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Article ; Online: The non-homologous end-joining factor Nej1 inhibits resection mediated by Dna2-Sgs1 nuclease-helicase at DNA double strand breaks.

Sorenson, Kyle S / Mahaney, Brandi L / Lees-Miller, Susan P / Cobb, Jennifer A

2017 Volume 292, Issue 35, Page(s) 14576–14586

Abstract: Double strand breaks (DSBs) represent highly deleterious DNA damage and need to be accurately repaired. Homology-directed repair and non-homologous end joining (NHEJ) are the two major DSB repair pathways that are highly conserved from yeast to mammals. ... ...

Abstract	Double strand breaks (DSBs) represent highly deleterious DNA damage and need to be accurately repaired. Homology-directed repair and non-homologous end joining (NHEJ) are the two major DSB repair pathways that are highly conserved from yeast to mammals. The choice between these pathways is largely based on 5' to 3' DNA resection, and NHEJ proceeds only if resection has not been initiated. In yeast, yKu70/80 rapidly localizes to the break, protecting DNA ends from nuclease accessibility, and recruits additional NHEJ factors, including Nej1 and Lif1. Cells harboring the
MeSH term(s)	Amino Acid Substitution ; DNA Breaks, Double-Stranded ; DNA End-Joining Repair ; DNA Helicases/chemistry ; DNA Helicases/genetics ; DNA Helicases/metabolism ; DNA-Binding Proteins/chemistry ; DNA-Binding Proteins/genetics ; DNA-Binding Proteins/metabolism ; Endodeoxyribonucleases/chemistry ; Endodeoxyribonucleases/genetics ; Endodeoxyribonucleases/metabolism ; Exodeoxyribonucleases/chemistry ; Exodeoxyribonucleases/genetics ; Exodeoxyribonucleases/metabolism ; Gene Deletion ; Microbial Viability ; Models, Molecular ; Point Mutation ; Protein Multimerization ; Protein Transport ; RecQ Helicases/chemistry ; RecQ Helicases/genetics ; RecQ Helicases/metabolism ; Saccharomyces cerevisiae/enzymology ; Saccharomyces cerevisiae/growth & development ; Saccharomyces cerevisiae/metabolism ; Saccharomyces cerevisiae Proteins/chemistry ; Saccharomyces cerevisiae Proteins/genetics ; Saccharomyces cerevisiae Proteins/metabolism ; Species Specificity
Chemical Substances	DNA-Binding Proteins ; LIF1 protein, S cerevisiae ; NEJ1 protein, S cerevisiae ; RAD50 protein, S cerevisiae ; Saccharomyces cerevisiae Proteins ; YKU70 protein, S cerevisiae ; YKU80 protein, S cerevisiae ; Endodeoxyribonucleases (EC 3.1.-) ; Exodeoxyribonucleases (EC 3.1.-) ; MRE11 protein, S cerevisiae (EC 3.1.-) ; exodeoxyribonuclease I (EC 3.1.11.1) ; SGS1 protein, S cerevisiae (EC 3.6.1.-) ; DNA Helicases (EC 3.6.4.-) ; DNA2 protein, S cerevisiae (EC 3.6.4.12) ; RecQ Helicases (EC 3.6.4.12)
Language	English
Publishing date	2017-07-05
Publishing country	United States
Document type	Journal Article
ZDB-ID	2997-x
ISSN	1083-351X ; 0021-9258
ISSN (online)	1083-351X
ISSN	0021-9258
DOI	10.1074/jbc.M117.796011
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Article ; Online: The C-terminus of Nej1 is critical for nuclear localization and non-homologous end-joining.

Mahaney, Brandi L / Lees-Miller, Susan P / Cobb, Jennifer A

DNA repair

2013 Volume 14, Page(s) 9–16

Abstract: Nej1 is an essential factor in the non-homologous end-joining (NHEJ) pathway and interacts with the DNA ligase complex, Lif1-Dnl4, through interactions with Lif1. We have mapped K331-V338 in the C-terminal region of Nej1 to be critical for its ... ...

