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(-) Description

Title :  SOLUTION STRUCTURE OF THE HUMAN HOMODIMERIC DNA REPAIR PROTEIN XPF
 
Authors :  D. Das, K. Tripsianes, G. Folkers, N. G. Jaspers, J. H. Hoeijmakers, R. Kaptein, R. Boelens
Date :  17 Aug 05  (Deposition) - 03 Oct 06  (Release) - 05 Aug 08  (Revision)
Method :  SOLUTION NMR
Resolution :  NOT APPLICABLE
Chains :  NMR Structure  :  A,B  (20x)
Keywords :  Nmr Spectroscopy, Dna Repair, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  D. Das, K. Tripsianes, N. G. Jaspers, J. H. Hoeijmakers, R. Kaptein, R. Boelens, G. Folkers
The Hhh Domain Of The Human Dna Repair Protein Xpf Forms Stable Homodimers
Proteins V. 70 1551 2008
PubMed-ID: 17912758  |  Reference-DOI: 10.1002/PROT.21635
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - DNA REPAIR ENDONUCLEASE XPF
    Chains: A, B
    EC Number: 3.1.-.-
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Fragment: RESIDUES 823-905
    Gene: ERCC4, ERCC11, XPF
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: DNA EXCISION REPAIR PROTEIN ERCC-4

 Structural Features

(-) Chains, Units

  
NMR Structure (20x): 

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (0, 0)

(no "Ligand,Modified Residues,Ions" information available for 2AQ0)

(-) Sites  (0, 0)

(no "Site" information available for 2AQ0)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2AQ0)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2AQ0)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (4, 8)

NMR Structure (4, 8)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_057479A860DXPF_HUMANPolymorphism4986933A
B		A28
128		D
2UniProtVAR_019201I873VXPF_HUMANPolymorphism2020957A
B		I41
141		V
3UniProtVAR_013408E875GXPF_HUMANPolymorphism1800124A
B		E43
143		G
4UniProtVAR_014772G912EXPF_HUMANPolymorphism2020956A
B		G80
180		E
  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2AQ0)

(-) Exons   (1, 2)

NMR Structure (1, 2)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1aENST000003118951aENSE00001307513chr16:14014014-14014229216XPF_HUMAN1-69690--
1.2ENST000003118952ENSE00001203019chr16:14015888-14016068181XPF_HUMAN70-130610--
1.3ENST000003118953ENSE00001203014chr16:14020418-14020613196XPF_HUMAN130-195660--
1.4ENST000003118954ENSE00001203009chr16:14021885-14022092208XPF_HUMAN195-264700--
1.5ENST000003118955ENSE00001203003chr16:14024567-14024747181XPF_HUMAN265-325610--
1.6bENST000003118956bENSE00001202996chr16:14026014-14026142129XPF_HUMAN325-368440--
1.8ENST000003118958ENSE00001202989chr16:14028049-14028159111XPF_HUMAN368-405380--
1.9aENST000003118959aENSE00001504946chr16:14029003-14029600598XPF_HUMAN405-6042000--
1.10bENST0000031189510bENSE00001202976chr16:14031623-1403171593XPF_HUMAN604-635320--
1.12ENST0000031189512ENSE00001202971chr16:14038580-14038692113XPF_HUMAN635-673390--
1.13cENST0000031189513cENSE00001203025chr16:14041471-140462054735XPF_HUMAN673-9162442A:1-84
B:101-184		84
84

(-) Sequences/Alignments

NMR Structure
   Reformat: Number of residues per line =  ('0' or empty: single-line sequence representation)
  Number of residues per labelling interval =   
  UniProt sequence: complete  aligned part    
   Show mapping: SCOP domains CATH domains Pfam domains Secondary structure (by author)
SAPs(SNPs) PROSITE motifs Exons
(details for a mapped element are shown in a popup box when the mouse pointer rests over it) 
Chain A from PDB  Type:PROTEIN  Length:84
 aligned with XPF_HUMAN | Q92889 from UniProtKB/Swiss-Prot  Length:916

