a polymeric post-translational modification synthesized transiently at sites of chromosomal damage to accelerate DNA strand break repair reactions. Displays apurinic-apyrimidinic (AP) endonuclease and 3'-5' exonuclease activities in vitro. Also able to introduce nicks at hydroxyuracil and other types of pyrimidine base damage.<ref>PMID:17396150</ref> <ref>PMID:17353262</ref>
+[https://www.uniprot.org/uniprot/APLF_HUMAN APLF_HUMAN] Nuclease involved in single-strand and double-strand DNA break repair. Recruited to sites of DNA damage through interaction with poly(ADP-ribose), a polymeric post-translational modification synthesized transiently at sites of chromosomal damage to accelerate DNA strand break repair reactions. Displays apurinic-apyrimidinic (AP) endonuclease and 3'-5' exonuclease activities in vitro. Also able to introduce nicks at hydroxyuracil and other types of pyrimidine base damage.<ref>PMID:17396150</ref> <ref>PMID:17353262</ref>
 == Evolutionary Conservation ==
 [[Image:Consurf_key_small.gif|200px|right]]
@@ Line 38: / Line 35: @@
 __TOC__
 </StructureSection>
-[[Category: Human]]
+[[Category: Homo sapiens]]
 [[Category: Large Structures]]
-[[Category: Brockmann, C]]
+[[Category: Brockmann C]]
-[[Category: Eustermann, S]]
+[[Category: Eustermann S]]
-[[Category: Neuhaus, D]]
+[[Category: Neuhaus D]]
-[[Category: Yang, J]]
+[[Category: Yang J]]
-[[Category: Adp-ribosylation]]
-[[Category: Dna damage]]
-[[Category: Dna repair]]
-[[Category: Lyase]]
-[[Category: Metal-binding]]
-[[Category: Nucleotide-binding]]
-[[Category: Nucleus]]
-[[Category: Zinc]]
-[[Category: Zinc-finger]]

2kqb: Difference between revisions

Revision as of 08:47, 14 June 2023

First PBZ domain of human APLF protein

Structural highlights

Function

Evolutionary Conservation

Publication Abstract from PubMed

See Also

References

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