Abstract	Nej1 is an essential factor in the non-homologous end-joining (NHEJ) pathway and interacts with the DNA ligase complex, Lif1-Dnl4, through interactions with Lif1. We have mapped K331-V338 in the C-terminal region of Nej1 to be critical for its functionality during repair. Truncation and alanine scanning mutagenesis have been used to identify a motif in Nej1, KKRK (331-334), which is important for both nuclear targeting and NHEJ repair after localization. We have identified F335-V338 to be important for proper interaction with Lif1, however this region is not required for Nej1 recruitment to HO endonuclease-induced DNA double-strand breaks in vivo. Phenylalanine at position 335 is particularly important for the role of Nej1 in repair and the loss of association between Nej1 and Lif1 correlates with a decrease in cell survival upon either transient or continuous HO expression in nej1 mutants.
MeSH term(s)	Active Transport, Cell Nucleus ; Cell Nucleus/metabolism ; DNA Damage ; DNA End-Joining Repair ; DNA Ligase ATP ; DNA Ligases/metabolism ; DNA-Binding Proteins/chemistry ; DNA-Binding Proteins/genetics ; DNA-Binding Proteins/metabolism ; Mutagenesis, Site-Directed ; Mutation ; Nuclear Localization Signals/genetics ; Saccharomyces cerevisiae/cytology ; Saccharomyces cerevisiae/genetics ; Saccharomyces cerevisiae/metabolism ; Saccharomyces cerevisiae Proteins/chemistry ; Saccharomyces cerevisiae Proteins/genetics ; Saccharomyces cerevisiae Proteins/metabolism
Chemical Substances	DNA-Binding Proteins ; LIF1 protein, S cerevisiae ; NEJ1 protein, S cerevisiae ; Nuclear Localization Signals ; Saccharomyces cerevisiae Proteins ; DNA Ligases (EC 6.5.1.-) ; DNA Ligase ATP (EC 6.5.1.1)
Language	English
Publishing date	2013-12-24
Publishing country	Netherlands
Document type	Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't
ZDB-ID	2071608-4
ISSN	1568-7856 ; 1568-7864
ISSN (online)	1568-7856
ISSN	1568-7864
DOI	10.1016/j.dnarep.2013.12.002
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Article ; Online: Interrogation of the active site of OMP decarboxylase from Escherichia coli with a substrate analogue bearing an anionic group at C6.

Thirumalairajan, Srinath / Mahaney, Brandi / Bearne, Stephen L

Chemical communications (Cambridge, England)

2010 Volume 46, Issue 18, Page(s) 3158–3160

Abstract: An analogue of orotidine 5'-monophosphate (OMP), 6-phosphonouridine 5'-monophosphate is a competitive inhibitor of OMP decarboxylase from E. coli, binding with an affinity similar to that of OMP. Hence the active site is capable of stabilizing negative ... ...

Abstract	An analogue of orotidine 5'-monophosphate (OMP), 6-phosphonouridine 5'-monophosphate is a competitive inhibitor of OMP decarboxylase from E. coli, binding with an affinity similar to that of OMP. Hence the active site is capable of stabilizing negative charge distributed out of the plane of the pyrimidine ring, consistent with the notion of ground state destabilization.
MeSH term(s)	Binding Sites ; Escherichia coli/enzymology ; Orotidine-5'-Phosphate Decarboxylase/chemistry ; Orotidine-5'-Phosphate Decarboxylase/metabolism ; Substrate Specificity
Chemical Substances	Orotidine-5'-Phosphate Decarboxylase (EC 4.1.1.23)
Language	English
Publishing date	2010-05-14
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	1472881-3
ISSN	1364-548X ; 1359-7345 ; 0009-241X
ISSN (online)	1364-548X
ISSN	1359-7345 ; 0009-241X
DOI	10.1039/b926894d
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Article ; Online: Repair of ionizing radiation-induced DNA double-strand breaks by non-homologous end-joining.