    Alignment length:84
                                   842       852       862       872       882       892       902       912    
            XPF_HUMAN   833 ADSETLPESEKYNPGPQDFLLKMPGVNAKNCRSLMHHVKNIAELAALSQDELTSILGNAANAKQLYDFIHTSFAEVVSKGKGKK 916
               SCOP domains d2aq0a_ A: DNA repair endonuclease XPF                                               SCOP domains
               CATH domains ------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..............hhhhhhhh....hhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh............. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------ PROSITE
               Transcript 1 Exon 1.13c  PDB: A:1-84 UniProt: 673-916 [INCOMPLETE]                                Transcript 1
                 2aq0 A   1 MDSETLPESEKYNPGPQDFLLKMPGVNAKNCRSLMHHVKNIAELAALSQDELTSILGNAANAKQLYDFIHTSFAEVVSKGKGKK  84
                                    10        20        30        40        50        60        70        80    


Chain B from PDB  Type:PROTEIN  Length:84
 aligned with XPF_HUMAN | Q92889 from UniProtKB/Swiss-Prot  Length:916

    Alignment length:84
                                   842       852       862       872       882       892       902       912    
            XPF_HUMAN   833 ADSETLPESEKYNPGPQDFLLKMPGVNAKNCRSLMHHVKNIAELAALSQDELTSILGNAANAKQLYDFIHTSFAEVVSKGKGKK 916
               SCOP domains d2aq0b_ B: DNA repair endonuclease XPF                                               SCOP domains
               CATH domains ------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ............hhhhhhhhhh....hhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.............. Sec.struct. author
                 SAPs(SNPs) ---------------------------D------------V-G------------------------------------E---- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------ PROSITE
               Transcript 1 Exon 1.13c  PDB: B:101-184 UniProt: 673-916 [INCOMPLETE]                             Transcript 1
                 2aq0 B 101 MDSETLPESEKYNPGPQDFLLKMPGVNAKNCRSLMHHVKNIAELAALSQDELTSILGNAANAKQLYDFIHTSFAEVVSKGKGKK 184
                                   110       120       130       140       150       160       170       180
   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
    → Modified Residue (blue background, lower-case, 'x' indicates undefined single-letter code, labelled with number + name)
  x → Chemical Group (purple background, 'x', labelled with number + name, e.g. ACE or NH2)
  extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '|'

 Classification and Annotation

(-) SCOP Domains  (1, 2)

NMR Structure
(-)
Class: All alpha proteins (14657)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2AQ0)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2AQ0)

(-) Gene Ontology  (40, 40)