Mahaney, Brandi L / Meek, Katheryn / Lees-Miller, Susan P

The Biochemical journal

2009 Volume 417, Issue 3, Page(s) 639–650

Abstract: DNA DSBs (double-strand breaks) are considered the most cytotoxic type of DNA lesion. They can be introduced by external sources such as IR (ionizing radiation), by chemotherapeutic drugs such as topoisomerase poisons and by normal biological processes ... ...

Abstract	DNA DSBs (double-strand breaks) are considered the most cytotoxic type of DNA lesion. They can be introduced by external sources such as IR (ionizing radiation), by chemotherapeutic drugs such as topoisomerase poisons and by normal biological processes such as V(D)J recombination. If left unrepaired, DSBs can cause cell death. If misrepaired, DSBs may lead to chromosomal translocations and genomic instability. One of the major pathways for the repair of IR-induced DSBs in mammalian cells is NHEJ (non-homologous end-joining). The main proteins required for NHEJ in mammalian cells are the Ku heterodimer (Ku70/80 heterodimer), DNA-PKcs [the catalytic subunit of DNA-PK (DNA-dependent protein kinase)], Artemis, XRCC4 (X-ray-complementing Chinese hamster gene 4), DNA ligase IV and XLF (XRCC4-like factor; also called Cernunnos). Additional proteins, including DNA polymerases mu and lambda, PNK (polynucleotide kinase) and WRN (Werner's Syndrome helicase), may also play a role. In the present review, we will discuss our current understanding of the mechanism of NHEJ in mammalian cells and discuss the roles of DNA-PKcs and DNA-PK-mediated phosphorylation in NHEJ.
MeSH term(s)	Animals ; DNA Breaks, Double-Stranded ; DNA Damage ; DNA Repair ; DNA Repair Enzymes/genetics ; DNA Repair Enzymes/metabolism ; DNA-Activated Protein Kinase/genetics ; DNA-Activated Protein Kinase/metabolism ; Humans ; Models, Biological ; Radiation, Ionizing
Chemical Substances	DNA-Activated Protein Kinase (EC 2.7.11.1) ; DNA Repair Enzymes (EC 6.5.1.-)
Language	English
Publishing date	2009-01-12
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't ; Review
ZDB-ID	2969-5
ISSN	1470-8728 ; 0006-2936 ; 0306-3275 ; 0264-6021
ISSN (online)	1470-8728
ISSN	0006-2936 ; 0306-3275 ; 0264-6021
DOI	10.1042/BJ20080413
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Article ; Online: XRCC4 and XLF form long helical protein filaments suitable for DNA end protection and alignment to facilitate DNA double strand break repair.

Mahaney, Brandi L / Hammel, Michal / Meek, Katheryn / Tainer, John A / Lees-Miller, Susan P

Biochemistry and cell biology = Biochimie et biologie cellulaire

2013 Volume 91, Issue 1, Page(s) 31–41

Abstract: DNA double strand breaks (DSBs), induced by ionizing radiation (IR) and endogenous stress including replication failure, are the most cytotoxic form of DNA damage. In human cells, most IR-induced DSBs are repaired by the nonhomologous end joining (NHEJ) ... ...

Abstract	DNA double strand breaks (DSBs), induced by ionizing radiation (IR) and endogenous stress including replication failure, are the most cytotoxic form of DNA damage. In human cells, most IR-induced DSBs are repaired by the nonhomologous end joining (NHEJ) pathway. One of the most critical steps in NHEJ is ligation of DNA ends by DNA ligase IV (LIG4), which interacts with, and is stabilized by, the scaffolding protein X-ray cross-complementing gene 4 (XRCC4). XRCC4 also interacts with XRCC4-like factor (XLF, also called Cernunnos); yet, XLF has been one of the least mechanistically understood proteins and precisely how XLF functions in NHEJ has been enigmatic. Here, we examine current combined structural and mutational findings that uncover integrated functions of XRCC4 and XLF and reveal their interactions to form long, helical protein filaments suitable to protect and align DSB ends. XLF-XRCC4 provides a global structural scaffold for ligating DSBs without requiring long DNA ends, thus ensuring accurate and efficient ligation and repair. The assembly of these XRCC4-XLF filaments, providing both DNA end protection and alignment, may commit cells to NHEJ with general biological implications for NHEJ and DSB repair processes and their links to cancer predispositions and interventions.
MeSH term(s)	Cell Transformation, Neoplastic/genetics ; Cell Transformation, Neoplastic/metabolism ; DNA/genetics ; DNA/metabolism ; DNA Breaks, Double-Stranded ; DNA End-Joining Repair ; DNA Ligase ATP ; DNA Ligases/genetics ; DNA Ligases/metabolism ; DNA Repair ; DNA Repair Enzymes/genetics ; DNA Repair Enzymes/metabolism ; DNA-Binding Proteins/genetics ; DNA-Binding Proteins/metabolism ; Humans ; Models, Molecular ; Protein Binding ; Radiation, Ionizing
Chemical Substances	DNA-Binding Proteins ; LIG4 protein, human ; NHEJ1 protein, human ; XRCC4 protein, human ; DNA (9007-49-2) ; DNA Ligases (EC 6.5.1.-) ; DNA Repair Enzymes (EC 6.5.1.-) ; DNA Ligase ATP (EC 6.5.1.1)
Language	English
Publishing date	2013-02-05
Publishing country	Canada
Document type	Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't ; Review
ZDB-ID	54104-7
ISSN	1208-6002 ; 0829-8211
ISSN (online)	1208-6002
ISSN	0829-8211
DOI	10.1139/bcb-2012-0058
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Article: Interrogation of the active site of OMP decarboxylase from Escherichia coli with a substrate analogue bearing an anionic group at C6

Thirumalairajan, Srinath / Bearne, Stephen L / Mahaney, Brandi

Chemical communications. 2010 Apr. 27, v. 46, no. 18

2010

Abstract: An analogue of orotidine 5′-monophosphate (OMP), 6-phosphonouridine 5′-monophosphate is a competitive inhibitor of OMP decarboxylase from E. coli, binding with an affinity similar to that of OMP. Hence the active site is capable of stabilizing negative ... ...

Abstract	An analogue of orotidine 5′-monophosphate (OMP), 6-phosphonouridine 5′-monophosphate is a competitive inhibitor of OMP decarboxylase from E. coli, binding with an affinity similar to that of OMP. Hence the active site is capable of stabilizing negative charge distributed out of the plane of the pyrimidine ring, consistent with the notion of ground state destabilization.
Keywords	active sites ; chemical communication ; chemical compounds ; chemical reactions ; enzymes ; Escherichia coli
Language	English
Dates of publication	2010-0427
Size	p. 3158-3160.
Publishing place	The Royal Society of Chemistry
Document type	Article
ZDB-ID	1472881-3
ISSN	1364-548X ; 1359-7345 ; 0009-241X
ISSN (online)	1364-548X
ISSN	1359-7345 ; 0009-241X
DOI	10.1039/b926894d
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Article: Proteomic investigation of glucose metabolism in the butyrate-producing gut anaerobe Fusobacterium varium.

Potrykus, Joanna / Mahaney, Brandi / White, Robert L / Bearne, Stephen L

Proteomics

2007 Volume 7, Issue 11, Page(s) 1839–1853

Abstract: ... with L-glutamate, an amino acid readily fermented by members of the Fusobacterium genus. A substrate pool ... both glucose and L-glutamate as energy sources. Enzymes involved in L-glutamate metabolism were also identified ... including an NAD-dependent glutamate dehydrogenase and two enzymes of the methylaspartate pathway of L ...