NMR Structure(hide GO term definitions)
Chain A,B   (XPF_HUMAN | Q92889)
molecular function
    GO:0003677    DNA binding    Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
    GO:0001094    TFIID-class transcription factor binding    Interacting selectively and non-covalently with a basal RNA polymerase II transcription factor of the TFIID class, one of the factors involved in formation of the preinitiation complex (PIC) by RNA polymerase II and defined as a basal or general transcription factor.
    GO:0003684    damaged DNA binding    Interacting selectively and non-covalently with damaged DNA.
    GO:0004520    endodeoxyribonuclease activity    Catalysis of the hydrolysis of ester linkages within deoxyribonucleic acid by creating internal breaks.
    GO:0004519    endonuclease activity    Catalysis of the hydrolysis of ester linkages within nucleic acids by creating internal breaks.
    GO:0016787    hydrolase activity    Catalysis of the hydrolysis of various bonds, e.g. C-O, C-N, C-C, phosphoric anhydride bonds, etc. Hydrolase is the systematic name for any enzyme of EC class 3.
    GO:0004518    nuclease activity    Catalysis of the hydrolysis of ester linkages within nucleic acids.
    GO:0003676    nucleic acid binding    Interacting selectively and non-covalently with any nucleic acid.
    GO:0008022    protein C-terminus binding    Interacting selectively and non-covalently with a protein C-terminus, the end of any peptide chain at which the 1-carboxy function of a constituent amino acid is not attached in peptide linkage to another amino-acid residue.
    GO:0047485    protein N-terminus binding    Interacting selectively and non-covalently with a protein N-terminus, the end of any peptide chain at which the 2-amino (or 2-imino) function of a constituent amino acid is not attached in peptide linkage to another amino-acid residue.
    GO:0005515    protein binding    Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules).
    GO:0003697    single-stranded DNA binding    Interacting selectively and non-covalently with single-stranded DNA.
    GO:0000014    single-stranded DNA endodeoxyribonuclease activity    Catalysis of the hydrolysis of ester linkages within a single-stranded deoxyribonucleic acid molecule by creating internal breaks.
biological process
    GO:0006259    DNA metabolic process    Any cellular metabolic process involving deoxyribonucleic acid. This is one of the two main types of nucleic acid, consisting of a long, unbranched macromolecule formed from one, or more commonly, two, strands of linked deoxyribonucleotides.
    GO:0006281    DNA repair    The process of restoring DNA after damage. Genomes are subject to damage by chemical and physical agents in the environment (e.g. UV and ionizing radiations, chemical mutagens, fungal and bacterial toxins, etc.) and by free radicals or alkylating agents endogenously generated in metabolism. DNA is also damaged because of errors during its replication. A variety of different DNA repair pathways have been reported that include direct reversal, base excision repair, nucleotide excision repair, photoreactivation, bypass, double-strand break repair pathway, and mismatch repair pathway.
    GO:0009650    UV protection    Any process in which an organism or cell protects itself from ultraviolet radiation (UV), which may also result in resistance to repeated exposure to UV.
    GO:0006974    cellular response to DNA damage stimulus    Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus indicating damage to its DNA from environmental insults or errors during metabolism.
    GO:0034644    cellular response to UV    Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of an ultraviolet radiation (UV light) stimulus. Ultraviolet radiation is electromagnetic radiation with a wavelength in the range of 10 to 380 nanometers.
    GO:0000724    double-strand break repair via homologous recombination    The error-free repair of a double-strand break in DNA in which the broken DNA molecule is repaired using homologous sequences. A strand in the broken DNA searches for a homologous region in an intact chromosome to serve as the template for DNA synthesis. The restoration of two intact DNA molecules results in the exchange, reciprocal or nonreciprocal, of genetic material between the intact DNA molecule and the broken DNA molecule.
    GO:0070911    global genome nucleotide-excision repair    The nucleotide-excision repair process in which DNA lesions are removed from nontranscribed strands and from transcriptionally silent regions over the entire genome.
    GO:0036297    interstrand cross-link repair    Removal of a DNA interstrand crosslink (a covalent attachment of DNA bases on opposite strands of the DNA) and restoration of the DNA. DNA interstrand crosslinks occur when both strands of duplex DNA are covalently tethered together (e.g. by an exogenous or endogenous agent), thus preventing the strand unwinding necessary for essential DNA functions such as transcription and replication.
    GO:0032205    negative regulation of telomere maintenance    Any process that stops, prevents, or reduces the frequency, rate or extent of a process that affects and monitors the activity of telomeric proteins and the length of telomeric DNA.
    GO:0006289    nucleotide-excision repair    A DNA repair process in which a small region of the strand surrounding the damage is removed from the DNA helix as an oligonucleotide. The small gap left in the DNA helix is filled in by the sequential action of DNA polymerase and DNA ligase. Nucleotide excision repair recognizes a wide range of substrates, including damage caused by UV irradiation (pyrimidine dimers and 6-4 photoproducts) and chemicals (intrastrand cross-links and bulky adducts).