Abstract	A proteome survey and MS analysis were conducted to investigate glucose metabolism in Fusobacterium varium, a butyrate-producing constituent of the indigenous human gut microflora. The bacterium was capable of catabolizing glucose as the main energy source via the Embden-Meyerhof-Parnas pathway. 2-DE analyses revealed that the apparent concentrations of the six identified glycolytic enzymes (pyruvate kinase, enolase, glucose-6-phosphate isomerase, phosphoglycerate kinase, triosephosphate isomerase, and glyceraldehyde-3-phosphate dehydrogenase) were specifically increased in response to the presence of glucose in the chemically defined minimal growth medium, and did not diminish when the medium was additionally supplemented with L-glutamate, an amino acid readily fermented by members of the Fusobacterium genus. A substrate pool depletion study revealed that the sugar, and not the amino acid, is the more efficient growth substrate. Both proteomics and substrate pool depletion studies revealed that F. varium can simultaneously utilize both glucose and L-glutamate as energy sources. Enzymes involved in L-glutamate metabolism were also identified, including an NAD-dependent glutamate dehydrogenase and two enzymes of the methylaspartate pathway of L-glutamate catabolism (glutamate mutase and methylaspartate ammonia-lyase). Their apparent intracellular concentrations were elevated when the bacterium was cultured in media supplemented with excess L-glutamate. Our observation that the apparent concentrations of specific proteins were elevated in response to a particular growth substrate supplied as an energy source provides the first evidence for the presence of a nutrient-responsive mechanism governing intracellular protein concentration in F. varium.
MeSH term(s)	Bacteria, Anaerobic/metabolism ; Bacterial Proteins/isolation & purification ; Bacterial Proteins/metabolism ; Butyrates/metabolism ; Chromatography, Liquid ; Culture Media ; Fusobacterium/metabolism ; Glucose/metabolism ; Humans ; Intestines/microbiology ; Mass Spectrometry ; Proteomics
Chemical Substances	Bacterial Proteins ; Butyrates ; Culture Media ; Glucose (IY9XDZ35W2)
Language	English
Publishing date	2007-06
Publishing country	Germany
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2032093-0
ISSN	1615-9861 ; 1615-9853
ISSN (online)	1615-9861
ISSN	1615-9853
DOI	10.1002/pmic.200600464
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Article: Proteomic investigation of glucose metabolism in the butyrate-producing gut anaerobe Fusobacterium varium

Potrykus, Joanna / Mahaney, Brandi / White, Robert L / Bearne, Stephen L

Proteomics. 2007 June, v. 7, no. 11

2007

Abstract	A proteome survey and MS analysis were conducted to investigate glucose metabolism in Fusobacterium varium, a butyrate-producing constituent of the indigenous human gut microflora. The bacterium was capable of catabolizing glucose as the main energy source via the Embden-Meyerhof-Parnas pathway. 2-DE analyses revealed that the apparent concentrations of the six identified glycolytic enzymes (pyruvate kinase, enolase, glucose-6-phosphate isomerase, phosphoglycerate kinase, triosephosphate isomerase, and glyceraldehyde-3-phosphate dehydrogenase) were specifically increased in response to the presence of glucose in the chemically defined minimal growth medium, and did not diminish when the medium was additionally supplemented with L-glutamate, an amino acid readily fermented by members of the Fusobacterium genus. A substrate pool depletion study revealed that the sugar, and not the amino acid, is the more efficient growth substrate. Both proteomics and substrate pool depletion studies revealed that F. varium can simultaneously utilize both glucose and L-glutamate as energy sources. Enzymes involved in L-glutamate metabolism were also identified, including an NAD-dependent glutamate dehydrogenase and two enzymes of the methylaspartate pathway of L-glutamate catabolism (glutamate mutase and methylaspartate ammonia-lyase). Their apparent intracellular concentrations were elevated when the bacterium was cultured in media supplemented with excess L-glutamate. Our observation that the apparent concentrations of specific proteins were elevated in response to a particular growth substrate supplied as an energy source provides the first evidence for the presence of a nutrient-responsive mechanism governing intracellular protein concentration in F. varium.
Language	English
Dates of publication	2007-06
Size	p. 1839-1853.
Publishing place	Wiley-VCH Verlag
Document type	Article
ZDB-ID	2032093-0
ISSN	1615-9861 ; 1615-9853
ISSN (online)	1615-9861
ISSN	1615-9853
DOI	10.1002/pmic.200600464
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Article: DNA-PK and ATM phosphorylation sites in XLF/Cernunnos are not required for repair of DNA double strand breaks.

Yu, Yaping / Mahaney, Brandi L / Yano, Ken-Ichi / Ye, Ruiqiong / Fang, Shujuan / Douglas, Pauline / Chen, David J / Lees-Miller, Susan P

DNA repair

2008 Volume 7, Issue 10, Page(s) 1680–1692

Abstract: Nonhomologous end joining (NHEJ) is the major pathway for the repair of DNA double strand breaks (DSBs) in human cells. NHEJ requires the catalytic subunit of the DNA-dependent protein kinase (DNA-PKcs), Ku70, Ku80, XRCC4, DNA ligase IV and Artemis, as ... ...

Abstract	Nonhomologous end joining (NHEJ) is the major pathway for the repair of DNA double strand breaks (DSBs) in human cells. NHEJ requires the catalytic subunit of the DNA-dependent protein kinase (DNA-PKcs), Ku70, Ku80, XRCC4, DNA ligase IV and Artemis, as well as DNA polymerases mu and lambda and polynucleotide kinase. Recent studies have identified an additional participant, XLF, for XRCC4-like factor (also called Cernunnos), which interacts with the XRCC4-DNA ligase IV complex and stimulates its activity in vitro, however, its precise role in the DNA damage response is not fully understood. Since the protein kinase activity of DNA-PKcs is required for NHEJ, we asked whether XLF might be a physiological target of DNA-PK. Here, we have identified two major in vitro DNA-PK phosphorylation sites in the C-terminal region of XLF, serines 245 and 251. We show that these represent the major phosphorylation sites in XLF in vivo and that serine 245 is phosphorylated in vivo by DNA-PK, while serine 251 is phosphorylated by Ataxia-Telangiectasia Mutated (ATM). However, phosphorylation of XLF did not have a significant effect on the ability of XLF to interact with DNA in vitro or its recruitment to laser-induced DSBs in vivo. Similarly, XLF in which the identified in vivo phosphorylation sites were mutated to alanine was able to complement the DSB repair defect as well as radiation sensitivity in XLF-deficient 2BN cells. We conclude that phosphorylation of XLF at these sites does not play a major role in the repair of IR-induced DSBs in vivo.
MeSH term(s)	Amino Acid Sequence ; Amino Acids/metabolism ; Ataxia Telangiectasia Mutated Proteins ; Cell Cycle Proteins/metabolism ; Cell Survival/radiation effects ; DNA/metabolism ; DNA Breaks, Double-Stranded/radiation effects ; DNA Repair/radiation effects ; DNA Repair Enzymes/chemistry ; DNA Repair Enzymes/isolation & purification ; DNA Repair Enzymes/metabolism ; DNA-Activated Protein Kinase/metabolism ; DNA-Binding Proteins/chemistry ; DNA-Binding Proteins/isolation & purification ; DNA-Binding Proteins/metabolism ; HeLa Cells ; Humans ; Molecular Sequence Data ; Mutant Proteins/metabolism ; Phosphorylation/radiation effects ; Phosphoserine/metabolism ; Protein Binding/radiation effects ; Protein Structure, Tertiary ; Protein Transport/radiation effects ; Protein-Serine-Threonine Kinases/metabolism ; Radiation, Ionizing ; Recombinant Proteins/isolation & purification ; Recombinant Proteins/metabolism ; Tumor Suppressor Proteins/metabolism
Chemical Substances	Amino Acids ; Cell Cycle Proteins ; DNA-Binding Proteins ; Mutant Proteins ; NHEJ1 protein, human ; Recombinant Proteins ; Tumor Suppressor Proteins ; Phosphoserine (17885-08-4) ; DNA (9007-49-2) ; ATM protein, human (EC 2.7.11.1) ; Ataxia Telangiectasia Mutated Proteins (EC 2.7.11.1) ; DNA-Activated Protein Kinase (EC 2.7.11.1) ; Protein-Serine-Threonine Kinases (EC 2.7.11.1) ; DNA Repair Enzymes (EC 6.5.1.-)
Language	English
Publishing date	2008-08-03
Publishing country	Netherlands
Document type	Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't
ZDB-ID	2071608-4
ISSN	1568-7856 ; 1568-7864
ISSN (online)	1568-7856
ISSN	1568-7864
DOI	10.1016/j.dnarep.2008.06.015
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Article ; Online: XRCC4 protein interactions with XRCC4-like factor (XLF) create an extended grooved scaffold for DNA ligation and double strand break repair.