    GO:1901255    nucleotide-excision repair involved in interstrand cross-link repair    Any nucleotide-excision repair that is involved in interstrand cross-link repair.
    GO:0033683    nucleotide-excision repair, DNA incision    A process that results in the endonucleolytic cleavage of the damaged strand of DNA. The incision occurs at the junction of single-stranded DNA and double-stranded DNA that is formed when the DNA duplex is unwound.
    GO:0006295    nucleotide-excision repair, DNA incision, 3'-to lesion    The endonucleolytic cleavage of the damaged strand of DNA 3' to the site of damage. The incision occurs at the junction of single-stranded DNA and double-stranded DNA that is formed when the DNA duplex is unwound. The incision precedes the incision formed 5' to the site of damage.
    GO:0006296    nucleotide-excision repair, DNA incision, 5'-to lesion    The endonucleolytic cleavage of the damaged strand of DNA 5' to the site of damage. The incision occurs at the junction of single-stranded DNA and double-stranded DNA that is formed when the DNA duplex is unwound. The incision follows the incision formed 3' to the site of damage.
    GO:0006293    nucleotide-excision repair, preincision complex stabilization    The stabilization of the multiprotein complex involved in damage recognition, DNA helix unwinding, and endonucleolytic cleavage at the site of DNA damage as well as the unwound DNA. The stabilization of the protein-DNA complex ensures proper positioning of the preincision complex before the phosphodiester backbone of the damaged strand is cleaved 3' and 5' of the site of DNA damage.
    GO:0000712    resolution of meiotic recombination intermediates    The cleavage and rejoining of intermediates, such as Holliday junctions, formed during meiotic recombination to produce two intact molecules in which genetic material has been exchanged.
    GO:0009411    response to UV    Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of an ultraviolet radiation (UV light) stimulus. Ultraviolet radiation is electromagnetic radiation with a wavelength in the range of 10 to 380 nanometers.
    GO:0000723    telomere maintenance    Any process that contributes to the maintenance of proper telomeric length and structure by affecting and monitoring the activity of telomeric proteins, the length of telomeric DNA and the replication and repair of the DNA. These processes includes those that shorten, lengthen, replicate and repair the telomeric DNA sequences.
    GO:0006283    transcription-coupled nucleotide-excision repair    The nucleotide-excision repair process that carries out preferential repair of DNA lesions on the actively transcribed strand of the DNA duplex. In addition, the transcription-coupled nucleotide-excision repair pathway is required for the recognition and repair of a small subset of lesions that are not recognized by the global genome nucleotide excision repair pathway.
cellular component
    GO:0070522    ERCC4-ERCC1 complex    A heterodimeric nucleotide-excision repair complex that has endonuclease activity specific for bubble structures characteristic of certain DNA lesions. The subunits are known as XPF/ERCC4 and ERCC1 in mammals, and Rad1p and Rad10p in S. cerevisiae.
    GO:0000781    chromosome, telomeric region    The terminal region of a linear chromosome that includes the telomeric DNA repeats and associated proteins.
    GO:0000784    nuclear chromosome, telomeric region    The terminal region of a linear nuclear chromosome that includes the telomeric DNA repeats and associated proteins.
    GO:0005654    nucleoplasm    That part of the nuclear content other than the chromosomes or the nucleolus.
    GO:0000109    nucleotide-excision repair complex    Any complex formed of proteins that act in nucleotide-excision repair.
    GO:0000110    nucleotide-excision repair factor 1 complex    One of several protein complexes involved in nucleotide-excision repair; possesses DNA damage recognition and endodeoxynuclease activities. In S. cerevisiae, it is composed of Rad1p, Rad10p, and Rad14p; in human the subunits are ERCC4/XPF, ERCC1 and XPA, respectively.
    GO:0005634    nucleus    A membrane-bounded organelle of eukaryotic cells in which chromosomes are housed and replicated. In most cells, the nucleus contains all of the cell's chromosomes except the organellar chromosomes, and is the site of RNA synthesis and processing. In some species, or in specialized cell types, RNA metabolism or DNA replication may be absent.
    GO:0005669    transcription factor TFIID complex    A complex composed of TATA binding protein (TBP) and TBP associated factors (TAFs); the total mass is typically about 800 kDa. Most of the TAFs are conserved across species. In TATA-containing promoters for RNA polymerase II (Pol II), TFIID is believed to recognize at least two distinct elements, the TATA element and a downstream promoter element. TFIID is also involved in recognition of TATA-less Pol II promoters. Binding of TFIID to DNA is necessary but not sufficient for transcription initiation from most RNA polymerase II promoters.

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 Related Entries

(-) Entries Sharing at Least One Protein Chain (UniProt ID)

UniProtKB/Swiss-Prot
        XPF_HUMAN | Q92889: 1z00 2a1j 2kn7 2mut

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