Hammel, Michal / Rey, Martial / Yu, Yaping / Mani, Rajam S / Classen, Scott / Liu, Mona / Pique, Michael E / Fang, Shujuan / Mahaney, Brandi L / Weinfeld, Michael / Schriemer, David C / Lees-Miller, Susan P / Tainer, John A

The Journal of biological chemistry

2011 Volume 286, Issue 37, Page(s) 32638–32650

Abstract: The XRCC4-like factor (XLF)-XRCC4 complex is essential for nonhomologous end joining, the major repair pathway for DNA double strand breaks in human cells. Yet, how XLF binds XRCC4 and impacts nonhomologous end joining functions has been enigmatic. Here, ...

Abstract	The XRCC4-like factor (XLF)-XRCC4 complex is essential for nonhomologous end joining, the major repair pathway for DNA double strand breaks in human cells. Yet, how XLF binds XRCC4 and impacts nonhomologous end joining functions has been enigmatic. Here, we report the XLF-XRCC4 complex crystal structure in combination with biophysical and mutational analyses to define the XLF-XRCC4 interactions. Crystal and solution structures plus mutations characterize alternating XRCC4 and XLF head domain interfaces forming parallel super-helical filaments. XLF Leu-115 ("Leu-lock") inserts into a hydrophobic pocket formed by XRCC4 Met-59, Met-61, Lys-65, Lys-99, Phe-106, and Leu-108 in synergy with pseudo-symmetric β-zipper hydrogen bonds to drive specificity. XLF C terminus and DNA enhance parallel filament formation. Super-helical XLF-XRCC4 filaments form a positively charged channel to bind DNA and align ends for efficient ligation. Collective results reveal how human XLF and XRCC4 interact to bind DNA, suggest consequences of patient mutations, and support a unified molecular mechanism for XLF-XRCC4 stimulation of DNA ligation.
MeSH term(s)	Cell Line ; Crystallography, X-Ray ; DNA/chemistry ; DNA/genetics ; DNA/metabolism ; DNA Breaks, Double-Stranded ; DNA Repair/physiology ; DNA Repair Enzymes/chemistry ; DNA Repair Enzymes/genetics ; DNA Repair Enzymes/metabolism ; DNA-Binding Proteins/chemistry ; DNA-Binding Proteins/genetics ; DNA-Binding Proteins/metabolism ; Humans ; Protein Binding/physiology ; Protein Structure, Quaternary ; Protein Structure, Secondary
Chemical Substances	DNA-Binding Proteins ; NHEJ1 protein, human ; XRCC4 protein, human ; DNA (9007-49-2) ; DNA Repair Enzymes (EC 6.5.1.-)
Language	English
Publishing date	2011-07-20
Publishing country	United States
Document type	Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't
ZDB-ID	2997-x
ISSN	1083-351X ; 0021-9258
ISSN (online)	1083-351X
ISSN	0021-9258
DOI	10.1074/jbc.M111.272641
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